0001047469-12-008730 | 10-K | XBRL Viewer

Document and Entity Information - USD ($)	12 Months Ended
Document and Entity Information - USD ($)	Jun. 30, 2012	Aug. 24, 2012	Dec. 31, 2011
Document and Entity Information
Entity Registrant Name	ACCURAY INC
Entity Central Index Key	0001138723
Document Type	10-K
Document Period End Date	Jun. 30, 2012
Amendment Flag	false
Amendment Description
Current Fiscal Year End Date	--06-30
Entity Well-known Seasoned Issuer	No
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Public Float			$ 176,019,053
Entity Common Stock, Shares Outstanding		72,006,666
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	FY

Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2012	Jun. 30, 2011
Current assets:
Cash and cash equivalents	$ 143,504	$ 95,906
Restricted cash	1,560	3,172
Accounts receivable, net of allowance for doubtful accounts of $1,700 and $324 at June 30, 2012 and 2011, respectively	67,890	61,853
Inventories	81,693	97,836
Prepaid expenses and other current assets	16,715	21,115
Deferred cost of revenue - current	4,896	5,840
Total current assets	316,258	285,722
Property and equipment, net	37,458	44,823
Goodwill	59,215	54,474
Intangible assets, net	49,819	66,039
Deferred cost of revenue - noncurrent	2,433	2,258
Other assets	7,987	2,468
Total assets	473,170	455,784
Current liabilities:
Accounts payable	18,209	38,645
Accrued compensation	23,071	27,406
Other accrued liabilities	31,646	43,012
Customer advances - current	18,177	25,829
Deferred revenue - current	83,071	68,152
Total current liabilities	174,174	203,044
Long-term liabilities:
Long-term other liabilities	5,988	6,321
Deferred revenue - noncurrent	9,675	6,092
Long-term debt	79,466
Total liabilities	269,303	215,457
Commitment and contingencies (Note 8)
Equity:
Preferred stock, $0.001 par value; authorized: 5,000,000 shares; no shares issued and outstanding
Common stock, $0.001 par value; authorized: 100,000,000 shares; issued: 71,864,268 and 72,199,837 shares at June 30, 2012 and 2011, respectively; outstanding: 71,864,268 and 70,059,819 shares at June 30, 2012 and 2011, respectively	72	70
Additional paid-in capital	409,143	373,963
Accumulated other comprehensive income	2,837	127
Accumulated deficit	(216,427)	(144,385)
Total stockholders' equity	195,625	229,775
Non-controlling interest	8,242	10,552
Total equity	203,867	240,327
Total liabilities and equity	$ 473,170	$ 455,784

Consolidated Balance Sheets (Parenthetical) - USD ($) $ in Thousands	Jun. 30, 2012	Jun. 30, 2011
Consolidated Balance Sheets
Accounts receivable, allowance for doubtful accounts (in dollars)	$ 1,700	$ 324
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, authorized shares	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, authorized shares	100,000,000	100,000,000
Common stock, issued shares	71,864,268	72,199,837
Common stock, outstanding shares	71,864,268	70,059,819

Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Net revenue:
Products	$ 240,472	$ 138,595	$ 143,187
Services	166,681	80,490	77,504
Other	2,070	3,199	934
Total net revenue	409,223	222,284	221,625
Cost of revenue:
Cost of products	136,180	55,524	66,216
Cost of services	134,562	56,218	50,732
Cost of other	1,209	3,300	659
Total cost of revenue	271,951	115,042	117,607
Gross profit	137,272	107,242	104,018
Operating expenses:
Selling and marketing	54,547	37,181	34,187
Research and development	87,114	41,687	31,523
General and administrative	58,598	56,657	35,472
Total operating expenses	200,259	135,525	101,182
Income (loss) from operations	(62,987)	(28,283)	2,836
Other income (expense), net	(12,871)	2,288	1
Income (loss) before provision for (benefit from) income taxes	(75,858)	(25,995)	2,837
Provision for (benefit from) income taxes	2,595	1,116	(4)
Net income (loss)	(78,453)	(27,111)	2,841
Non-controlling interest	(6,411)	(429)
Net income (loss) attributable to stockholders	$ (72,042)	$ (26,682)	$ 2,841
Net income (loss) per share attributable to stockholders
Basic (in dollars per share)	$ (1.02)	$ (0.44)	$ 0.05
Diluted (in dollars per share)	$ (1.02)	$ (0.44)	$ 0.05
Weighted average common shares used in computing net income (loss) per share
Basic (in shares)	70,887	60,085	57,560
Diluted (in shares)	70,887	60,085	60,191

Consolidated Statement of Stockholders' Equity - USD ($) $ in Thousands	Total	Total Stockholders' Equity	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit	Non-controlling Interest	Comprehensive Income (Loss)
Balance at Jun. 30, 2009	$ 153,902	$ 153,902	$ 57	$ 273,946	$ 416	$ (120,517)
Balance (in shares) at Jun. 30, 2009			56,643,529
Increase (Decrease) in Stockholders' Equity
Exercise of stock options, net	2,030	2,030	$ 2	2,028
Exercise of stock options, net (in shares)			1,313,749
Issuance of common stock under employee stock purchase plan	1,807	1,807		1,807
Issuance of common stock under employee stock purchase plan (in shares)			399,283
Issuance of restricted stock (in shares)			170,395
Share-based compensation	10,397	10,397		10,397
Income tax charges from employee stock plans	(414)	(414)		(414)
Net (loss) income	2,841	2,841				2,841		$ 2,841
Cumulative translation adjustment	(57)	(57)			(57)			(57)
Unrealized loss on investments, net	(430)	(430)			(430)			(430)
Total comprehensive (loss) income	2,354	2,354						2,354
Balance at Jun. 30, 2010	170,076	170,076	$ 59	287,764	(71)	(117,676)
Balance (in shares) at Jun. 30, 2010			58,526,956
Increase (Decrease) in Stockholders' Equity
Deconsolidation of Morphormics	(27)	(27)				(27)
Exercise of stock options, net	3,601	3,601	$ 1	3,600
Exercise of stock options, net (in shares)			1,396,685
Issuance of common stock under employee stock purchase plan	2,000	2,000		2,000
Issuance of common stock under employee stock purchase plan (in shares)			392,084
Issuance of restricted stock (in shares)			201,992
Share-based compensation	9,842	9,842		9,842
Shares issued in connection with acquisition of TomoTherapy	67,342	67,342	$ 10	67,332
Shares issued in connection with acquisition of TomoTherapy (in shares)			9,112,511
Shares issued in connection with the assumption of restricted stock awards related to acquisition of TomoTherapy			429,591
Restricted stock awards assumed in connection with acquisition of TomoTherapy	1,191	1,191		1,191
Stock options assumed in connection with acquisition of TomoTherapy	2,234	2,234		2,234
Non-controlling interest in CPAC resulting from acquisition of TomoTherapy	10,981						$ 10,981
Net (loss) income	(27,111)	(26,682)				(26,682)	(429)	(27,111)
Cumulative translation adjustment	236	236			236			236
Unrealized loss on investments, net	(38)	(38)			(38)			(38)
Total comprehensive (loss) income	(26,913)	(26,484)					(429)	(26,913)
Balance at Jun. 30, 2011	$ 240,327	229,775	$ 70	373,963	127	(144,385)	10,552
Balance (in shares) at Jun. 30, 2011	70,059,819		70,059,819
Increase (Decrease) in Stockholders' Equity
Exercise of stock options, net	$ 1,866	1,866	$ 1	1,865
Exercise of stock options, net (in shares)			746,441
Issuance of common stock under employee stock purchase plan	2,581	2,581	$ 1	2,580
Issuance of common stock under employee stock purchase plan (in shares)			755,532
Issuance of restricted stock (in shares)			302,476
Share-based compensation	7,546	7,546		7,546
Embedded conversion feature on Convertible Note	23,189	23,189		23,189
Non-controlling interest in CPAC resulting from acquisition of TomoTherapy	4,101						4,101
Net (loss) income	(78,453)	(72,042)				(72,042)	(6,411)	(78,453)
Cumulative translation adjustment	2,710	2,710			2,710			2,710
Total comprehensive (loss) income	(75,743)	(69,332)					(6,411)	$ (75,743)
Balance at Jun. 30, 2012	$ 203,867	$ 195,625	$ 72	$ 409,143	$ 2,837	$ (216,427)	$ 8,242
Balance (in shares) at Jun. 30, 2012	71,864,268		71,864,268

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Cash Flows From Operating Activities
Net income (loss)	$ (78,453)	$ (27,111)	$ 2,841
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities
Depreciation and amortization	32,592	7,566	7,122
Share-based compensation	8,458	13,365	10,232
Realized and unrealized (gain) loss on investments, net		(27)	65
Accretion of interest on long-term debt	3,596
Provision for (recovery of) bad debt	1,392	239	(380)
Provision for write-down of inventories	2,129	1,698	626
Loss on disposal of property and equipment	296	312	195
Changes in assets and liabilities:
Restricted cash	1,605		438
Accounts receivable	(9,162)	8,698	(2,448)
Inventories	11,927	(4,321)	244
Prepaid expenses and other current assets	5,533	(1,340)	(4,230)
Deferred cost of revenue	2,080	7,586	8,980
Other assets	(2,647)	214	(228)
Accounts payable	(21,425)	10,662	(5,364)
Accrued liabilities	(10,043)	9,831	4,382
Customer advances	(7,044)	(909)	20
Deferred revenue	20,887	(14,060)	(27,568)
Net cash provided by (used in) operating activities	(38,279)	12,403	(5,073)
Cash Flows From Investing Activities
Purchases of property and equipment, net	(10,769)	(4,022)	(5,130)
Acquisition of business, net of cash acquired	(1,384)	(70,265)
Purchase of investments		(100,710)	(111,429)
Sale and maturity of investments		206,414	127,086
Net cash provided by (used in) investing activities	(12,153)	31,417	10,527
Cash Flows From Financing Activities
Proceeds from issuance of common stock	1,867	3,601	2,030
Proceeds from employee stock purchase plan	2,582	2,000	1,807
Proceeds from debt, net of costs	96,100
Net cash provided by financing activities	100,549	5,601	3,837
Effect of exchange rate changes on cash and cash equivalents	(2,519)	1,051	(692)
Net increase in cash and cash equivalent	47,598	50,472	8,599
Cash and cash equivalents at beginning of period	95,906	45,434	36,835
Cash and cash equivalents at end of period	143,504	95,906	45,434
Supplemental Disclosure of Cash Flow Information
Cash paid for income taxes	1,198	1,392	$ 60
Cash paid for interest	$ 1,875
Non-cash financing activity:
Fair value of common stock issued and vested options and restricted stock awards assumed in connection with acquisition of TomoTherapy		$ 73,845

Description of Business

12 Months Ended

Jun. 30, 2012

Description of Business

Description of Business

1. Description of Business

Organization

Accuray Incorporated (together with its subsidiaries, the "Company") is incorporated in Delaware. The Company designs, develops and sells advanced medical radiation systems for the treatment of tumors throughout the body. The CyberKnife Systems are advanced, image-guided robotic systems used to deliver radiosurgery for the treatment of solid tumors anywhere in the body.

On June 10, 2011, the Company completed the acquisition of TomoTherapy Incorporated ("TomoTherapy") by acquiring all of TomoTherapy's common stock in exchange for cash and shares of Accuray common stock (for further information, see Note 12, Acquisition). TomoTherapy designs, manufactures and sells systems used to deliver advanced radiation therapy for the treatment of a wide range of cancer types. The consolidated financial statements include the financial results of TomoTherapy prospectively from the date of acquisition.

Summary of Significant Accounting Policies

12 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Basis of Presentation and Principles of Consolidation

The accompanying consolidated financial statements have been prepared in accordance with United States generally accepted accounting principles, ("GAAP"), pursuant to the rules and regulations of the Securities and Exchange Commission (the "SEC"). The consolidated financial statements include the accounts of the Company, its wholly-owned subsidiaries and a variable interest entity, Compact Particle Acceleration Corporation ("CPAC") (for further information, see Note 13, Investment in CPAC). All significant inter-company transactions and balances have been eliminated in consolidation.

Use of Estimates

The preparation of consolidated financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosures at the date of the financial statements. Key estimates and assumptions made by the Company relate to revenue recognition, business combinations and intangible asset impairment, inventories, share-based compensation expense, income taxes, loss contingencies and corporate bonus expenses and accruals. Actual results could differ materially from those estimates.

Foreign Currency

The Company's international subsidiaries use their local currencies as their functional currencies. For those subsidiaries, assets and liabilities are translated at exchange rates in effect at the balance sheet date and income and expense accounts at the average exchange rate. Resulting translation adjustments are excluded from the determination of net income (loss) and are recorded in accumulated other comprehensive income (loss) as a separate component of stockholders' equity. Net foreign currency exchange transaction gains or losses are included as a component of other income (expense), net, in the Company's consolidated statements of operations.

Cash and Cash Equivalents

Cash equivalents consist of amounts invested in highly liquid investment accounts with original maturities of three months or less on the date of purchase. Cash equivalents are comprised of money market funds and certificates of deposit and amounted to $46.8 million and $19,000 at June 30, 2012 and 2011, respectively. Cash and cash equivalent balances denominated in foreign currencies amounted to $43.2 million and $28.3 million at June 30, 2012 and 2011, respectively.

Restricted Cash

Restricted cash primarily relates to funds held related to Value-Added Tax ("VAT") guarantees in a foreign jurisdiction and certain performance obligation guarantees.

Fair Value Measurements

In May 2011, the Financial Accounting Standards Board ("FASB") issued additional guidance on fair value measurements and related disclosures. The new guidance clarifies the application of existing guidance on fair value measurement for non-financial assets and requires the disclosure of quantitative information about the unobservable inputs used in a fair value measurement. This guidance is effective on a prospective basis for interim and annual periods beginning after December 15, 2011. The adoption of this guidance during the year ended June 30, 2012 did not have any impact on the Company's financial statements.

The carrying values of the Company's financial instruments including cash equivalents, restricted cash, accounts receivable and accounts payable are approximately equal to their respective fair values due to the relatively short-term nature of these instruments. Also refer to Note 4, Financial Instruments, for further details.

Other-than-Temporary Impairment Assessment

The Company regularly reviews all of its investments for other-than-temporary declines in fair value. The review includes but is not limited to (i) the consideration of the cause of the impairment, (ii) the creditworthiness of the security issuers, (iii) the length of time a security is in an unrealized loss position, and (iv) the Company's positive intent and ability to hold the security for a period of time sufficient to allow for any anticipated recovery in fair value.

Concentration of Credit Risk and Other Risks and Uncertainties

The Company's cash and cash equivalents are mainly deposited with several major financial institutions. At times, deposits in these institutions exceed the amount of insurance provided on such deposits. The Company has not experienced any losses in such accounts and believes that it is not exposed to any significant risk on these balances.

There were no customers that represented 10% or more of total net revenue for the years ended June 30, 2012, 2011 and 2010. At June 30, 2012 and 2011, there were two customers and one customer, respectively, whose accounts receivable balance was 10% or more of the Company's total accounts receivable.

Accounts receivable are typically not collateralized. The Company performs ongoing credit evaluations of its customers and maintains reserves for potential credit losses. Accounts receivable are deemed past due in accordance with the contractual terms of the agreement. Accounts are charged against the allowance for doubtful accounts once collection efforts are unsuccessful. Historically, such losses have been within management's expectations.

Single-source suppliers presently provide the Company with several components. In most cases, if a supplier was unable to deliver these components, the Company believes that it would be able to find other sources for these components subject to any regulatory qualifications, if required.

Inventories

Inventories are stated at the lower of cost (on a first-in, first-out basis) or market value. Excess and obsolete inventories are written down based on historical sales and forecasted demand, as judged by management. The Company determines inventory and product costs, which include allocated production overheads, through use of standard costs.

Revenue Recognition

The Company earns revenue from the sale of products, the operation of its shared ownership program, and the provision of related services, which include installation services, post-contract customer support ("PCS"), training and other professional services. The Company records its revenues net of any value added or sales tax. From time to time, the Company introduces customers to third party financing organizations. No amounts received from these third party financing organizations are at risk.

In the first quarter of fiscal 2011, the Company adopted Accounting Standards Update ("ASU") 2009-13, Multiple-Deliverable Revenue Arrangements, and ASU 2009-14, Certain Arrangements That Include Software Elements. These standards changed the requirements for establishing separate units of accounting in a multiple element arrangement and require the allocation of arrangement consideration to each deliverable to be based on the relative selling price. The FASB also amended the accounting standards for revenue recognition to exclude software that is contained in a tangible product from the scope of software revenue guidance if the software is essential to the tangible product's functionality. The Company adopted these new standards on a prospective basis. For revenue arrangements that were entered into or materially modified after the adoption of these standards, implementation of this new authoritative guidance had an insignificant impact on the Company's reported net revenue since the first quarter of fiscal 2011 as compared to net revenue if the related arrangements entered into or modified after the effective date were subject to the accounting requirements in effect prior to the first quarter of fiscal 2011.

The Company frequently enters into sales arrangements with customers that contain multiple elements or deliverables. For revenue arrangements with multiple elements that were entered into prior to the adoption of the new standards and that have not subsequently been materially modified, the Company allocated arrangement consideration to each element based upon vendor specific objective evidence ("VSOE") of fair value of the respective elements. VSOE of fair value for each element is based upon the Company's standard rates charged for the product or service when such product or service is sold separately or based upon the price established by the Company's pricing committee when that product or service is not yet being sold separately. When contracts contain multiple elements, and VSOE of fair value exists for all undelivered elements, the Company accounts for the delivered elements, principally the system and optional product upgrades, based upon the residual method. If VSOE of fair value does not exist for all the undelivered elements, all revenue is deferred until the earlier of: (1) delivery of all elements, or (2) establishment of VSOE of fair value for all remaining undelivered elements.

Under the new accounting guidance, in evaluating revenue recognition for arrangements which contain multiple deliverables, the Company determined that in certain instances it was not able to establish VSOE for all deliverables in an arrangement as the Company infrequently sells each element on a stand-alone basis, does not price products within a narrow range, or has a limited sales history. When VSOE cannot be established, the Company attempts to establish the selling price of each element based on relevant third-party evidence ("TPE"). TPE is determined based on competitors' prices for similar deliverables when sold separately. Generally, the Company's offerings contain a significant level of proprietary technology, customization or differentiation such that the comparable pricing of products with similar functionality cannot be obtained. Furthermore, the Company is unable to reliably determine what similar competitors' products' selling prices are on a stand-alone basis. Therefore, the Company typically is not able to determine TPE.

When the Company is unable to establish selling price using VSOE or TPE, the Company uses its best estimate of selling price ("BESP") in the Company's allocation of arrangement consideration. The objective of BESP is to determine the price at which the Company would transact a sale if the product or service were sold on a stand-alone basis. BESP is generally used for offerings that are not typically sold on a stand-alone basis or for new or highly customized offerings. The Company determines BESP for a product or service by considering multiple factors including, but not limited to, pricing practices, internal costs, geographies and gross margin. The determination of BESP is made through consultation with the Company's pricing committee, taking into consideration the overall go-to-market pricing strategy.

As the Company's go-to-market strategies and other factors evolve, the Company may modify its pricing practices in the future, which could result in changes in selling prices, including VSOE, TPE and BESP. As a result, the Company's future revenue recognition for multiple element arrangements could differ materially from that recorded in the current period. The Company regularly reviews VSOE, TPE and BESP and maintains internal controls over the establishment and update of these inputs.

The Company has a limited number of software offerings which are not required to deliver the tangible product's essential functionality and can be sold separately. Revenues from sales of these software products and related post-contract support are accounted for under software revenue recognition rules. The Company's multiple-element arrangements may therefore have a software deliverable that is subject to the existing software revenue recognition guidance. The revenue for these multiple-element arrangements is allocated to the software deliverable or group of software deliverables and the non-software deliverables based on the relative selling prices of all of the deliverables in the arrangement using the hierarchy in the new revenue recognition accounting guidance.

The Company recognizes product revenues when there is persuasive evidence of an arrangement, the fee is fixed or determinable, collection of the fee is probable and delivery has occurred. Payments received in advance of product shipment are recorded as customer advances and are recognized as revenue or deferred revenue upon product shipment or installation.

The Company assesses the probability of collection based on a number of factors, including past transaction history with the customer and the credit-worthiness of the customer. The Company generally does not request collateral from its customers. If the Company determines that collection is not probable, the Company will defer the fee and recognize revenue upon receipt of cash.

The Company records revenues from sales of systems to distributors on either a sell-through or sell-in basis, depending on the terms of the distribution agreement as well as terms and conditions executed for each sale, and once all revenue recognition criteria have been met. For sales of product upgrades and accessories to distributors, revenue is recognized on either a sell-through or sell-in basis, depending upon the terms of the purchase order or signed quotation and once all revenue recognition criteria have been met.

The Company's agreements with customers and distributors for system sales generally do not contain product return rights. Certain distributor agreements include parts inventory buy-back provisions upon distributorship termination. The Company accrues an inventory buy-back liability when and if such distributorship termination is expected and the liability can be estimated.

Product Revenue

The majority of product revenue is generated from sales of CyberKnife and TomoTherapy systems. The Company sells its systems with PCS contracts, training points, and at times, professional services. PCS contracts provide planned and corrective maintenance services, software updates, bug fixes, as well as call-center support. If the Company is responsible for installation, the Company recognizes revenue after installation and acceptance of the system. Otherwise, revenue is recognized upon delivery.

Service Revenue

Service revenue is generated primarily from warranty services, post warranty services, installation services, unspecified when and if available product upgrades, training, and professional services. Warranty and post warranty service revenue is deferred and recognized ratably over the service period, generally 12-18 months, until no further obligation exists. The warranty service period generally starts upon product acceptance. Training and consulting service revenues that are not deemed essential to the functionality of the systems are recognized as such services are performed. Installation service revenue is recognized concurrent with system revenue.

Costs associated with service revenue are expensed when incurred, except when those costs are related to system upgrades where revenue recognition has been deferred. In those cases, the costs are deferred and are recognized over the period of revenue recognition.

Other revenue

Other revenue primarily consists of research and development and construction contract revenues.

Shared ownership program

The Company also enters into arrangements under its shared ownership program with certain customers. Agreements under the shared ownership program typically have a term of five years, during which the customer has the option to purchase the system, either at the end of the contractual period or in advance, at the customer's request, at pre-determined prices. Under the terms of this program, the Company retains title to its system, while the customer has use of the system. The Company generally receives a minimum monthly payment and earns additional revenues from the customer based upon its use of the system. The Company may provide unspecified upgrades during the term of each program when and if available. Upfront non-refundable payments and minimum monthly payments from the customer are recognized as revenue over the contractual period. Additional revenues beyond the minimum payments from the shared ownership program are recorded as they become earned and receivable and are included within shared ownership program revenues, which are included in products revenue in the consolidated statements of operations.

Future minimum revenues under shared ownership arrangements as of June 30, 2012 are as follows (in thousands):

Year Ending June 30,	Amount

2013	$	1,744
2014		1,789
2015		1,789
2016		1,394
2017		540

Total	$	7,256

Total usage-based fee revenues, which are included in products revenue, earned from the systems under the shared ownership program amounted to $1.7 million, $1.5 million and $1.6 million for the years ended June 30, 2012, 2011 and 2010, respectively.

Under the terms of the shared ownership program, the customer has the option to purchase the CyberKnife or TomoTherapy System at pre-determined prices based on the period the system has been in use and considering the lease payments already received. Revenue from such sales is recorded in accordance with the Company's revenue recognition policy, taking into account the PCS and any other elements that might be sold as part of the arrangement. At June 30, 2012, the Company had four systems installed under its shared ownership program. During the years ended June 30, 2012, 2011 and 2010, nil, $3.6 million and nil, respectively, of revenue was recognized in the consolidated statements of operations for the sale of nil, one and nil systems, respectively, that were formerly under the shared ownership program.

The systems associated with the Company's shared ownership program are recorded within property and equipment on the accompanying consolidated balance sheets. Depreciation and warranty expenses attributable to the shared ownership systems are recorded within cost of products in the accompanying consolidated statements of operations.

Long-term construction and manufacturing contracts

The Company recognizes revenue and cost of revenue related to long-term construction and manufacturing contracts using contract accounting on the percentage-of-completion or the completed contract method. The Company records such revenue under other revenue and cost of such revenue under cost of other in the consolidated statements of operations. Any loss provision identified from the total contract in the period is recorded as an increase to cost of revenue.

Deferred Revenue and Deferred Cost of Revenue

Deferred revenue consists of deferred product revenue, deferred shared ownership program revenue and deferred service revenue. Deferred product revenue arises from timing differences between the shipment of product and satisfaction of all revenue recognition criteria consistent with the Company's revenue recognition policy. Deferred shared ownership program revenue results from the receipt of advance payments that will be recognized ratably over the term of the shared ownership program. Deferred service revenue results from the advance payment for services to be delivered over a period of time, usually one year. Service revenue is recognized ratably over the service period. Deferred cost of revenue consists of the direct costs associated with the manufacturing of units and direct service costs for which the revenue has been deferred in accordance with the Company's revenue recognition policies. Deferred revenue and associated deferred cost of revenue expected to be realized within one year are classified as current liabilities and current assets, respectively.

Customer Advances

Customer advances represent payments made by customers in advance of product shipment.

Property and Equipment

Property and equipment are stated at cost and are depreciated using the straight-line method over the estimated useful lives of the related assets. Leasehold improvements are depreciated on a straight-line basis over the remaining term of the lease or the estimated useful life of the asset, whichever is shorter. Machinery and equipment are depreciated over five years. Furniture and fixtures are depreciated over four years. Computer and office equipment and computer software are depreciated over three years. Repairs and maintenance costs, which are not considered improvements and do not extend the useful life of the property and equipment, are expensed as incurred.

Software Capitalization Costs

The Company capitalizes certain costs associated with obtaining or developing internal use software, including external direct costs of material and services. Software development costs relating to assets to be sold in the normal course of business are included in research and development and are expensed as incurred until technological feasibility is established. After technological feasibility is established, material software development costs are capitalized. The capitalized cost is then amortized on a straight-line basis over the estimated product life, or on the ratio of current revenues to total projected product revenue, whichever is greater. To date, the period between achieving technological feasibility, which the Company has defined as the establishment of a working model which typically occurs when the beta testing commences, and the general availability of such software has been short and software development costs qualifying for capitalization have been insignificant.

Capitalized software costs are included in property, plant and equipment and amortized beginning when the software project is complete and the assets is ready for its intended use. The Company has capitalized software development costs relating to internal use software as identified and discussed below at Note 5, Balance Sheet Components.

Impairment of Long-Lived Assets

The Company reviews long-lived assets, including property and equipment, for impairment whenever events or changes in business circumstances indicate that the carrying amount of the assets may not be fully recoverable using pretax undiscounted cash flows. Impairment, if any, is measured as the amount by which the carrying value of a long-lived asset exceeds its fair value. Through June 30, 2012, there have been no such impairment losses.

Goodwill and Acquired Intangible Assets

Goodwill represents the excess of acquisition cost over the fair value of tangible and identified intangible net assets of businesses acquired. Goodwill is not amortized, but is evaluated for impairment on an annual basis or when impairment indicators are present. The Company has assessed that it has one reporting unit and the consolidated net assets, including existing goodwill and other intangible assets, are considered to be the carrying value of the reporting unit. The Company estimates the fair value of the reporting unit based on the Company's closing stock price on the trading day closest to the annual review date multiplied by the outstanding shares on that date. If the carrying value of the reporting unit is in excess of its fair value, an impairment may exist, and the Company must perform the second step of the analysis, in which the implied fair value of the goodwill is compared to its carrying value to determine the impairment charge, if any. If the estimated fair value of the reporting unit exceeds the carrying value of the reporting unit, goodwill is not impaired and no further analysis is required. Through June 30, 2012, there have been no such impairment losses.

Purchased intangible assets other than goodwill, including developed technology, in-process research and development, backlog and distributor license, are amortized on a straight-line basis over their estimated useful lives unless their lives are determined to be indefinite. Purchased intangible assets are carried at cost, less accumulated amortization. Amortization is computed over the estimated useful lives of the respective assets which range from approximately one to six years.

Business Combinations

In fiscal 2011, the Company accounted for the acquisition of TomoTherapy using the acquisition method of accounting. The underlying principles of this method require that the Company recognize separately from goodwill the assets acquired and the liabilities assumed, generally at their acquisition date fair values. Goodwill as of the acquisition date is measured as the excess of consideration transferred and the net of the acquisition date fair values of the assets acquired and the liabilities assumed. While the Company uses its best estimates and assumptions as a part of the purchase price allocation process to accurately value assets acquired and liabilities assumed at the acquisition date, its estimates are inherently uncertain and subject to refinement. As a result, during the measurement period, which may be up to one year from the acquisition date, the Company may record adjustments to the assets acquired and liabilities assumed, with the corresponding offset to goodwill. Upon the conclusion of the measurement period or final determination of the values of assets acquired or liabilities assumed, whichever comes first, subsequent adjustments, if any, are recorded to the Company's consolidated statements of operations. Transaction costs and costs to restructure the acquired company are expensed as incurred. The operating results of the acquired company are reflected in the Company's consolidated financial statements after the date of the merger or acquisition.

Shipping and Handling

The Company's billings for shipping and handling for product shipments to customers are included in cost of products. Shipping and handling costs incurred for inventory purchases are capitalized in inventory and expensed in cost of products.

Advertising Expenses

The Company expenses the costs of advertising and promoting its products and services as incurred. Advertising expenses were approximately $0.5 million, $0.4 million and $0.4 million for the years ended June 30, 2012, 2011 and 2010, respectively.

Research and Development Costs

Costs related to research, design and development of products are charged to research and development expense as incurred. These costs include direct salaries, benefits, and other headcount related costs for research and development personnel; costs for materials used in research and development activities; costs for outside services and allocated portions of facilities and other corporate costs. The Company has entered into research and clinical study arrangements with selected hospitals, cancer treatment centers, academic institutions and research institutions worldwide. These agreements support the Company's internal research and development capabilities.

Share-Based Compensation

The Company accounts for share-based compensation by measuring and recognizing the fair value of all share-based payment awards made to employees based on the estimated grant date fair values, including employee stock options, restricted stock units ("RSUs"), restricted stock awards ("RSAs"), performance stock units ("PSUs") and the employee stock purchase plan ("ESPP"). The determination of fair value involves a number of significant estimates. The Company uses the Black-Scholes model to estimate the value of employee stock options and ESPP, which requires a number of assumptions to determine the model inputs. These include the expected volatility of the Company's stock, the expected term of the option, the expected risk free rate of interest and dividend yields. As share-based compensation expense is based on awards ultimately expected to vest, the expense is recorded net of estimated forfeitures. Forfeitures are estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. As the Company has been operating as a public company for a period of time that is shorter than its estimated expected option term, the Company concluded that its historical price volatility does not provide a reasonable basis for the expected volatility input assumption within its Black-Scholes model when determining the fair value of its stock options. Expected volatility was based on the historical volatility of a peer group of publicly traded companies. The Company continues to use the "simplified" method for the estimated term of the awards. Management's estimate of forfeitures is based on historical experience, but actual forfeitures could differ materially as a result of voluntary employee terminations which could result in a significant change in future share-based compensation expense. See Note 9, Stockholders' Equity, for additional information.

Net Income (Loss) Per Common Share

Basic net income (loss) per share is computed by dividing net income (loss) attributable to stockholders by the weighted- average number of common shares outstanding during the period. Diluted net income (loss) per share is computed by dividing net income (loss) attributable to stockholders by the weighted average number of common shares outstanding and other dilutive common shares outstanding during the period. The potential dilutive shares of the Company's common stock resulting from the assumed exercise of outstanding stock options, the vesting of RSUs and PSUs, and the purchase of ESPP shares, as determined under the treasury stock method, are included in the computation of diluted net income (loss) per share if their effect would have been dilutive.

A reconciliation of the numerator and denominator used in the calculation of basic and diluted net income (loss) per share follows (in thousands):

	Years ended June 30,

	2012			2011			2010
Numerator:
Net income (loss) used in computing basic and diluted net income (loss) per share		(72,042	)		(26,682	)		2,841

Denominator:
Weighted average shares used in computing basic net income (loss) per share		70,887			60,085			57,560
Add: Dilutive stock options and awards outstanding		—			—			2,631

Weighted average shares used in computing diluted net income (loss) per share		70,887			60,085			60,191

The following table sets forth all potentially dilutive securities excluded from the computation in the table above because their effect would have been anti-dilutive (in thousands):

	As of June 30,

	2012		2011		2010
Option to purchase common stock		7,873		8,337		4,057
Restricted stock units		1,171		658		260
Performance stock units		926		—		—

		9,970		8,995		4,317

The 3.75% Convertible Senior Notes due August 1, 2016 (the "Convertible Notes") are included in the calculation of diluted net income per share if their inclusion is dilutive under the if-converted method. For the year ended June 30, 2012, the potential dilutive shares under the convertible notes were excluded from the calculation of diluted net loss per share as their inclusion would be anti-dilutive. See Note 14, Debt, for further details.

Income Taxes

The Company is required to estimate its income taxes in each of the tax jurisdictions in which it operates prior to the completion and filing of tax returns for such periods. This process involves estimating actual current tax expense together with assessing temporary differences in the treatment of items for tax purposes versus financial accounting purposes that may create net deferred tax assets and liabilities. The Company accounts for income taxes under the asset and liability method, which requires, among other things, that deferred income taxes be provided for temporary differences between the tax bases of the Company's assets and liabilities and their financial statement reported amounts. In addition, deferred tax assets are recorded for the future benefit of utilizing net operating losses, research and development credit carryforwards, and other deferred tax assets.

The Company records a valuation allowance to reduce its deferred tax assets to the amount the Company believes is more likely than not to be realized. Because of the uncertainty of the realization of the deferred tax assets, the Company has recorded a full valuation allowance against its domestic and certain foreign net deferred tax assets.

The calculation of unrecognized tax benefits involves dealing with uncertainties in the application of complex global tax regulations. Management regularly assesses the Company's tax positions in light of legislative, bilateral tax treaty, regulatory and judicial developments in the countries in which the Company does business. The Company anticipates that except for $0.3 million in uncertain tax positions that may be reduced related to the lapse of various statutes of limitation, there will be no material changes in uncertain tax positions in the next 12 months.

Comprehensive Income (Loss)

Comprehensive income (loss) is comprised of net income (loss) and other comprehensive income (loss). Other comprehensive income (loss) consists of foreign currency translation adjustments for years ended June 30, 2012, 2011 and 2010, and unrealized gains and losses on investments for years ended June 30, 2011 and 2010, that have been excluded from the determination of net income (loss). The Company has reported the components of comprehensive income (loss) for the years ended June 30, 2012, 2011 and 2010 in its consolidated statement of stockholders' equity.

Segment Information

The Company has determined that it operates in only one segment, as it only reports profit and loss information on an aggregate basis to its chief operating decision maker. The Company's long-lived assets maintained outside the United States are not material. Revenue by geographic region is based on the shipping addresses of the Company's customers. The following summarizes revenue by geographic region (in thousands):

	Years ended June 30,

	2012		2011		2010
Americas (including Puerto Rico)	$	189,072	$	122,636	$	147,381
Europe		110,331		67,244		58,049
Asia (excluding Japan)		64,026		16,158		5,608
Japan		45,794		16,246		10,587

Total	$	409,223	$	222,284	$	221,625

Recent Accounting Pronouncements

In July 2012, the FASB issued ASU 2012-02, Testing Indefinite-Lived Intangible Assets for Impairment (Topic 350—the revised standard). The revised standard allows an entity the option to first assess qualitatively whether it is more likely than not that an indefinite-lived intangible asset is impaired, thus necessitating that it perform the quantitative impairment test. An entity is not required to calculate the fair value of an indefinite-lived intangible asset and perform the quantitative impairment test unless the entity determined that it is more likely than not that the asset is impaired. The revised standard is effective for annual and interim impairment tests performed for fiscal years beginning after September 15, 2012. Early adoption is permitted for annual and interim goodwill impairment tests if an entity's financial statements for the most recent interim period have not yet been issued. The Company does not expect that adoption of this guidance during fiscal 2013 will have a material impact on the Company's consolidated financial position, results of operations or cash flows.

In September 2011, the FASB issued ASU 2011-08, Intangibles—Goodwill and Other (Topic 350): Testing Goodwill for Impairment, applicable for annual and interim goodwill impairment tests performed for fiscal years beginning after December 15, 2011. The guidance allows an entity the option to make a qualitative evaluation about the likelihood of goodwill impairment for a reporting unit. If, after assessing the totality of events or circumstances, an entity determines it is not more likely than not that the fair value of a reporting unit is less than its carrying amount, then performing the quantitative two-step impairment test is unnecessary. Early adoption is permitted for annual and interim goodwill impairment tests if an entity's financial statements for the most recent interim period have not yet been issued. The Company does not expect that adoption of this guidance during fiscal 2013 will have a material impact on the Company's consolidated financial position, results of operations or cash flows.

In June 2011, the FASB issued ASU 2011-05, Comprehensive Income (Topic 220)—Presentation of Comprehensive Income, to require an entity to present the total of comprehensive income, the components of net income, and the components of other comprehensive income either in a single continuous statement of comprehensive income or in two separate but consecutive statements. ASU 2011-05 eliminates the option to present the components of other comprehensive income as part of the statement of equity. The FASB issued ASU 2011-12 in December 2011 to defer certain presentation requirements of the new guidance. ASU 2011-05 is effective for the Company in the first quarter of fiscal year 2013 and will be applied retrospectively. The adoption of these standards will only result in changes in the financial statement presentation.

Alliance Agreement

12 Months Ended

Jun. 30, 2012

Alliance Agreement

Alliance Agreement

3. Alliance Agreement

In June 2010, the Company entered into a Strategic Alliance Agreement (the "Alliance Agreement") with Siemens AG ("Siemens"), pursuant to which (1) the Company granted Siemens certain distribution rights to our CyberKnife Systems, (2) Siemens agreed to incorporate certain Accuray technology into certain of its linear accelerator ("linac") products, and (3) the Company created a research and development relationship with Siemens for the pursuit and implementation of other potential collaboration opportunities. Siemens terminated the Alliance Agreement effective December 23, 2011, thereby terminating the elements described in clauses (2) and (3) above. On December 26, 2011, Siemens and the Company entered into a distribution agreement pursuant to which Siemens has the right to distribute both CyberKnife and TomoTherapy Systems. The term of this agreement ends in March 2013. Sales to date under the Siemens Alliance Agreement and subsequent distribution agreement with Accuray have not been material.

In April 2012, Siemens and Varian Medical Systems, Inc. ("Varian") announced that they had entered into a strategic global partnership involving mutual marketing and representation of products for imaging and treatment in the global radiation oncology business, the development of software interfaces between Siemens and Varian treatment systems and potential joint development of new products. Given this announcement, the Company anticipates that Siemens will distribute few, if any, CyberKnife or TomoTherapy Systems during the remaining term of its distribution agreement.

Financial Instruments

12 Months Ended

Jun. 30, 2012

Financial Instruments

Financial Instruments

4. Financial Instruments

The Company defines fair value as the price that would be received to sell an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. The fair value hierarchy contains three levels of inputs that may be used to measure fair value, as follows:

Level 1— Unadjusted quoted prices that are available in active markets for the identical assets or liabilities at the measurement date.

Level 2— Other observable inputs available at the measurement date, other than quoted prices included in Level 1, either directly or indirectly, including:
- •
  
  Quoted prices for similar assets or liabilities in active markets;
  
  •
  
  Quoted prices for identical or similar assets in non-active markets;
  
  •
  
  Inputs other than quoted prices that are observable for the asset or liability; and
  
  •
  
  Inputs that are derived principally from or corroborated by other observable market data.
Level 3— Unobservable inputs that cannot be corroborated by observable market data and reflect the use of significant management judgment. These values are generally determined using pricing models for which the assumptions utilize management's estimates of market participant assumptions.

At June 30, 2012, the Company held money market funds totaling $40.1 million, which are included in cash equivalents on the consolidated balance sheet. These money market funds are measured on a recurring basis using Level 1 inputs.

The fair value of the 3.75% Convertible Senior Notes due August 1, 2016 (the "Convertible Notes") was approximately $101.4 million at June 30, 2012 and is measured on a non-recurring basis using Level 2 inputs based upon observable inputs of the Company's underlying stock price and the time value of the conversion option, since an observable quoted price of the Convertible Notes is not readily available. Refer to "Note 14, Debt" for details.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 820
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=7578670&loc=d3e19207-110258

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
-SubTopic 10
-Section 50
-Paragraph 30
-URI http://asc.fasb.org/extlink&oid=6957238&loc=d3e14172-108612

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
-SubTopic 10
-Section 50
-Paragraph 21
-URI http://asc.fasb.org/extlink&oid=7491637&loc=d3e13537-108611

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
-SubTopic 10
-Section 50
-Paragraph 28
-URI http://asc.fasb.org/extlink&oid=6957238&loc=d3e14064-108612

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
-SubTopic 10
-Section 50
-Paragraph 16
-URI http://asc.fasb.org/extlink&oid=7491637&loc=d3e13504-108611

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
-SubTopic 10
-Section 50
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=7491637&loc=d3e13433-108611

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 15B
-Subparagraph a, b
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 133
-Paragraph 44A, 44B
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 159
-Paragraph 17-22, 27, 28
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 15A
-Subparagraph a-d
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 15C, 15D
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 157
-Paragraph 32, 33, 34
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 3, 10, 14, 15
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Balance Sheet Components

12 Months Ended

Jun. 30, 2012

Balance Sheet Components

Balance Sheet Components

5. Balance Sheet Components

Accounts receivable, net

Accounts receivable, net consisted of the following (in thousands):

	June 30,

	2012			2011
Accounts receivable	$	69,285		$	59,858
Unbilled fees and services		305			2,319

		69,590			62,177
Less: Allowance for doubtful accounts		(1,700	)		(324	)

Accounts receivable, net	$	67,890		$	61,853

Financing receivables

A financing receivable is a contractual right to receive money, on demand or on fixed or determinable dates, that is recognized as an asset in the creditor's balance sheet. The Company's financing receivables, consisting of its accounts receivable with contractual maturities of more than one year, was $2.5 million and nil at June 30, 2012 and 2011, respectively and are included in Other Assets in the consolidated balance sheet. There was no balance or activity in the allowance for doubtful financing receivable accounts as of or during the years ended June 30, 2012 and 2011.

Inventories

Inventories consisted of the following (in thousands):

	June 30,

	2012		2011(1)
Raw materials	$	42,951	$	32,988
Work-in-process		16,932		28,216
Finished goods		21,810		36,632

Inventories	$	81,693	$	97,836

(1): Prior year numbers have been reclassified to conform to current year classification and presentation.

Property and Equipment, net

Property and equipment consisted of the following (in thousands):

	June 30,

	2012			2011
Furniture and fixtures	$	5,921		$	5,317
Computer and office equipment		9,126			8,280
Software		9,429			8,107
Leasehold improvements		16,065			15,386
Machinery and equipment		33,493			33,692
Shared ownership systems		4,979			4,923
Construction in progress		3,787			602

		82,800			76,307
Less: Accumulated depreciation and amortization		(45,342	)		(31,484	)

Property and equipment, net	$	37,458		$	44,823

Depreciation and amortization expense related to property and equipment for the years ended June 30, 2012, 2011 and 2010 was $16.4 million, $6.4 million and $6.8 million, respectively. Accumulated depreciation related to the CyberKnife and TomoTherapy Systems attributable to the shared ownership program at June 30, 2012 and 2011 was $1.3 million and $2.1 million, respectively.

Investment

12 Months Ended

Jun. 30, 2012

Investment

Investment

6. Investment

Morphormics

In 2008, the Company purchased 120,000 shares of Morphormics Series C Preferred Stock at $12.50 per share, for a total purchase price of $1.5 million. The investment is carried at zero value as of June 30, 2012 and 2011. See Note 18, Subsequent Events, for further details.

- Definition

The entire disclosure for investments in certain debt and equity securities.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-Glossary Debt Security
-URI http://asc.fasb.org/extlink&oid=6509901

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 310
-SubTopic 30
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6379141&loc=d3e15032-111544

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27290-111563

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-Glossary Equity Security
-URI http://asc.fasb.org/extlink&oid=6511694

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27232-111563

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 320
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62557-112803

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 9
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27357-111563

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27161-111563

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27405-111563

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 3, 19, 20, 21, 22, 137
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Goodwill and Intangible Assets

12 Months Ended

Jun. 30, 2012

Goodwill and Intangible Assets

Goodwill and Intangible Assets

7. Goodwill and Intangible Assets

Goodwill

Goodwill as of June 30, 2012 and 2011 and changes in the carrying amount of goodwill for the respective periods are as follows (in thousands):

	Year Ended June 30, 2012		Year Ended June 30, 2011

Balance at the beginning of the period	$	54,474	$	4,495
Addition related to acquisition		—		49,979
Adjustments related to prior year acquisition(1)		4,741		—

Balance at the end of the period	$	59,215	$	54,474

(1): Primarily represents liabilities related to the TomoTherapy acquisition.

Intangible Assets

The Company's intangible assets associated with completed acquisitions at June 30, 2012 and 2011 are as follows: (in thousands):

		June 30, 2012							June 30, 2011

	Useful Lives	Gross Carrying Amount		Accumulated Amortization			Net Amount		Gross Carrying Amount		Accumulated Amortization			Net Amount
	(in years)
Developed technology	6.0	$	43,455	$	(9,161	)	$	34,294	$	43,455	$	(2,069	)	$	41,386
Backlog	1.25		10,500		(8,867	)		1,633		10,500		(467	)		10,033
Distributor license	2.5		1,860		(768	)		1,092		1,860		(40	)		1,820
In-process research and development (CPAC)	Indefinite		12,800		—			12,800		12,800		—			12,800

		$	68,615	$	(18,796	)	$	49,819	$	68,615	$	(2,576	)	$	66,039

During the year ended June 30, 2011, the Company recorded additions to intangible assets of $66.8 million related to the acquisition of TomoTherapy. See Note 12, Acquisition, for additional information on the acquisition of TomoTherapy. Amortization expense related to intangible assets was $16.2 million, $1.2 million and $0.3 million for the years ended June 30, 2012, 2011 and 2010, respectively. During the years ended June 30, 2012, 2011 and 2010, the Company did not record any impairment charges as a result of its analysis of its intangible assets.

The estimated future amortization expense of purchased intangible assets, excluding in-process research and development, as of June 30, 2012, is as follows (in thousands):

Year Ending June 30,	Amount

2013	$	9,306
2014		7,298
2015		6,933
2016		6,933
2017		6,549

	$	37,019

- Definition

The entire disclosure for the aggregate amount of goodwill and a description of intangible assets, which may include (a) for amortizable intangible assets (also referred to as finite-lived intangible assets), the carrying amount, the amount of any significant residual value, and the weighted-average amortization period, (b) for intangible assets not subject to amortization (also referred to as indefinite-lived intangible assets), the carrying amount, and (c) the amount of research and development assets acquired and written off in the period, including the line item in the income statement in which the amounts written off are aggregated, if not readily apparent from the income statement. Also discloses (a) for amortizable intangibles assets in total and by major class, the gross carrying amount and accumulated amortization, the total amortization expense for the period, and the estimated aggregate amortization expense for each of the five succeeding fiscal years, (b) for intangible assets not subject to amortization the carrying amount in total and by major class, and (c) for goodwill, in total and for each reportable segment, the changes in the carrying amount of goodwill during the period (including the aggregate amount of goodwill acquired, the aggregate amount of impairment losses recognized, and the amount of goodwill included in the gain (loss) on disposal of a reporting unit). If any part of goodwill has not been allocated to a reportable segment, discloses the unallocated amount and the reasons for not allocating. For each impairment loss recognized related to an intangible asset (excluding goodwill), discloses: (a) a description of the impaired intangible asset and the facts and circumstances leading to the impairment, (b) the amount of the impairment loss and the method for determining fair value, (c) the caption in the income statement or the statement of activities in which the impairment loss is aggregated, and (d) the segment in which the impaired intangible asset is reported. For each goodwill impairment loss recognized, discloses: (a) a description of the facts and circumstances leading to the impairment, (b) the amount of the impairment loss and the method of determining the fair value of the associated reporting unit, and (c) if a recognized impairment loss is an estimate not finalized and the reasons why the estimate is not final. May also disclose the nature and amount of any significant adjustments made to a previous estimate of an impairment loss.

+ References + Details

Commitments and Contingencies

12 Months Ended

Jun. 30, 2012

Commitments and Contingencies.

Commitments and Contingencies

8. Commitments and Contingencies

Operating Lease Agreements and Long-term Debt

The Company leases office and manufacturing space under non-cancelable operating leases with various expiration dates through December 2018. Rent expense, including common area maintenance, was $7.1 million, $4.8 million and $5.2 million for the years ended June 30, 2012, 2011 and 2010, respectively. The terms of the facility leases provide for rental payments on a graduated scale. The Company recognizes rent expense on a straight-line basis over the lease period, and has accrued for rent expense incurred but not paid.

The Company is required to make semi-annual interest payments on the Convertible Notes. See Note 14, Debt, for details.

Future minimum lease payments under non-cancelable operating lease agreements and long-term principal and interest on the Convertible Note as of June 30, 2012 are as follows (in thousands):

Year Ending June 30,	Operating Leases		Long-term Debt(1)

2013	$	8,021	$	3,750
2014		7,245		3,750
2015		4,681		3,750
2016		2,272		3,750
2017		2,325		100,313
Thereafter		2,645		—

Total	$	27,189	$	115,313

(1): These amounts represent principal and interest cash payments over the life of the debt obligations, including anticipated interest payments that are not recorded on the Company's consolidated balance sheet. Any conversion, redemption or purchase of Convertible Notes would impact cash payments.

The Company enters into standard indemnification agreements with its landlords and all superior mortgagees and their respective directors, officers' agents, and employees in the ordinary course of business. Pursuant to these agreements, the Company will indemnify, hold harmless, and agree to reimburse the indemnified party for losses suffered or incurred by the indemnified party, generally the landlords, in connection with any loss, accident, injury, or damage by any third party with respect to the leased facilities. The term of these indemnification agreements is from the commencement of the lease agreements until termination of the lease agreements. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, historically the Company has not incurred claims or costs to defend lawsuits or settle claims related to these indemnification agreements. The Company has recorded no liability associated with its indemnification agreements as it is not aware of any pending or threatened actions that represent probable losses as of June 30, 2012.

Royalty Agreements

In March 2007, the Company entered into a license and royalty agreement with Deutsches Krebsforschungszentrum ("DKFZ"), a German cancer research center. Under this agreement, the Company has a non-exclusive license to use certain technology. The Company is obligated to pay DKFZ $12,500 for each CyberKnife System sold that includes the licensed technology, with the stipulation that the Company must make minimum annual payments of $50,000. Royalty expense under this agreement recorded in cost of revenue or deferred cost of revenue was $0.1 million, $0.6 million and $0.6 million for the years ended June 30, 2012, 2011 and 2010, respectively. At June 30, 2012 and 2011, the Company accrued approximately $25,000 and $0.3 million, respectively, under this agreement and the amounts are included in other accrued liabilities in the accompanying consolidated balance sheets.

The Company, as a result of the acquisition of TomoTherapy, has a license and royalty agreement with RaySearch Laboratories AB, a Swedish provider of treatment planning software. Under this agreement, the Company has a non-exclusive license to use certain technology until September 2013. The Company is obligated to pay RaySearch $25,000 for each TomoTherapy System sold that includes the licensed technology, with the stipulation that the Company must make minimum annual payments of $750,000 for the remainder of the licensing term. Royalty expense under this agreement recorded in cost of revenue or deferred cost of revenue was $0.7 million, $40,000 and nil for the years ended June 30, 2012, 2011 and 2010, respectively. At June 30, 2012 and 2011, the Company accrued approximately $0.6 million and $0.6 million, respectively, under this agreement and the amounts are included in other accrued liabilities in the accompanying consolidated balance sheets.

The Company, as result of the acquisition of TomoTherapy, has an exclusive license agreement with the Wisconsin Alumni Research Foundation (WARF), a shareholder of the Company, to make, use, sell and otherwise distribute products under certain of WARF's patents anywhere in the world. The Company is required to pay WARF a royalty for each product sold. The license agreement expires upon expiration of the patents and may be terminated earlier if the Company so elects. The Company may also grant sublicenses to third parties but must pay WARF 50% of all fees, royalties and other payments received. WARF has the right to terminate the license agreement if the Company does not meet the minimum royalty obligations, which are $0.3 million per year, or if the Company commits any breach of the license agreement's covenants. If the Company were to lose this license, it would be unable to produce or sell the TomoTherapy Systems. Royalty expense under this agreement recorded in cost of revenue or deferred cost of revenue was $1.0 million, nil and nil for the years ended June 30, 2012, 2011 and 2010, respectively. At June 30, 2012 and 2011, the Company accrued approximately $0.1 million and $0.3 million, respectively, under this agreement and the amounts are included in other accrued liabilities in the accompanying consolidated balance sheets.

Contingencies

From time to time, the Company may become involved in litigation relating to claims arising during the ordinary course of business. Management does not believe the final disposition of these matters will have a material adverse effect on the financial position, results of operations or future cash flows of the Company.

Software License Indemnity

Under the terms of the Company's software license agreements with its customers, the Company agrees that in the event the software sold infringes upon any patent, copyright, trademark, or any other proprietary right of a third party, it will indemnify its customer licensees against any loss, expense, or liability from any damages that may be awarded against its customer. The Company includes this infringement indemnification in all of its software license agreements and selected managed services arrangements. In the event the customer cannot use the software or service due to infringement and the Company cannot obtain the right to use, replace or modify the license or service in a commercially feasible manner so that it no longer infringes, then the Company may terminate the license and provide the customer a refund of the fees paid by the customer for the infringing license or service. The Company has recorded no liability associated with this indemnification, as it is not aware of any pending or threatened actions that represent probable losses as of June 30, 2012.

Litigation

From time to time, the Company is involved in legal proceedings arising in the ordinary course of its business. Currently, management believes the Company does not have any probable and estimable loss related to any current legal proceedings and claims that would individually or in the aggregate materially adversely affect its financial condition or operating results. Litigation is inherently unpredictable and is subject to significant uncertainties, some of which are beyond the Company's control. Should any of these estimates and assumptions change or prove to have been incorrect, the Company could incur significant charges related to legal matters which could have a material impact on its results of operations, financial position and cash flows.

Accuray Securities Litigation

On July 22, 2009, a securities class action lawsuit was filed in the U.S. District Court for the Northern District of California against the Company and certain of its current and former directors and officers. On August 7, 2009 and August 9, 2009, two securities class action complaints, both similar to the one filed on July 22, 2009, were filed against the same defendants in the same court. These three actions were consolidated. The consolidated complaint generally alleged that the Company and the individual defendants made false or misleading public statements regarding its operations and sought unspecified monetary damages and other relief. On August 31, 2010, the Court granted defendants' motion to dismiss the consolidated complaint and granted plaintiffs leave to file an amended complaint. On September 27, 2010, plaintiffs filed an amended complaint. The amended complaint named the Company and certain of its current and former officers and directors as defendants and generally alleged that the defendants made false or misleading public statements regarding its operations. The amended complaint sought unspecified monetary damages and other relief. Defendants filed a motion to dismiss the amended complaint. On April 28, 2011, the parties filed a stipulation of settlement with the court, providing for the settlement of the litigation for a payment of $13.5 million which was covered by insurance. The court preliminarily approved the settlement on June 10, 2011. A hearing on the terms of the settlement was held on September 1, 2011. On December 8, 2011, the Court issued its final judgment and order of dismissal with prejudice.

Litigation relating to the TomoTherapy Acquisition

On March 11, 2011, a purported class action complaint was filed in the Circuit Court for the State of Wisconsin, Dane County, on behalf of a putative class of TomoTherapy shareholders and naming as defendants TomoTherapy and TomoTherapy's board of directors (prior to the acquisition of TomoTherapy by the Company). Thereafter, four additional complaints were filed in the same court on behalf of the same class and against the same defendants, and two such complaints also named the Company and Jaguar Acquisition, Inc., a wholly-owned subsidiary of the Company ("Merger Sub"). On April 4, 2011, all five actions were consolidated. The complaints generally alleged that, in connection with the Company's then proposed merger transaction with TomoTherapy, TomoTherapy's board breached their fiduciary duties by, among other things, failing to maximize the value of TomoTherapy to its shareholders and purportedly agreeing to certain terms in the merger agreement, which were allegedly preclusive and onerous. The complaints further alleged that the Company and Merger Sub aided and abetted TomoTherapy's board of directors in their alleged breaches of fiduciary duties. The plaintiffs sought, among other things, an injunction barring consummation of the merger, rescission or recessionary damages, costs and attorney's fees. The Company and Merger Sub were dismissed from the litigation without prejudice on April 19, 2011. The consolidated complaint against TomoTherapy and the former directors of TomoTherapy was dismissed with prejudice and without costs to either party on July 5, 2011.

Best Medical Trade Secret Litigation

On September 3, 2009, Best Medical International, Inc. ("Best Medical") filed a lawsuit against the Company in the U.S. District Court for the Western District of Pennsylvania, claiming that the Company induced certain individuals to leave the employment of Best Medical and join the Company in order to gain access to Best Medical's confidential information and trade secrets. Best Medical is seeking monetary damages and other relief. The Company filed a motion for summary judgment on May 20, 2011, Best Medical filed its response on June 21, 2011, and the Company filed a response to their response on July 8, 2011. On October 25, 2011, the court granted summary judgment in favor of the Company on all counts. On November 21, 2011 Best Medical filed a notice of appeal, and the parties await a ruling by the appellate court. At this time, the Company does not have enough information to estimate what, if any, financial impact this claim will have.

Best Medical Patent Litigation

On August 6, 2010, Best Medical filed an additional lawsuit against the Company in the U.S. District Court for the Western District of Pennsylvania, claiming that the Company has infringed U.S. Patent No. 5,596,619; a patent that Best Medical alleges protects a method and apparatus for conformal radiation therapy. On December 2, 2010, the Court granted the Company's motion to dismiss, with leave to amend. On December 16, 2010, Best Medical filed an amended complaint, claiming that the Company also infringed U.S. Patent Nos. 6,038,283 and 7,266,175, both of which Best Medical alleges cover methods and apparatus for conformal radiation therapy. On March 9, 2011, the Court dismissed with prejudice all counts against the Company, except for two counts of alleged willful infringement of two of the patents. The Court issued a Scheduling Order on May 12, 2011 appointing a special master for claim construction, and setting a claim construction hearing on January 10, 2012. Best Medical moved to voluntarily dismiss one of the two remaining patent claims on June 28, 2011, which the court granted on June 30, 2011, leaving only one patent (U.S. Patent No. 6,038,283) at issue in the case. The Court held a claim construction hearing on May 16, 2012, and we await a ruling by the Court. Best Medical is seeking declaratory and injunctive relief, as well as unspecified compensatory and treble damages and other relief. At this time, the Company does not have enough information to estimate what, if any, financial impact this claim will have.

TomoTherapy Former Distributor in Japan

On July 17, 2009, Hi-Art Co., Ltd. (Hi-Art), TomoTherapy's former distributor in Japan, filed a complaint against TomoTherapy in the Tokyo District Court seeking compensation it claimed was owed by TomoTherapy. The Company and Hi-Art entered into a settlement agreement pursuant to which the Company agreed to pay 190,000,000 yen (or approximately $2.3 million) and Hi-Art dropped all claims against TomoTherapy and the Company. On July 26, 2011, the Court approved the settlement and issued a decree dismissing the case. The settlement amount was paid during the fiscal quarter ended September 30, 2011.

Rotary Systems

On April 28, 2011, a former supplier to TomoTherapy, Rotary Systems Incorporated, filed suit in Minnesota state court, Tenth Judicial District, Anoka County, against TomoTherapy alleging misappropriation of trade secrets, as well as several other counts alleging various theories of injury. Rotary Systems alleges TomoTherapy misappropriated Rotary Systems' trade secrets pertaining to a component previously purchased from Rotary Systems, which component TomoTherapy now purchases from a different supplier. The suit alleges TomoTherapy improperly supplied the alleged trade secrets to its present supplier, Dynamic Sealing Technologies Inc. (also a named defendant in the suit). Rotary Systems has made an unspecified claim for damages of greater than $50,000. TomoTherapy moved to dismiss the case in June 2011, and on August 29, 2011, the court granted the motion to dismiss with respect to all counts other than the count alleging misappropriation of trade secrets. At this time, the Company does not have enough information to estimate what, if any, financial impact this claim will have.

Radiation Stabilization Solutions Patent Litigation

On September 15, 2011, Radiation Stabilization Solutions LLC ("Radiation Stabilization Solutions") filed a patent infringement complaint in the United States District Court for the Northern District of Illinois, Eastern Division. The complaint, alleged the Company's sale of the TomoHD product induces infringement of or contributorily infringes U.S. Patent No. 6,118,848, or the '848 Patent, and sought unspecified monetary damages for the alleged infringement. The complaint also named Varian Medical Systems, Inc., BrainLab AG, BrainLab, Inc., Elekta AB and Elekta, Inc. as defendants, alleging that certain of their products also infringe the '848 patent. On October 27, 2011, the Court dismissed the complaint without prejudice because non-resident defendants had been improperly named in the complaint.

On October 28, 2011, Radiation Stabilization Solutions filed a new complaint against the Company and a customer of the Company in the United States District Court for the Northern District of Illinois, Eastern Division. The new complaint repeats the original complaint's allegations against the Company and seeks unspecified monetary damages for the alleged infringement. The complaint further alleges that the customer directly and indirectly infringes the '848 patent, and seeks unspecified monetary damages for the alleged infringement. Radiation Stabilization Solutions also filed individual suits against each of Varian and Elekta and several of their respective customers. Radiation Stabilization Solutions served the complaint on Accuray and its customer on December 7, 2011. On January 30, 2012 the Company filed a motion to dismiss the complaint, and the Court heard oral argument for the motion on June 29, 2012. The parties await a ruling by the Court. At this time, the Company does not have enough information to estimate what, if any, financial impact this claim will have.

- Definition

The entire disclosure for commitments and contingencies.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
-SubTopic 20
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6449706&loc=d3e16207-108621

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 460
-SubTopic 10
-Section 50
-Paragraph 8
-URI http://asc.fasb.org/extlink&oid=6398077&loc=d3e12565-110249

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6952336&loc=d3e14435-108349

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.25)
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 440
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6394976&loc=d3e25287-109308

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Interpretation (FIN)
-Number 14
-Paragraph 3
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 5
-Paragraph 9, 10, 11, 12
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Stockholders' Equity

12 Months Ended

Jun. 30, 2012

Stockholders' Equity

Stockholders' Equity

9. Stockholders' Equity

In August 2007, the Company announced that the Board of Directors had approved a stock repurchase plan that authorized the Company to repurchase shares of its common stock. Under the plan, the Company had the ability to acquire up to $25.0 million of common shares in the open market over a period of one year. The stock repurchase plan expired in August 2008 and was not renewed by the Board of Directors. During the year ended June 30, 2012, the Company retired 2,140,018 shares of its common stock that had been repurchased in prior years. At June 30, 2012, the Company has reserved approximately 13.2 million shares of its authorized common stock for future issuance to the 3.75% Convertible Senior Note-holders, while 14.7 million shares of authorized common stock are reserved for issuance under the share-based compensation plans and the employee stock purchase plan.

Stock Options, Restricted Stock Units, Performance Stock Units and Restricted Stock Awards

At June 30, 2012, the Company has one active share-based compensation plan, the 2007 Incentive Award Plan (the '2007 Plan'). Options may be granted to employees, directors and non-employee consultants to purchase shares of the Company's common stock. Additionally, the Company grants Restricted Stock Units, or RSUs, and Performance Stock Units, or PSUs, to employees that entitle the holder to receive shares of common stock as the awards vest.

Under the 2007 Plan, the Company may issue up to 10.5 million shares, of which 2.3 million were available for future issuances as of June 30, 2012. As of June 30, 2012, the 1993 Plan and the 1998 Plan continued to remain in effect along with the 2007 Plan; however, options can no longer be granted from the 1993 and 1998 Plans, and all options which expire or are forfeited will be retired from the pool.

Only employees are eligible to receive incentive stock options. Non-employees may be granted non-qualified options. The Board of Directors has the authority to set the exercise price of all options granted, subject to the exercise price of incentive stock options being no less than 100% of the fair value of a share of common stock on the date of grant; and no less than 85% of the fair value for non-qualified stock options.

Generally, the Company's outstanding options and RSUs vest at a rate of 25% per year. However, certain RSUs granted vest 10% upon the first anniversary year of the grant date, 20% upon the second anniversary year of the grant date, 30% upon the third anniversary year of the grant date and 40% upon the fourth anniversary year of the grant date. Continued vesting typically terminates when the employment or consulting relationship ends. The maximum term of the options granted to persons who own at least 10% of the voting rights of all outstanding stock on the date of grant is five years. The maximum term of all other options is ten years. The Company's current practice with options is to issue new shares to satisfy share option exercises.

In connection with the Company's acquisition of TomoTherapy, the Company assumed 1,539,255 outstanding stock options and 429,591 RSAs under TomoTherapy's stock plans. The remaining vesting term, remaining contractual term range and exercise price range for the assumed stock options is 0 years, 0.1 to 3.4 years and $0.48 to $44.24, respectively. The remaining vesting term for the RSAs is 1.2 years.

As of June 30, 2012, there was approximately $4.5 million of unrecognized compensation cost, net of estimated forfeitures, related to RSUs, which is expected to be recognized over a weighted average period of 1.9 years. As of June 30, 2012, there was approximately $5.5 million of unrecognized compensation cost, net of estimated forfeitures, related to unvested stock options, which is expected to be recognized over a weighted average period of 2.7 years. As of June 30, 2012, there was approximately $0.5 million of unrecognized compensation cost related to RSAs, which is expected to be recognized over a weighted-average period of 1.2 years.

The Company uses the Black-Scholes option pricing model for determining the fair value of option grants. During the years ended June 30, 2012, 2011 and 2010, the following weighted average assumptions were used:

	Years Ended June 30,

	2012			2011			2010
Risk-free interest rate		0.85% - 1.72	%		1.88% - 2.44	%		2.11% - 3.04	%
Dividend yield		—			—			—
Expected life		6.25			6.25			6.25
Expected volatility		52.0% - 52.9	%		52.8% - 54.9	%		56.6% - 64.7	%

The following table summarizes the share-based compensation charges included in the Company's consolidated statements of operations (in thousands):

	Years ended June 30,

	2012		2011		2010
Cost of revenue	$	1,672	$	1,312	$	1,721
Selling and marketing		729		695		1,433
Research and development		2,340		2,922		2,850
General and administrative		3,717		8,436		4,642

	$	8,458	$	13,365	$	10,646

During the years ended June 30, 2011, the Company recognized $4.4 million of share-based compensation expense related to accelerated vesting of stock options, RSUs and RSAs in conjunction with employee separation costs. No such expenses were recognized during the year ended June 30, 2012 and 2010. At June 30, 2012 and 2011, $0.4 million and $0.3 million, respectively, of capitalized share-based compensation costs were included as components of inventory.

The aggregate intrinsic value in the table below represents the total pre-tax intrinsic value (the difference between the fair value of the Company's common stock on June 30, 2012 of $6.82 and the exercise price of the options) that would have been received by option holders if all options exercisable had been exercised on June 30, 2012. The total intrinsic value of options exercised in the years ended June 30, 2012, 2011, and 2010 was approximately $2.9 million, $6.1 million and $6.6 million, respectively. The total fair value of shares vested during the years ended June 30, 2012, 2011 and 2010 was $2.8 million, $3.4 million and $1.1 million, respectively.

Option activity during the year ended June 30, 2012 was as follows:

			Weighted Average Exercise Price			Aggregate Intrinsic Value (in thousands)

Balance at June 30, 2011	8,336,220		$	7.39	5.13	$	19,131
Options granted	1,399,424		$	4.53
Options exercised	(746,441	)	$	2.50
Options forfeited/expired	(1,116,603	)	$	9.79

Balance at June 30, 2012	7,872,600		$	7.00	5.57	$	12,359

Vested or Expected to vest at June 30, 2012	7,871,741		$	7.00	5.57	$	12,359

Exercisable at June 30, 2012	5,816,292		$	7.57	4.46	$	9,242

During the years ended June 30, 2012, 2011 and 2010, the Company recognized $3.5 million, $4.7 million and $6.6 million, respectively, of share-based compensation expense for stock options granted to employees. The weighted average fair value of options granted was $2.30, $3.91 and $3.45 per share for the years ended June 30, 2012, 2011 and 2010, respectively.

Tax benefits from tax deductions for exercised options and disqualifying dispositions in excess of the deferred tax asset attributable to stock compensation costs for such options are credited to additional paid-in capital. Realized excess tax benefits for the years ended June 30, 2012, 2011 and 2010 were nil, nil and $0.4 million, respectively.

Combined activity under the share based compensation plans were as follows:

					Weighted Average Exercise Price				Weighted Average Grant Date Fair Value

Balance at June 30, 2009	2,645,757		8,455,316		$	5.70	519,609		$	18.15
Additional shares reserved	1,500,000		—
Expirations	(325,120	)	—
Grants	(1,686,498	)	1,498,740		$	6.09	187,758		$	6.12
Forfeitures or cancellations	904,502		(831,716	)	$	9.86	(72,786	)	$	18.92
Exercises or releases	—		(1,313,749	)	$	1.55	(170,395	)	$	6.32

Balance at June 30, 2010	3,038,641		7,808,591		$	6.03	464,186		$	12.52
Additional shares reserved	1,500,000		—				—
Expirations	(151,042	)	—				—
Grants	(1,389,949	)	914,770		$	7.30	475,179		$	6.77
Options assumed	—		1,539,255		$	10.41	—		$	—
Forfeitures or cancellations	602,945		(529,711	)	$	8.60	(79,180	)	$	9.85
Exercises or releases	—		(1,396,685	)	$	2.58	(201,992	)	$	7.57

Balance at June 30, 2011	3,600,595		8,336,220		$	7.39	658,193		$	6.97

Additional shares reserved	1,500,000		—				—
Expirations	—		—				—
Grants	(3,400,449	)	1,399,424		$	4.53	2,001,025		$	4.53
Forfeitures or cancellations	617,864		(1,116,603	)	$	9.79	(259,107	)	$	5.67
Exercises or releases	—		(746,441	)	$	2.50	(302,476	)	$	4.47

Balance at June 30, 2012	2,318,010		7,872,600		$	7.00	2,097,635		$	5.16

Vested during year ended June 30, 2012							296,905		$	4.47
Non-vested at June 30, 2011							652,622		$	6.97
Non-vested at June 30, 2012							2,097,635		$	5.16

Under the 2007 Plan, the Company issued RSUs to employees and recognized $2.5 million, $2.9 million and $3.0 million of share-based compensation expense, net of estimated forfeitures, during the years ended June 30, 2012, 2011 and 2010, at a weighted average grant date fair value of $4.53, $6.77 and $6.12 per share, respectively.

The activity under the RSA Plan was as follows:

			Weighted Average Grant Date Fair Value

Balance at June 30, 2011	190,522		$	7.39
Grants	—		$	—
Forfeitures	(10,804	)	$	7.39
Releases	(147,290	)	$	7.39

Balance at June 30, 2012	32,428		$	7.39

The Company recognized $1.4 million and $5.0 million of share-based compensation expense during the years ended June 30, 2012 and 2011, respectively, for RSAs assumed in connection with the acquisition of TomoTherapy.

Employee Stock Purchase Plan

Under the Company's 2007 Employee Stock Purchase Plan ("ESPP"), qualified employees are permitted to purchase the Company's common stock at 85% of the lower of the fair market value of the common stock on the commencement date of each offering period or the fair market value on the specified purchase date. The ESPP is deemed compensatory and compensation costs are accounted for under ASC 718, Stock Compensation. The maximum number of shares authorized for sale under the ESPP is 1.2 million.

Employees' payroll deductions may not exceed 10% of their salaries. Employees may purchase up to 2,500 shares per period provided that the value of the shares purchased in any calendar year may not exceed $25,000, as calculated pursuant to the purchase plan.

The estimated fair value of ESPP shares was determined at the date of grant using the Black-Scholes option pricing model. Expected volatility was based on the historical volatility of a peer group of publicly traded companies. The expected term of six months was based upon the offering period of the ESPP. The risk-free rate for the expected term of the ESPP option was based on the U.S. Treasury Constant Maturity rate for each offering period. For the years ended June 30, 2012, 2011 and 2010, the Company recognized $1.1 million, $0.8 million and $0.8 million, respectively, of compensation expense related to its ESPP. The weighted average assumptions were as follows:

	Years Ended June 30,

	2012			2011			2010
Risk-free interest rate		0.05% - 0.12	%		0.11% - 0.23	%		0.15% - 0.29	%
Dividend yield		—			—			—
Expected life		0.50			0.50			0.50
Expected volatility		33.6% - 50.6	%		33.6% - 56.7	%		56.7% - 78.3	%

As of June 30, 2012, there was approximately $0.6 million of unrecognized compensation cost related to the ESPP, which is expected to be recognized over a weighted average period of 0.4 years. The weighted average fair value of ESPP shares was $1.80, $2.03 and $2.21 per share for the years ended June 30, 2012, 2011 and 2010, respectively.

Performance-Based Awards

During fiscal 2012, the Compensation Committee of the Board of Directors of the Company approved the granting of Performance-Based Stock Units ("PSUs") to employees of the Company which vest only upon meeting certain financial performance criteria during the performance period commencing on the first day of the Company's 2012 fiscal year and ending on the last day of the Company's 2013 fiscal year. If the PSUs do not become vested as a result of the Company's performance during the performance period, all PSUs are automatically forfeited by the participants effective as of the last day of the performance period. During the year ended June 30, 2012, approximately 1.0 million PSUs have been granted to employees valued at approximately $3.9 million which was based on the fair value of the Company's common stock on the grant date and will be recognized over the requisite performance period based on management's assessment of the probability of achieving the performance criteria. Approximately 0.9 million PSUs are outstanding as of June 30, 2012.

As of June 30, 2012, management assessed that it was not probable that the performance criteria would be met during the performance period and accordingly, no compensation cost has been recognized for the PSUs during the year ended June 30, 2012. If in a future period management revises its assessment and concludes that it is probable that the performance criteria will be met, the Company will record a cumulative catch up compensation charge for the PSUs in that period. Remaining compensation charges would be recognized ratably over the remaining performance period.

Income Taxes

12 Months Ended

Jun. 30, 2012

Income Taxes

Income Taxes

10. Income Taxes

Income (loss) before provision for (benefit from) income taxes on the accompanying statements of operations included the following components (in thousands):

	Years Ended June 30,

	2012			2011			2010
Domestic	$	(82,494	)	$	(28,621	)	$	1,169
Foreign		6,636			2,626			1,668

Total worldwide		(75,858	)		(25,995	)		2,837

The provision for (benefit from) income taxes consisted of the following (in thousands):

	Years Ended June 30,

	2012			2011		2010
Current:
Federal	$	—		$	—	$	(876	)
State		(7	)		114		265
Foreign		2,107			939		724

Total current		2,100			1,053		113
Deferred:
Federal		—			—		—
State		—			—		—
Foreign		495			63		(117	)

Total deferred		495			63		(117	)

Total provision for (benefit from) income taxes	$	2,595		$	1,116	$	(4	)

Income tax payable was $1.1 million and $0.4 million at June 30, 2012 and 2011 respectively. A reconciliation of income taxes at the statutory federal income tax rate to net income taxes included in the accompanying consolidated statements of operations is as follows (in thousands):

	Years Ended June 30,

	2012			2011			2010
U.S. federal taxes (benefit):
At federal statutory rate	$	(26,551	)	$	(8,961	)	$	993
State tax, net of federal benefit		(7	)		114			265
Stock-based compensation expense		3,645			33			389
Change in valuation allowance		24,796			8,883			(32	)
Credits		(846	)		(1,373	)		(877	)
Federal alternative minimum tax		—			—			(873	)
Meals and entertainment		335			214			178
Acquisition costs		89			2,451			—
Other		818			(251	)		(71	)
Foreign taxes		316			6			24

Total	$	2,595		$	1,116		$	(4	)

Deferred income taxes reflect the net tax effects of temporary differences between the carrying amounts of assets and liabilities for financial reporting purposes and the amounts used for income tax purposes. Significant components of the Company's net deferred tax assets at June 30, 2012 and 2011 were as follows (in thousands):

	June 30,

	2012			2011
Deferred tax assets:
Federal and state net operating losses	$	80,834		$	46,110
Accrued vacation		1,973			2,184
Accrued bonus		—			2,315
Deferred revenue		1,125			13,981
Deferred rent		1,165			1,355
Credits		13,985			12,500
Share-based compensation expense		13,103			15,007
Reserves not deductible for tax purposes		4,085			9,678
Unicap		1,347			1,818
Other		689			1,642

Total deferred tax assets		118,306			106,590
Deferred tax liabilities:
Fixed assets/intangibles		(15,198	)		(21,629	)
Foreign currency differences		(594	)		(3,034	)

Total deferred tax liabilities		(15,792	)		(24,663	)
Valuation allowance		(102,142	)		(81,800	)

Net deferred tax assets	$	372		$	127

The Company has not provided for U.S. income taxes on undistributed earnings of its foreign subsidiaries because it intends to permanently re-invest these earnings outside the U.S. The cumulative amount of such undistributed earnings upon which no U.S. income taxes have been provided as of June 30, 2012 was $6.6 million. It is not practicable to determine the income tax liability that might be incurred if these earnings were to be repatriated to the U.S.

As of June 30, 2012, the Company had approximately $209.0 million and $43.0 million in federal and state net operating loss carryforwards, respectively. The federal and state carryforwards expire in varying amounts beginning in 2019 for federal and 2015 for state purposes. Such net operating loss carryforwards includes excess tax benefits from employee stock option exercises which, in accordance with guidance for income tax accounting, have not been recorded within the Company's deferred tax asset balances. The Company will record approximately $5.5 million as a credit to additional paid-in capital as and when such excess benefits are ultimately realized.

In addition, as of June 30, 2012, the Company had federal and state research and development tax credits of approximately $13.5 million and $13.1 million, respectively. The federal research credits will begin to expire in 2025, the California research credits have no expiration date, and the other state research credits will begin to expire in 2013.

Utilization of the Company's net operating loss and credit carryforwards is subject to annual limitation due to the ownership change limitations provided by Section 382 of the Internal Revenue Code and similar state provisions. The acquisition of TomoTherapy and the resulting Section 382 limitation should not result in the expiration of net operating losses or credits due to the Section 382 limitation.

Based on the available objective evidence and history of losses, the Company has established a 100% valuation allowance against its domestic and certain foreign net deferred tax assets due to the uncertainty surrounding the realization of such assets.

The aggregate changes in the balance of gross unrecognized tax benefits were as follows at June 30, 2012, 2011, and 2010 (in thousands):

	Years Ended June 30,

	2012			2011			2010
Balance at beginning of year	$	14,158		$	3,669		$	3,364
Tax positions related to current year:
Additions		1,129			10,468			347
Tax positions related to prior years:
Additions		40			58			6
Reductions		(180	)		(37	)		(48	)

Balance at end of year	$	15,147		$	14,158		$	3,669

The calculation of unrecognized tax benefits involves dealing with uncertainties in the application of complex global tax regulations. Management regularly assesses the Company's tax positions in respect to legislative, bilateral tax treaty, regulatory and judicial developments in the countries in which the Company does business. The Company anticipates that except for $0.3 million in uncertain tax positions that may be reduced related to the lapse of various statutes of limitation, there will be no material changes in uncertain tax positions in the next 12 months. As of June 30, 2012, the amount of gross unrecognized tax benefits was $15.1 million of which $2.5 million would affect the Company's effective tax rate if realized.

The Company's practice is to recognize interest and/or penalties related to income tax matters in income tax expense. As of June 30, 2012 and 2011, respectively, the Company had approximately $0.6 million and $0.4 million of accrued interest and penalties related to uncertain tax positions.

The Company files income tax returns in the United States federal, various states and foreign jurisdictions. Due to attributes being carried forward and utilized during open years, the statute of limitations remains open for the U.S. federal jurisdiction and domestic states for tax years from 1999 and forward. The statute of limitations for Accuray France and Accuray Japan remain open from 2008 and 2011, respectively. For legacy TomoTherapy foreign entities, the statute of limitations in most foreign jurisdictions remain open from 2008, with the exception of TomoTherapy China which remains open from 2011.

The Company is also subject to the periodic examination of our income tax returns by the Internal Revenue Service (IRS) and other tax authorities, and in some cases we have received additional tax assessments. Currently, certain tax years are under audit by the relevant tax authorities, including an examination of our U.S. federal tax returns for the calendar year 2009 for TomoTherapy Incorporated and an examination in France for fiscal years 2009 through 2011. Both audits are in the information gathering stage.

- Definition

The entire disclosure for income taxes. Disclosures may include net deferred tax liability or asset recognized in an enterprise's statement of financial position, net change during the year in the total valuation allowance, approximate tax effect of each type of temporary difference and carryforward that gives rise to a significant portion of deferred tax liabilities and deferred tax assets, utilization of a tax carryback, and tax uncertainties information.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(h))
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e23780-122690

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32559-109319

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 15
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32718-109319

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 9
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32639-109319

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32537-109319

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 109
-Paragraph 136, 172
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 08
-Paragraph h
-Article 4

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 109
-Paragraph 43, 44, 45, 46, 47, 48, 49
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Other Income (Expense), Net

12 Months Ended

Jun. 30, 2012

Other Income (Expense), Net

Other Income (Expense), Net

11. Other Income (Expense), Net

For the years ended June 30, 2012, 2011 and 2010, other income (expense), net consisted of the following (in thousands):

	Years Ended June 30,

	2012			2011			2010
Interest income	$	360		$	543		$	1,813
Foreign currrency transaction gain		—			2,193			—
Realized gain on investments		—			27			318
Other		170			69			270

Total interest and other income		530			2,832			2,401

Interest expense on convertible notes		(7,397	)		—			—
Other interest expenses		(414	)		(23	)		(32	)
Foreign currrency transaction loss		(4,386	)		—			(1,920	)
Loss on asset disposition		(296	)		(254	)		(195	)
State sales, use and local taxes		(877	)		(267	)		(226	)
Fines and penalties		(31	)		—			(27	)

Total interest and other expense		(13,401	)		(544	)		(2,400	)

Total other income (expense), net	$	(12,871	)	$	2,288		$	1

Acquisition

12 Months Ended

Jun. 30, 2012

Acquisition

Acquisition

12. Acquisition

Fiscal year 2011

On June 10, 2011, the Company completed the acquisition of TomoTherapy by acquiring all of TomoTherapy's common stock in exchange for cash and shares of Accuray common stock. TomoTherapy is a creator of advanced radiation therapy solutions for cancer care. The objective of the acquisition is to create a company that can provide patients with radiation treatments tailored to their specific needs, from high-precision radiosurgery to image-guided, intensity-modulated radiation therapy. The Company has included the financial results of TomoTherapy in its consolidated financial statements from the date of acquisition. TomoTherapy's revenues and net loss from the acquisition date through June 30, 2011 were $11.1 million and $20.6 million, respectively.

The total purchase price for TomoTherapy was approximately $248.0 million and was comprised of the following (in thousands):


Cash	$	174,178
Common stock issued (9,112,511 shares)		67,341
Stock options assumed (1,539,255 shares)		2,234
RSAs assumed (429,591 shares)		4,270

	$	248,023

The fair value of the Common Stock issued was based on the per share price of Accuray's Common Stock on the date of acquisition. The fair value of the stock options assumed was determined using the Black-Scholes option pricing model utilizing the following assumptions:


Risk Free Rate		0.10% - 1.36%
Dividend Yield		0%
Expected Life		0.44 - 4.44
Volatility		34% - 56%

The fair value of the stock options assumed was attributed to purchase price and post-transaction compensation expense based on the ratio of the past service period to the total service period for each award.

The fair value of the RSA's assumed was based on a combination of the per share price of Accuray's common stock on the date of acquisition and $3.15 for each pre-adjusted RSA. The fair value of the RSA's assumed was attributed to purchase price and post-transaction compensation expense based on the ratio of the past service period to the total service period for each award.

The preliminary allocation of the purchase price to TomoTherapy's tangible and identifiable intangible assets acquired and liabilities assumed was based on their estimated fair values at the date of acquisition as determined by the Company's management. The excess of the purchase price over the tangible and identifiable intangible assets acquired and liabilities assumed has been allocated to goodwill. As of June 30, 2011, the purchase price has been allocated as follows (in thousands):


Cash	$	105,932
Accounts receivable		31,563
Inventories		72,383
Other assets		10,666
Property and equipment		28,878
Goodwill		49,979
Identified intangible assets		66,805
Accounts payable		(14,974	)
Customer advances		(13,045	)
Deferred revenue		(39,856	)
Other liabilities		(39,327	)
Noncontrolling interest		(10,981	)

Total purchase price	$	248,023

The Company has estimated the fair value of the acquired identifiable intangible assets, which are subject to amortization, using the income approach, which included an analysis of the completion costs, cash flows, other required assets and risk associated with achieving such cash flows. The goodwill of $50.0 million represents the value that is expected from combining TomoTherapy with Accuray to provide customers with a broader range of product offerings and generate greater opportunity for service revenue and for replacement business over time to customers who have purchased these best-in-class technologies. No amount of goodwill is expected to be deductible for tax purposes.

In conjunction with the acquisition, the Company recorded an expense of $10.5 million for severance payments to certain TomoTherapy employees, most of which was paid as of June 30, 2011. These charges were recorded in operating expenses in the consolidated statements of operations for the year ended June 30, 2011. The Company incurred $18.5 million in acquisition-related costs for TomoTherapy during fiscal year 2011, including the severance liability above, and additional acquisition-related costs, such as bankers' fees, legal and accounting fees and integration costs.

The identifiable intangible assets assumed in the acquisition of TomoTherapy were recognized as follows based upon their fair values as of June 10, 2011 (in thousands):

	Fair Value		Useful Life

			(in years)
Developed technology	$	41,645	6
Backlog		10,500	1.25
Distributor license		1,860	2.5

Total intangible assets subject to amortization		54,005
In-process research and development (CPAC)		12,800	Indefinite

Total intangible assets	$	66,805

Acquired developed technology represents the fair value of TomoTherapy's products that have reached technological feasibility and are part of the existing product line. Backlog represents existing production or sales orders not yet fulfilled as of June 10, 2011. In-process research and development represents TomoTherapy's research and development projects that had not reached technological feasibility and had no alternative future use when acquired.

The unaudited pro forma results presented below include the effects of pro forma adjustments as if TomoTherapy was acquired on July 1, 2009. The nonrecurring pro forma adjustments are primarily the result of fair value adjustments to intangible assets, inventory, fixed assets and deferred revenue. The pro forma financial results do not include any anticipated synergies or other expected benefits of the acquisition. The table below is presented for informational purposes only and is not indicative of future operations or results that would have been achieved had the acquisition been completed as of July 1, 2009 (in thousands, except per share amounts).

	Years Ended June 30,

	2011			2010
	(unaudited)
Net revenue	$	407,963		$	409,313
Net loss attributable to stockholders	$	(74,522	)	$	(50,037	)
Diluted earnings per share	$	(1.08	)	$	(0.75	)

- Definition

The entire disclosure for a business combination (or series of individually immaterial business combinations) completed during the period, including background, timing, and recognized assets and liabilities. The disclosure may include leverage buyout transactions (as applicable).

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=7659399&loc=d3e1497-128463

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=7659399&loc=d3e1490-128463

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=7659399&loc=d3e1392-128463

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 30
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=7488404&loc=d3e7008-128479

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=7659399&loc=d3e1486-128463

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 30
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=7488404&loc=d3e6927-128479

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 20
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6910749&loc=d3e4845-128472

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=7659399&loc=d3e1500-128463

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 10
-Section 50
-Paragraph 7
-URI http://asc.fasb.org/extlink&oid=7659399&loc=d3e1524-128463

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 30
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=7488404&loc=d3e7000-128479

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 20
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6910749&loc=d3e4922-128472

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 20
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6910749&loc=d3e4934-128472

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 20
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6910749&loc=d3e4926-128472

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 30
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=7488404&loc=d3e6996-128479

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 805
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=7659399&loc=d3e1383-128463

Reference 16: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 88-16
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 17: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 141R
-Paragraph F4
-Subparagraph e
-Appendix F

Reference 18: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 141
-Paragraph 51, 52
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 19: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 141R
-Paragraph 67-73
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Investment in CPAC

12 Months Ended

Jun. 30, 2012

Investment in CPAC

Investment in CPAC

13. Investment in CPAC

In April 2008, TomoTherapy established a new affiliate, CPAC, to develop a compact proton therapy system for the treatment of cancer. As its initial investment in CPAC, TomoTherapy contributed intellectual property with a fair market value of approximately $1.9 million. Since then, CPAC has raised additional funds from TomoTherapy, the Company and other investors through the sale of stock and issuance of promissory notes. As of June 30, 2012, the Company and its wholly owned subsidiary, TomoTherapy, together own approximately 15.4% of the outstanding stock of CPAC and approximately 16.3% on a fully diluted basis. Although TomoTherapy's and the Company's combined ownership in CPAC is less than 50%, the Company includes CPAC in its consolidated financial statements because the Company and TomoTherapy are the primary beneficiaries of CPAC (a variable interest entity, or VIE). The Company and TomoTherapy were involved in the design of CPAC, from which CPAC cannot depart due to restrictions that are part of its financing arrangements. The Company also provided intellectual property, which is the basis of CPAC and also holds influence over the VIE through representation on CPAC's board of directors. Further, the Company has an option to either acquire CPAC or enter into a distribution arrangement for the technology developed by CPAC as further described below. CPAC's outside stockholders' interests are shown in the Company's consolidated financial statements as "Non-controlling interest." The liabilities of the VIE do not represent additional claims on the Company's general assets; rather they represent claims against the specific assets of the VIE. Likewise, the assets of the VIE consolidated by the Company do not represent additional assets available to satisfy claims against the Company's general assets. The creditors of the VIE do not have recourse to the Company. Total assets and liabilities of CPAC were $15.0 million and $0.6 million, respectively, as of June 30, 2012 and $16.0 million and $1.6 million, respectively, as of June 30, 2011, which are included within the Company's consolidated balance sheets. The largest component of CPAC assets as of June 30, 2012 and 2011 is its in-process research and development intangible asset valued at $12.8 million. See Note 7, Goodwill and Intangible Assets for details.

From December 2010 through March 2012, the Company, TomoTherapy and certain other CPAC investors purchased convertible promissory notes from CPAC. Total consideration for the notes that the Company and TomoTherapy purchased was $1.2 million. Under the terms of the December 2010 notes, TomoTherapy received warrants for 1,386,981 common shares of CPAC. Other participating investors also purchased $3.3 million of the convertible notes which were included in "other accrued liabilities" in the Company's consolidated balance sheets prior to their conversion to equity in April 2012. The other investors also received warrants under the terms of the December 2010 notes for an aggregate of 1,386,983 shares of CPAC, which were equity classified. The notes bore interest at 12% and were convertible based on a per share conversion price as defined in the notes. The CPAC warrants described above are exercisable through November 2020 at an exercise price of $0.57 per CPAC common share. At June 30, 2012, none of these warrants had been exercised.

On March 9, 2011, TomoTherapy entered into a revolving promissory note with CPAC. On May 10, 2011, the revolving note was amended to increase the maximum amount available to borrow to $1.9 million. As of June 30, 2012, $2.2 million of principal and accrued interest was outstanding under the revolving note. The revolving note bears interest at 12% per annum compounded quarterly. This note and related interest is eliminated in consolidation.

On April 20, 2012, the Company entered into various transactions with CPAC and its other stockholders pursuant to which the Company invested $1.1 million and agreed, under certain circumstances, to invest up to an additional $0.7 million in exchange for preferred stock of CPAC and warrants to purchase common stock. The Company (including TomoTherapy) also converted the outstanding principal and accrued interest on its convertible promissory notes, amounting to $1.3 million, into preferred stock. The other note holders also converted their outstanding principal and accrued interest, amounting to $3.6 million into preferred stock. Certain other investors also participated in the financing. In connection with such transactions, the Company received warrants for 338,839 common shares of CPAC. These warrants are exercisable through April 2017 at an exercise price of $0.8725 per CPAC common share. At June 30, 2012, none of these warrants had been exercised.

The $1.9 million principal amount revolving promissory note remains outstanding but its maturity date was extended from December 31, 2011 to December 31, 2012 as part of the April 2012 transaction. The Company can convert all or any part of the revolving note into preferred stock of CPAC at any time until September 30, 2012. If the second closing of the preferred stock financing occurs, then the Company will be obligated to convert the revolving note to the extent such conversion will not result in the Company owning more than 19.0% of CPAC. If any portion of the revolving note remains outstanding following the second closing, the note will be amended to change the maturity date to December 31, 2015 and to decrease the interest rate from 12% per annum to 8% per annum compounded quarterly.

In connection with the April 2012 transactions, the Company modified the option it previously held to purchase a portion of the CPAC stock held by other CPAC investors. The Company now has the option, upon the occurrence of certain events, to elect to either acquire CPAC at the then-determined fair value or enter into a non-exclusive supply and distribution agreement for CPAC's compact proton therapy products. The triggers for the option becoming exercisable include CPAC achieving certain technical milestones or the CPAC board approving a proposal for the acquisition of CPAC.

The Company and CPAC also amended certain licensing relationships for the DWA technology by and between the Company, CPAC and Lawrence Livermore National Security, LLC ("LLNS") and terminated a previous arrangement pursuant to which the Company had provided CPAC with certain accounting and back office support and management services.

Debt

12 Months Ended

Jun. 30, 2012

Debt

Debt

14. Debt

On August 1, 2011, the Company issued $100 million aggregate principal amount of 3.75% Convertible Senior Notes due August 1, 2016 (the "Convertible Notes") to certain qualified institutional buyers or QIBs. The Convertible Notes were offered and sold to the QIBs pursuant to Rule 144A under the Securities Act of 1933, as amended. The net proceeds from the offering, after deducting the initial purchaser's discount and commission and the related offering costs, were approximately $96.1 million. The offering costs and the initial purchaser's discount and commission (which are recorded in Other Assets) are both being amortized to interest expense using the effective interest method over five years. The Convertible Notes bear interest at a rate of 3.75% per year, payable semi-annually in arrears in cash on February 1 and August 1 of each year, beginning on February 1, 2012. The Convertible Notes will mature on August 1, 2016, unless earlier repurchased, redeemed or converted.

The Convertible Notes were issued under an Indenture between the Company and The Bank of New York Mellon Trust Company, N.A., as trustee. Holders of the Convertible Notes may convert their Convertible Notes at any time on or after May 1, 2016 until the close of business on the business day immediately preceding the maturity date. Prior to May 1, 2016, holders of the Convertible Notes may convert their Convertible Notes only under the following circumstances: (1) during any calendar quarter after the calendar quarter ending September 30, 2011, and only during such calendar quarter, if the closing sale price of the Company's common stock for each of 20 or more trading days in the 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter exceeds 130% of the conversion price in effect on the last trading day of the immediately preceding calendar quarter; (2) during the five consecutive business days immediately after any five consecutive trading-day period (such five consecutive trading-day period, the "Note Measurement Period") in which the trading price per $1,000 principal amount of Convertible Notes for each trading day of that Note Measurement Period was equal to or less than 98% of the product of the closing sale price of shares of the Company's common stock and the applicable conversion rate for such trading day; (3) if the Company calls any or all of the Convertible Notes for redemption, at any time prior to the close of business on the business day immediately preceding the redemption date; or (4) upon the occurrence of specified corporate transactions as described in the Indenture. Upon conversion by holders of the Convertible Notes, the Company will have the right to pay or deliver, as the case may be, cash, shares of common stock of the Company or a combination thereof, at the Company's election. At any time on or prior to the 33rd business day immediately preceding the maturity date, the Company may irrevocably elect to (a) deliver solely shares of common stock of the Company in respect of the Company's conversion obligation or (b) pay cash up to the aggregate principal amount of the Convertible Notes to be converted and pay or deliver, as the case may be, cash, shares of common stock of the Company or a combination thereof in respect of the remainder, if any, of the Company's conversion obligation in excess of the aggregate principal amount of the Convertible Notes being converted. The initial conversion rate will be 105.5548 shares of the Company's common stock per $1,000 principal amount of Convertible Notes (which represents an initial conversion price of approximately $9.47 per share of the Company's common stock). The conversion rate, and thus the conversion price, will be subject to adjustment as further described below.

Holders of the Convertible Notes who convert their Convertible Notes in connection with a "make-whole fundamental change", as defined in the Indenture, may be entitled to a make-whole premium in the form of an increase in the conversion rate. Additionally, in the event of a fundamental change, as defined in the Indenture, holders of the Convertible Notes may require the Company to purchase all or a portion of their Convertible Notes at a fundamental change repurchase price equal to 100% of the principal amount of Convertible Notes, plus accrued and unpaid interest, if any, to, but not including, the fundamental change repurchase date.

On or after August 1, 2014 and prior to the maturity date, the Company may redeem for cash all or a portion of the Convertible Notes if the closing sale price of its common stock exceeds 130% of the applicable conversion price (the initial conversion price is approximately $9.47 per share of common stock) of such Convertible Notes for at least 20 trading days during any consecutive 30 trading-day period (including the last trading day of such period).

In accordance with ASC 470-20 Debt with Conversion and Other Options, the Company separately accounts for the liability and equity conversion components of the Convertible Notes. The principal amount of the liability component of the Convertible Notes was $75.9 million as of date of issuance based on the present value of its cash flows using a discount rate of 10%, our approximate borrowing rate at the date of the issuance for a similar debt instrument without the conversion feature. The carrying value of the equity conversion component was $24.1 million. A portion of the initial purchaser's discount and commission and the offering costs totaling $0.9 million was allocated to the equity conversion component. The liability component will be accreted to the principal amount of the Convertible Notes using the effective interest method over five years.

The following table presents the carrying value of the Convertible Notes as of June 30, 2012 (in thousands):


Carrying amount of the equity conversion component	$	23,189

Principal amount of the Convertible Notes	$	100,000
Unamortized debt discount(1)		(20,534	)

Net carrying amount	$	79,466

(1): As of June 30, 2012, the remaining period over which the unamortized debt discount will be amortized is 49 months.

A summary of interest expense and effective interest rate on the liability component related to the Convertible Notes for the year ended June 30, 2012 is as follows (in thousands):

	Year ended June 30, 2012

Effective interest rate		10.0	%
Interest expense related to contractual interest coupon	$	3,438
Interest expense related to amortization of debt discount		3,596

Total interest expense recognized	$	7,034

- Definition

The entire disclosure for information about short-term and long-term debt arrangements, which includes amounts of borrowings under each line of credit, note payable, commercial paper issue, bonds indenture, debenture issue, own-share lending arrangements and any other contractual agreement to repay funds, and about the underlying arrangements, rationale for a classification as long-term, including repayment terms, interest rates, collateral provided, restrictions on use of assets and activities, whether or not in compliance with debt covenants, and other matters important to users of the financial statements, such as the effects of refinancing and noncompliance with debt covenants.

+ References + Details

Employee Benefit Plans

12 Months Ended

Jun. 30, 2012

Employee Benefit Plans

Employee Benefit Plans

15. Employee Benefit Plans

The Company's employee savings and retirement plan is qualified under Section 401(k) of the United States Internal Revenue Code. Employees may make voluntary, tax-deferred contributions to the 401(k) Plan up to the statutorily prescribed annual limit. The Company makes discretionary matching contributions to the 401(k) Plan on behalf of employees up to the limit determined by the Board of Directors. The Company contributed $1.7 million, $0.7 million and $0.7 million to the 401(k) Plan during the years ended June 30, 2012, 2011 and 2010, respectively.

- Definition

The entire disclosure for pension and other postretirement benefits.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 715
-URI http://asc.fasb.org/topic&trid=2235017

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Implementation Guide (Q and A)
-Number FAS88
-Paragraph 63
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 132R
-Paragraph 5
-Subparagraph b
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 106
-Paragraph 518
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 132R
-Paragraph 5
-Subparagraph a
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 03-2
-Paragraph 8
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 87
-Paragraph 264
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 132R
-Paragraph 5
-Subparagraph q
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 132R
-Paragraph 5
-Subparagraph h
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 132R
-Paragraph 8
-Subparagraph m
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 132R
-Paragraph 5, 6, 7, 8
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 158
-Paragraph 7, 21, 22
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Staff Position (FSP)
-Number FAS106-2
-Paragraph 20, 21, 22
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Principles Board Opinion (APB)
-Number 30
-Paragraph 26
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Restructuring Charges

12 Months Ended

Jun. 30, 2012

Restructuring Charges

Restructuring Charges

16. Restructuring Charges

In the second quarter of fiscal 2012, the Company implemented a Workforce Re-alignment Program ("WFA") which affected approximately 51 full-time positions across the organization. The WFA was designed to position the workforce more appropriately for the Company's growth strategy and to help achieve cost synergies associated with the acquisition of TomoTherapy during fiscal 2011. The Company originally estimated the total restructuring-related charges associated with the WFA to be approximately $1.7 million in cash related to employee severance pay and related expenses. The WFA program has been completed by the end of the fourth quarter of fiscal 2012 and the Company reduced its global workforce under this program by 51 full-time employees and recorded $1.9 million in charges for severance and related benefits, which has been paid as of June 30, 2012. Restructuring charges are reflected within the respective operating expenses in the consolidated statements of operations.

- Definition

The entire disclosure for restructuring and related activities. Description of restructuring activities such as exit and disposal activities, include facts and circumstances leading to the plan, the expected plan completion date, the major types of costs associated with the plan activities, total expected costs, the accrual balance at the end of the period, and the periods over which the remaining accrual will be settled.

+ References + Details

Quarterly Financial Data (unaudited)

12 Months Ended

Jun. 30, 2012

Quarterly Financial Data (unaudited)

Quarterly Financial Data (unaudited)

17. Quarterly Financial Data (unaudited)

	Quarters ended

	September 30, 2011			December 31, 2011			March 31, 2012			June 30, 2012
Net revenue	$	100,451		$	106,423		$	101,816		$	100,533
Gross profit	$	24,428		$	40,243		$	36,111		$	36,490
Net loss	$	(28,083	)	$	(12,191	)	$	(16,533	)	$	(21,646	)
Net loss attributable to stockholders	$	(26,510	)	$	(10,387	)	$	(14,881	)	$	(20,264	)
Basic net loss per share attributable to stockholders	$	(0.38	)	$	(0.15	)	$	(0.21	)	$	(0.28	)
Diluted net loss per share attributable to stockholders	$	(0.38	)	$	(0.15	)	$	(0.21	)	$	(0.28	)
Shares used in basic per share calculation		70,263			70,698			71,120			71,473
Shares used in diluted per share calculation		70,263			70,698			71,120			71,473

	Quarters ended

	September 30, 2010			December 31, 2010		March 31, 2011			June 30, 2011
Net revenue	$	38,068		$	54,246	$	54,747		$	75,223
Gross profit	$	18,237		$	29,466	$	27,313		$	32,226
Net income (loss)	$	(4,640	)	$	4,098	$	(1,160	)	$	(25,409	)
Net income (loss) attributable to stockholders	$	(4,640	)	$	4,098	$	(1,160	)	$	(24,980	)
Basic net (loss) per share attributable to stockholders	$	(0.08	)	$	0.07	$	(0.02	)	$	(0.40	)
Diluted net (loss) per share attributable to stockholders	$	(0.08	)	$	0.07	$	(0.02	)	$	(0.40	)
Shares used in basic per share calculation		58,667			59,282		59,960			62,451
Shares used in diluted per share calculation		58,667			61,376		59,960			62,451

- Definition

The entire disclosure for the quarterly financial data in the annual financial statements. The disclosure may include a tabular presentation of financial information for each fiscal quarter for the current and previous year, including revenues, gross profit, income or loss before extraordinary items and earnings per share data. It also includes an indication if the information in the note is unaudited, comments on the aggregate effect of year-end adjustments, and an explanation of matters or transactions that affect comparability or are pertinent to an understanding of the information furnished.

+ References + Details

Subsequent Events

12 Months Ended

Jun. 30, 2012

Subsequent Events

Subsequent Events

18. Subsequent Events

Acquisition of Morphormics, Inc.

On July 15, 2012, the Company acquired all of the remaining outstanding equity of Morphormics, Inc. that it did not previously own for a cash payment of approximately $5.7 million. Morphormics is a privately-held developer of medical imaging software. This acquisition will enable the Company to extend auto-contouring capabilities for both the CyberKnife and TomoTherapy systems to improve disease specific workflows. The purchase price is primarily attributable to developed technology which is expected to be amortized over 5 years. Given the proximity of this acquisition, the initial accounting for the business combination was incomplete at the time the financial statements were issued.

SCHEDULE II Valuation and Qualifying Accounts

12 Months Ended

Jun. 30, 2012

Valuation and Qualifying Accounts

SCHEDULE II Valuation and Qualifying Accounts

SCHEDULE II
Valuation and Qualifying Accounts

	Beginning Balance		Additions (Deductions)			Write-offs			Ending Balance

Accounts receivable allowances
Year ended June 30, 2010	$	484	$	(358	)	$	(11	)	$	115
Year ended June 30, 2011	$	115	$	239		$	(30	)	$	324
Year ended June 30, 2012	$	324	$	1,392		$	(16	)	$	1,700

	Beginning Balance		Increase Due to Acquisition		Additions		Deductions			Ending Balance

Accrued warranty
Year ended June 30, 2011	$	—	$	7,600	$	—	$	(805	)	$	6,795
Year ended June 30, 2012	$	6,795	$	—	$	48	$	(6,095	)	$	748

Summary of Significant Accounting Policies (Policies)

12 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies

Basis of Presentation and Principles of Consolidation

Use of Estimates

Foreign Currency

Cash and Cash Equivalents

Restricted Cash

Restricted cash primarily relates to funds held related to Value-Added Tax ("VAT") guarantees in a foreign jurisdiction and certain performance obligation guarantees.

Fair Value Measurements

Other-than-Temporary Impairment Assessment

Concentration of Credit Risk and Other Risks and Uncertainties

Inventories

Revenue Recognition

Product Revenue

Service Revenue

Other revenue

Other revenue primarily consists of research and development and construction contract revenues.

Shared ownership program

Future minimum revenues under shared ownership arrangements as of June 30, 2012 are as follows (in thousands):

Year Ending June 30,	Amount

2013	$	1,744
2014		1,789
2015		1,789
2016		1,394
2017		540

Total	$	7,256

Long-term construction and manufacturing contracts

Deferred Revenue and Deferred Cost of Revenue

Customer Advances

Customer advances represent payments made by customers in advance of product shipment.

Property and Equipment

Software Capitalization Costs

Impairment of Long-Lived Assets

Goodwill and Acquired Intangible Assets

Business Combinations

Shipping and Handling

Advertising Expenses

Research and Development Costs

Share-Based Compensation

Net Income (Loss) Per Common Share

A reconciliation of the numerator and denominator used in the calculation of basic and diluted net income (loss) per share follows (in thousands):

	Years ended June 30,

	2012			2011			2010
Numerator:
Net income (loss) used in computing basic and diluted net income (loss) per share		(72,042	)		(26,682	)		2,841

Denominator:
Weighted average shares used in computing basic net income (loss) per share		70,887			60,085			57,560
Add: Dilutive stock options and awards outstanding		—			—			2,631

Weighted average shares used in computing diluted net income (loss) per share		70,887			60,085			60,191

The following table sets forth all potentially dilutive securities excluded from the computation in the table above because their effect would have been anti-dilutive (in thousands):

	As of June 30,

	2012		2011		2010
Option to purchase common stock		7,873		8,337		4,057
Restricted stock units		1,171		658		260
Performance stock units		926		—		—

		9,970		8,995		4,317

Income Taxes

Comprehensive Income (Loss)

Segment Information

	Years ended June 30,

	2012		2011		2010
Americas (including Puerto Rico)	$	189,072	$	122,636	$	147,381
Europe		110,331		67,244		58,049
Asia (excluding Japan)		64,026		16,158		5,608
Japan		45,794		16,246		10,587

Total	$	409,223	$	222,284	$	221,625

Recent Accounting Pronouncements

Summary of Significant Accounting Policies (Tables)

12 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies

Schedule of future minimum revenues under shared ownership arrangements

Year Ending June 30,	Amount

2013	$	1,744
2014		1,789
2015		1,789
2016		1,394
2017		540

Total	$	7,256

Schedule of reconciliation of the numerator and denominator used in the calculation of basic and diluted net income (loss) per share

	Years ended June 30,

	2012			2011			2010
Numerator:
Net income (loss) used in computing basic and diluted net income (loss) per share		(72,042	)		(26,682	)		2,841

Denominator:
Weighted average shares used in computing basic net income (loss) per share		70,887			60,085			57,560
Add: Dilutive stock options and awards outstanding		—			—			2,631

Weighted average shares used in computing diluted net income (loss) per share		70,887			60,085			60,191

Schedule of all potentially dilutive securities excluded from the computation of net income (loss) per share

	As of June 30,

	2012		2011		2010
Option to purchase common stock		7,873		8,337		4,057
Restricted stock units		1,171		658		260
Performance stock units		926		—		—

		9,970		8,995		4,317

Schedule of revenue by geographic region

	Years ended June 30,

	2012		2011		2010
Americas (including Puerto Rico)	$	189,072	$	122,636	$	147,381
Europe		110,331		67,244		58,049
Asia (excluding Japan)		64,026		16,158		5,608
Japan		45,794		16,246		10,587

Total	$	409,223	$	222,284	$	221,625

Balance Sheet Components (Tables)

12 Months Ended

Jun. 30, 2012

Balance Sheet Components

Schedule of accounts receivable, net

	June 30,

	2012			2011
Accounts receivable	$	69,285		$	59,858
Unbilled fees and services		305			2,319

		69,590			62,177
Less: Allowance for doubtful accounts		(1,700	)		(324	)

Accounts receivable, net	$	67,890		$	61,853

Schedule of inventories

	June 30,

	2012		2011(1)
Raw materials	$	42,951	$	32,988
Work-in-process		16,932		28,216
Finished goods		21,810		36,632

Inventories	$	81,693	$	97,836

(1): Prior year numbers have been reclassified to conform to current year classification and presentation.

Schedule of property and equipment

	June 30,

	2012			2011
Furniture and fixtures	$	5,921		$	5,317
Computer and office equipment		9,126			8,280
Software		9,429			8,107
Leasehold improvements		16,065			15,386
Machinery and equipment		33,493			33,692
Shared ownership systems		4,979			4,923
Construction in progress		3,787			602

		82,800			76,307
Less: Accumulated depreciation and amortization		(45,342	)		(31,484	)

Property and equipment, net	$	37,458		$	44,823

Goodwill and Intangible Assets (Tables)

12 Months Ended

Jun. 30, 2012

Goodwill and Intangible Assets

Schedule of goodwill

	Year Ended June 30, 2012		Year Ended June 30, 2011

Balance at the beginning of the period	$	54,474	$	4,495
Addition related to acquisition		—		49,979
Adjustments related to prior year acquisition(1)		4,741		—

Balance at the end of the period	$	59,215	$	54,474

(1): Primarily represents liabilities related to the TomoTherapy acquisition.

Schedule of intangible assets associated with completed acquisitions

		June 30, 2012							June 30, 2011

	Useful Lives	Gross Carrying Amount		Accumulated Amortization			Net Amount		Gross Carrying Amount		Accumulated Amortization			Net Amount
	(in years)
Developed technology	6.0	$	43,455	$	(9,161	)	$	34,294	$	43,455	$	(2,069	)	$	41,386
Backlog	1.25		10,500		(8,867	)		1,633		10,500		(467	)		10,033
Distributor license	2.5		1,860		(768	)		1,092		1,860		(40	)		1,820
In-process research and development (CPAC)	Indefinite		12,800		—			12,800		12,800		—			12,800

		$	68,615	$	(18,796	)	$	49,819	$	68,615	$	(2,576	)	$	66,039

Schedule of estimated future amortization expense of purchased intangible assets, excluding in-process research and development

Year Ending June 30,	Amount

2013	$	9,306
2014		7,298
2015		6,933
2016		6,933
2017		6,549

	$	37,019

- Definition

Tabular disclosure of goodwill by reportable segment and in total which includes a rollforward schedule.

+ References + Details

Commitments and Contingencies (Tables)

12 Months Ended

Jun. 30, 2012

Commitments and Contingencies.

Schedule of future minimum lease payments under non-cancelable operating lease agreements and long-term principal and interest on Convertible Note

Year Ending June 30,	Operating Leases		Long-term Debt(1)

2013	$	8,021	$	3,750
2014		7,245		3,750
2015		4,681		3,750
2016		2,272		3,750
2017		2,325		100,313
Thereafter		2,645		—

Total	$	27,189	$	115,313

(1): These amounts represent principal and interest cash payments over the life of the debt obligations, including anticipated interest payments that are not recorded on the Company's consolidated balance sheet. Any conversion, redemption or purchase of Convertible Notes would impact cash payments.

Stockholders' Equity (Tables)

12 Months Ended

Jun. 30, 2012

Stockholders' Equity

Schedule of weighted average assumptions used for determining fair value of option grants

	Years Ended June 30,

	2012			2011			2010
Risk-free interest rate		0.85% - 1.72	%		1.88% - 2.44	%		2.11% - 3.04	%
Dividend yield		—			—			—
Expected life		6.25			6.25			6.25
Expected volatility		52.0% - 52.9	%		52.8% - 54.9	%		56.6% - 64.7	%

Summary of share-based compensation charges

	Years ended June 30,

	2012		2011		2010
Cost of revenue	$	1,672	$	1,312	$	1,721
Selling and marketing		729		695		1,433
Research and development		2,340		2,922		2,850
General and administrative		3,717		8,436		4,642

	$	8,458	$	13,365	$	10,646

Schedule of option activity

			Weighted Average Exercise Price			Aggregate Intrinsic Value (in thousands)

Balance at June 30, 2011	8,336,220		$	7.39	5.13	$	19,131
Options granted	1,399,424		$	4.53
Options exercised	(746,441	)	$	2.50
Options forfeited/expired	(1,116,603	)	$	9.79

Balance at June 30, 2012	7,872,600		$	7.00	5.57	$	12,359

Vested or Expected to vest at June 30, 2012	7,871,741		$	7.00	5.57	$	12,359

Exercisable at June 30, 2012	5,816,292		$	7.57	4.46	$	9,242

Schedule of combined activity under the Plans

					Weighted Average Exercise Price				Weighted Average Grant Date Fair Value

Balance at June 30, 2009	2,645,757		8,455,316		$	5.70	519,609		$	18.15
Additional shares reserved	1,500,000		—
Expirations	(325,120	)	—
Grants	(1,686,498	)	1,498,740		$	6.09	187,758		$	6.12
Forfeitures or cancellations	904,502		(831,716	)	$	9.86	(72,786	)	$	18.92
Exercises or releases	—		(1,313,749	)	$	1.55	(170,395	)	$	6.32

Balance at June 30, 2010	3,038,641		7,808,591		$	6.03	464,186		$	12.52
Additional shares reserved	1,500,000		—				—
Expirations	(151,042	)	—				—
Grants	(1,389,949	)	914,770		$	7.30	475,179		$	6.77
Options assumed	—		1,539,255		$	10.41	—		$	—
Forfeitures or cancellations	602,945		(529,711	)	$	8.60	(79,180	)	$	9.85
Exercises or releases	—		(1,396,685	)	$	2.58	(201,992	)	$	7.57

Balance at June 30, 2011	3,600,595		8,336,220		$	7.39	658,193		$	6.97

Additional shares reserved	1,500,000		—				—
Expirations	—		—				—
Grants	(3,400,449	)	1,399,424		$	4.53	2,001,025		$	4.53
Forfeitures or cancellations	617,864		(1,116,603	)	$	9.79	(259,107	)	$	5.67
Exercises or releases	—		(746,441	)	$	2.50	(302,476	)	$	4.47

Balance at June 30, 2012	2,318,010		7,872,600		$	7.00	2,097,635		$	5.16

Vested during year ended June 30, 2012							296,905		$	4.47
Non-vested at June 30, 2011							652,622		$	6.97
Non-vested at June 30, 2012							2,097,635		$	5.16

Schedule of activity under the RSA Plan

			Weighted Average Grant Date Fair Value

Balance at June 30, 2011	190,522		$	7.39
Grants	—		$	—
Forfeitures	(10,804	)	$	7.39
Releases	(147,290	)	$	7.39

Balance at June 30, 2012	32,428		$	7.39

Schedule of weighted average assumptions used for determining fair value of ESPP shares

	Years Ended June 30,

	2012			2011			2010
Risk-free interest rate		0.05% - 0.12	%		0.11% - 0.23	%		0.15% - 0.29	%
Dividend yield		—			—			—
Expected life		0.50			0.50			0.50
Expected volatility		33.6% - 50.6	%		33.6% - 56.7	%		56.7% - 78.3	%

- Definition

Tabular disclosure of the allocation of equity-based compensation costs to a given line item on the balance sheet and income statement for the period. This may include the reporting line for the costs and the amount capitalized and expensed.

+ References + Details

Income Taxes (Tables)

12 Months Ended

Jun. 30, 2012

Income Taxes

Schedule of components of income (loss) before provision for income taxes

	Years Ended June 30,

	2012			2011			2010
Domestic	$	(82,494	)	$	(28,621	)	$	1,169
Foreign		6,636			2,626			1,668

Total worldwide		(75,858	)		(25,995	)		2,837

Schedule of components of provision for (benefit from) income taxes

	Years Ended June 30,

	2012			2011		2010
Current:
Federal	$	—		$	—	$	(876	)
State		(7	)		114		265
Foreign		2,107			939		724

Total current		2,100			1,053		113
Deferred:
Federal		—			—		—
State		—			—		—
Foreign		495			63		(117	)

Total deferred		495			63		(117	)

Total provision for (benefit from) income taxes	$	2,595		$	1,116	$	(4	)

Schedule of reconciliation of income taxes at the statutory federal income tax rate to net income taxes

	Years Ended June 30,

	2012			2011			2010
U.S. federal taxes (benefit):
At federal statutory rate	$	(26,551	)	$	(8,961	)	$	993
State tax, net of federal benefit		(7	)		114			265
Stock-based compensation expense		3,645			33			389
Change in valuation allowance		24,796			8,883			(32	)
Credits		(846	)		(1,373	)		(877	)
Federal alternative minimum tax		—			—			(873	)
Meals and entertainment		335			214			178
Acquisition costs		89			2,451			—
Other		818			(251	)		(71	)
Foreign taxes		316			6			24

Total	$	2,595		$	1,116		$	(4	)

Schedule of significant components of deferred tax assets

	June 30,

	2012			2011
Deferred tax assets:
Federal and state net operating losses	$	80,834		$	46,110
Accrued vacation		1,973			2,184
Accrued bonus		—			2,315
Deferred revenue		1,125			13,981
Deferred rent		1,165			1,355
Credits		13,985			12,500
Share-based compensation expense		13,103			15,007
Reserves not deductible for tax purposes		4,085			9,678
Unicap		1,347			1,818
Other		689			1,642

Total deferred tax assets		118,306			106,590
Deferred tax liabilities:
Fixed assets/intangibles		(15,198	)		(21,629	)
Foreign currency differences		(594	)		(3,034	)

Total deferred tax liabilities		(15,792	)		(24,663	)
Valuation allowance		(102,142	)		(81,800	)

Net deferred tax assets	$	372		$	127

Schedule of aggregate changes in the balance of gross unrecognized tax benefits

	Years Ended June 30,

	2012			2011			2010
Balance at beginning of year	$	14,158		$	3,669		$	3,364
Tax positions related to current year:
Additions		1,129			10,468			347
Tax positions related to prior years:
Additions		40			58			6
Reductions		(180	)		(37	)		(48	)

Balance at end of year	$	15,147		$	14,158		$	3,669

Other Income (Expense), Net (Tables)

12 Months Ended

Jun. 30, 2012

Other Income (Expense), Net

Schedule of other income, net

	Years Ended June 30,

	2012			2011			2010
Interest income	$	360		$	543		$	1,813
Foreign currrency transaction gain		—			2,193			—
Realized gain on investments		—			27			318
Other		170			69			270

Total interest and other income		530			2,832			2,401

Interest expense on convertible notes		(7,397	)		—			—
Other interest expenses		(414	)		(23	)		(32	)
Foreign currrency transaction loss		(4,386	)		—			(1,920	)
Loss on asset disposition		(296	)		(254	)		(195	)
State sales, use and local taxes		(877	)		(267	)		(226	)
Fines and penalties		(31	)		—			(27	)

Total interest and other expense		(13,401	)		(544	)		(2,400	)

Total other income (expense), net	$	(12,871	)	$	2,288		$	1

Acquisition (Tables)

12 Months Ended

Jun. 30, 2012

Acquisition

Schedule of components of purchase price


Cash	$	174,178
Common stock issued (9,112,511 shares)		67,341
Stock options assumed (1,539,255 shares)		2,234
RSAs assumed (429,591 shares)		4,270

	$	248,023

Schedule of assumptions utilized for determining the fair value of the stock options assumed


Risk Free Rate		0.10% - 1.36%
Dividend Yield		0%
Expected Life		0.44 - 4.44
Volatility		34% - 56%

Schedule of purchase price allocation


Cash	$	105,932
Accounts receivable		31,563
Inventories		72,383
Other assets		10,666
Property and equipment		28,878
Goodwill		49,979
Identified intangible assets		66,805
Accounts payable		(14,974	)
Customer advances		(13,045	)
Deferred revenue		(39,856	)
Other liabilities		(39,327	)
Noncontrolling interest		(10,981	)

Total purchase price	$	248,023

Schedule of identifiable intangible assets assumed in the acquisition

	Fair Value		Useful Life

			(in years)
Developed technology	$	41,645	6
Backlog		10,500	1.25
Distributor license		1,860	2.5

Total intangible assets subject to amortization		54,005
In-process research and development (CPAC)		12,800	Indefinite

Total intangible assets	$	66,805

Schedule of pro forma results

	Years Ended June 30,

	2011			2010
	(unaudited)
Net revenue	$	407,963		$	409,313
Net loss attributable to stockholders	$	(74,522	)	$	(50,037	)
Diluted earnings per share	$	(1.08	)	$	(0.75	)

Debt (Tables)

12 Months Ended

Jun. 30, 2012

Debt

Schedule of carrying value of the Convertible Notes


Carrying amount of the equity conversion component	$	23,189

Principal amount of the Convertible Notes	$	100,000
Unamortized debt discount(1)		(20,534	)

Net carrying amount	$	79,466

(1): As of June 30, 2012, the remaining period over which the unamortized debt discount will be amortized is 49 months.

Summary of interest expense and effective interest rate on the liability component related to the Convertible Notes

	Year ended June 30, 2012

Effective interest rate		10.0	%
Interest expense related to contractual interest coupon	$	3,438
Interest expense related to amortization of debt discount		3,596

Total interest expense recognized	$	7,034

Quarterly Financial Data (unaudited) (Tables)

12 Months Ended

Jun. 30, 2012

Quarterly Financial Data (unaudited)

Schedule of quarterly financial data (unaudited)

	Quarters ended

	September 30, 2011			December 31, 2011			March 31, 2012			June 30, 2012
Net revenue	$	100,451		$	106,423		$	101,816		$	100,533
Gross profit	$	24,428		$	40,243		$	36,111		$	36,490
Net loss	$	(28,083	)	$	(12,191	)	$	(16,533	)	$	(21,646	)
Net loss attributable to stockholders	$	(26,510	)	$	(10,387	)	$	(14,881	)	$	(20,264	)
Basic net loss per share attributable to stockholders	$	(0.38	)	$	(0.15	)	$	(0.21	)	$	(0.28	)
Diluted net loss per share attributable to stockholders	$	(0.38	)	$	(0.15	)	$	(0.21	)	$	(0.28	)
Shares used in basic per share calculation		70,263			70,698			71,120			71,473
Shares used in diluted per share calculation		70,263			70,698			71,120			71,473

	Quarters ended

	September 30, 2010			December 31, 2010		March 31, 2011			June 30, 2011
Net revenue	$	38,068		$	54,246	$	54,747		$	75,223
Gross profit	$	18,237		$	29,466	$	27,313		$	32,226
Net income (loss)	$	(4,640	)	$	4,098	$	(1,160	)	$	(25,409	)
Net income (loss) attributable to stockholders	$	(4,640	)	$	4,098	$	(1,160	)	$	(24,980	)
Basic net (loss) per share attributable to stockholders	$	(0.08	)	$	0.07	$	(0.02	)	$	(0.40	)
Diluted net (loss) per share attributable to stockholders	$	(0.08	)	$	0.07	$	(0.02	)	$	(0.40	)
Shares used in basic per share calculation		58,667			59,282		59,960			62,451
Shares used in diluted per share calculation		58,667			61,376		59,960			62,451

Summary of Significant Accounting Policies (Details) - USD ($)	12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011
Cash and Cash Equivalents
Maximum term of original maturity of highly-liquid investments to be considered as cash equivalents	3 months
Money market funds and certificates of deposit	$ 46,800,000	$ 19,000
Cash and cash equivalent balances in foreign currencies	$ 43,200,000	$ 28,300,000

Summary of Significant Accounting Policies (Details 2) - customer	12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Total net revenue \| Customer concentration risk \| Minimum
Concentration of Credit Risk and Other Risks and Uncertainties
Threshold percentage of concentration risk	10.00%	10.00%	10.00%
Total accounts receivable \| Customer concentration risk \| Major customer one
Concentration of Credit Risk and Other Risks and Uncertainties
Percentage of concentration risk	10.00%
Total accounts receivable \| Credit concentration risk \| Major customer one
Concentration of Credit Risk and Other Risks and Uncertainties
Number of significant customers		1
Percentage of concentration risk		10.00%
Total accounts receivable \| Credit concentration risk \| Major customer two
Concentration of Credit Risk and Other Risks and Uncertainties
Number of significant customers	2

Summary of Significant Accounting Policies (Details 3) $ in Thousands	12 Months Ended
	Jun. 30, 2012 USD ($) system	Jun. 30, 2011 USD ($) system	Jun. 30, 2010 USD ($) system
Revenue recognition
Term of agreements under the shared ownership program	5 years
Future minimum revenues under shared ownership arrangements
2013	$ 1,744
2014	1,789
2015	1,789
2016	1,394
2017	540
Total	7,256
Usage-based fee revenues earned under the shared ownership program	$ 1,700	$ 1,500	$ 1,600
Number of systems installed under the shared ownership program \| system	4
Deferred Revenue and Deferred Cost of Revenue
Period over which deferred service revenue resulting from advance payment for services are to be delivered	1 year
Maximum expected period to classify deferred revenue as current liabilities and deferred costs of revenue as current assets	1 year
CyberKnife shared ownership systems
Sale of shared ownership system
Revenue recognized	$ 0	$ 3,600	$ 0
Number of systems, formerly under the shared ownership program, sold \| system	0	1	0
Minimum
Revenue recognition
Period for revenue recognition of warranty and post warranty service revenue (in months)	12 months
Maximum
Revenue recognition
Period for revenue recognition of warranty and post warranty service revenue (in months)	18 months

Summary of Significant Accounting Policies (Details 4)	12 Months Ended
Summary of Significant Accounting Policies (Details 4)	Jun. 30, 2012
Machinery and equipment
Property and Equipment
Period over which property and equipment are depreciated	5 years
Furniture and fixtures
Property and Equipment
Period over which property and equipment are depreciated	4 years
Computer and office equipment
Property and Equipment
Period over which property and equipment are depreciated	3 years
Computer software
Property and Equipment
Period over which property and equipment are depreciated	3 years

Summary of Significant Accounting Policies (Details 5) $ in Millions	12 Months Ended
	Jun. 30, 2012 USD ($) item	Jun. 30, 2011 USD ($)	Jun. 30, 2010 USD ($)
Goodwill and Acquired Intangible Assets
Number of reporting unit \| item	1
Business Combinations
Maximum measurement period from the acquisition date up to record adjustments to the assets acquired and liabilities assumed		1 year
Advertising Expenses
Advertising expenses \| $	$ 0.5	$ 0.4	$ 0.4
Minimum
Goodwill and Acquired Intangible Assets
Estimated useful lives of respective assets	1 year
Maximum
Goodwill and Acquired Intangible Assets
Estimated useful lives of respective assets	6 years

Summary of Significant Accounting Policies (Details 6) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2010	Sep. 30, 2010	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Numerator:
Net income (loss) used in computing basic and diluted net income (loss) per share	$ (20,264)	$ (14,881)	$ (10,387)	$ (26,510)	$ (24,980)	$ (1,160)	$ 4,098	$ (4,640)	$ (72,042)	$ (26,682)	$ 2,841
Denominator:
Weighted-average shares used in computing basic net income (loss) per share	71,473	71,120	70,698	70,263	62,451	59,960	59,282	58,667	70,887	60,085	57,560
Add: dilutive stock options and awards outstanding (in shares)											2,631
Diluted (in shares)	71,473	71,120	70,698	70,263	62,451	59,960	61,376	58,667	70,887	60,085	60,191
Anti-dilutive securities excluded from computation of earnings per share
Anti-dilutive securities excluded from the computation of diluted net income (loss) per share (in shares)									9,970	8,995	4,317
Income Taxes
Subsequent period within which no material changes in unrecognized tax benefits are expected (in months)									12 months
Reduction in uncertain tax position due to lapse of various statutes of limitation									$ 300
Convertible Notes
Anti-dilutive securities excluded from computation of earnings per share
Interest rate (as a percent)	3.75%								3.75%
Option to purchase common stock
Anti-dilutive securities excluded from computation of earnings per share
Anti-dilutive securities excluded from the computation of diluted net income (loss) per share (in shares)									7,873	8,337	4,057
Restricted stock units
Anti-dilutive securities excluded from computation of earnings per share
Anti-dilutive securities excluded from the computation of diluted net income (loss) per share (in shares)									1,171	658	260
Performance stock units
Anti-dilutive securities excluded from computation of earnings per share
Anti-dilutive securities excluded from the computation of diluted net income (loss) per share (in shares)									926

Summary of Significant Accounting Policies (Details 7) $ in Thousands	3 Months Ended								12 Months Ended
	Jun. 30, 2012 USD ($)	Mar. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)	Sep. 30, 2011 USD ($)	Jun. 30, 2011 USD ($)	Mar. 31, 2011 USD ($)	Dec. 31, 2010 USD ($)	Sep. 30, 2010 USD ($)	Jun. 30, 2012 USD ($) segment	Jun. 30, 2011 USD ($)	Jun. 30, 2010 USD ($)
Summary of Significant Accounting Policies
Number of operating segments \| segment									1
Revenue by geographic region
Total	$ 100,533	$ 101,816	$ 106,423	$ 100,451	$ 75,223	$ 54,747	$ 54,246	$ 38,068	$ 409,223	$ 222,284	$ 221,625
Americas (including Puerto Rico)
Revenue by geographic region
Total									189,072	122,636	147,381
Europe
Revenue by geographic region
Total									110,331	67,244	58,049
Asia (excluding Japan)
Revenue by geographic region
Total									64,026	16,158	5,608
Japan
Revenue by geographic region
Total									$ 45,794	$ 16,246	$ 10,587

Financial Instruments (Details) $ in Millions	Jun. 30, 2012 USD ($)
Convertible Notes
Fair value measurement
Interest rate (as a percent)	3.75%
Non-recurring basis \| Fair Value Measurements Using Inputs Considered as Level 2 \| Convertible Notes
Fair value measurement
Interest rate (as a percent)	3.75%
Fair value	$ 101.4
Recurring basis \| Fair Value Measurements Using Inputs Considered as Level 1 \| Money market funds
Fair value measurement
Total	$ 40.1

Balance Sheet Components (Details) - USD ($) $ in Thousands	12 Months Ended
Balance Sheet Components (Details) - USD ($) $ in Thousands	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Accounts receivable, net
Accounts receivable	$ 69,285	$ 59,858
Unbilled fees and services	305	2,319
Accounts and other receivable, gross	69,590	62,177
Less: Allowance for doubtful accounts	(1,700)	(324)
Accounts receivable, net	67,890	61,853
Financing receivables
Accounts receivable with contractual maturities of more than one year	2,500	0
Inventories
Raw materials	42,951	32,988
Work-in-process	16,932	28,216
Finished goods	21,810	36,632
Total inventories	81,693	97,836
Property and Equipment, net
Property and equipment, gross	82,800	76,307
Less: Accumulated depreciation and amortization	(45,342)	(31,484)
Property and equipment, net	37,458	44,823
Depreciation and amortization expense	16,400	6,400	$ 6,800
Furniture and fixtures
Property and Equipment, net
Property and equipment, gross	5,921	5,317
Computer and office equipment
Property and Equipment, net
Property and equipment, gross	9,126	8,280
Software
Property and Equipment, net
Property and equipment, gross	9,429	8,107
Leasehold improvements
Property and Equipment, net
Property and equipment, gross	16,065	15,386
Machinery and equipment
Property and Equipment, net
Property and equipment, gross	33,493	33,692
CyberKnife shared ownership systems
Property and Equipment, net
Property and equipment, gross	4,979	4,923
Construction in progress
Property and Equipment, net
Property and equipment, gross	3,787	602
CyberKnife and TomoTherapy shared ownership systems
Property and Equipment, net
Less: Accumulated depreciation and amortization	$ (1,300)	$ (2,100)

Investment (Details) - USD ($)	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2008
Investment
Purchase price (in dollars per share)	$ 6.82
Morphormics \| Series C Preferred Stock
Investment
Shares purchased			120,000
Purchase price (in dollars per share)			$ 12.50
Total purchase price			$ 1,500,000
Fair value of investment	$ 0	$ 0

- Definition

Value of the investment at close of period. For schedules of investments that are categorized, the value would be aggregated by category. For investment in and advances to affiliates, if operations of any controlled companies are different in character from those of the company, group such affiliates within divisions and by type of activities.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 946
-SubTopic 320
-Section S99
-Paragraph 1
-Subparagraph (SX 210.12-12.Column C.3,4)
-URI http://asc.fasb.org/extlink&oid=6955306&loc=d3e611133-123010

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 946
-SubTopic 320
-Section S99
-Paragraph 4
-Subparagraph (SX 210.12-12C.Column C.7)
-URI http://asc.fasb.org/extlink&oid=6955306&loc=d3e611225-123010

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 946
-SubTopic 320
-Section S99
-Paragraph 6
-Subparagraph (SX 210.12-14.Column E.2,3)
-URI http://asc.fasb.org/extlink&oid=6955306&loc=d3e611322-123010

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 946
-SubTopic 320
-Section S99
-Paragraph 5
-Subparagraph (SX 210.12-13.Column C.6)
-URI http://asc.fasb.org/extlink&oid=6955306&loc=d3e611282-123010

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 12
-Paragraph Column C
-Article 12

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 12
-Paragraph 3, 4
-Article 12

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 14
-Paragraph 2, 3
-Article 12

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 13
-Paragraph 6
-Article 12

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 12C
-Paragraph 7
-Article 12

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 14
-Paragraph Column E
-Article 12

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 12C
-Paragraph Column C
-Article 12

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 13
-Paragraph Column C
-Article 12

+ Details

Goodwill and Intangible Assets (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010	Jun. 10, 2011
Changes in the carrying amount of goodwill
Balance at the beginning of the period	$ 54,474	$ 4,495
Goodwill resulting from acquisition of TomoTherapy		49,979
Adjustments related to acquisition of TomoTherapy	4,741
Balance at the end of the period	59,215	54,474	$ 4,495
Intangible Assets
Accumulated Amortization	(18,796)	(2,576)
Net Amount	37,019
Total gross carrying amount	68,615	68,615
Total net carrying amount	49,819	66,039
Amortization expense	16,200	1,200	$ 300
Estimated future amortization expense of purchased intangible assets
2013	9,306
2014	7,298
2015	6,933
2016	6,933
2017	6,549
Net Amount	37,019
TomoTherapy
Intangible Assets
Additions to intangible assets related to the acquisition		66,805		$ 66,805
In-process research and development (CPAC)
Intangible Assets
Gross Carrying Amount	12,800	12,800
Net Amount	$ 12,800	12,800
Developed technology
Intangible Assets
Useful Lives	6 years
Gross Carrying Amount	$ 43,455	43,455
Accumulated Amortization	(9,161)	(2,069)
Net Amount	34,294	41,386
Estimated future amortization expense of purchased intangible assets
Net Amount	$ 34,294	41,386
Backlog
Intangible Assets
Useful Lives	1 year 3 months
Gross Carrying Amount	$ 10,500	10,500
Accumulated Amortization	(8,867)	(467)
Net Amount	1,633	10,033
Estimated future amortization expense of purchased intangible assets
Net Amount	$ 1,633	10,033
Distributor license
Intangible Assets
Useful Lives	2 years 6 months
Gross Carrying Amount	$ 1,860	1,860
Accumulated Amortization	(768)	(40)
Net Amount	1,092	1,820
Estimated future amortization expense of purchased intangible assets
Net Amount	$ 1,092	$ 1,820

Commitments and Contingencies (Details) - USD ($)	12 Months Ended
Commitments and Contingencies (Details) - USD ($)	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Future minimum lease payments under non-cancelable operating lease agreements
2013	$ 8,021,000
2014	7,245,000
2015	4,681,000
2016	2,272,000
2017	2,325,000
Thereafter	2,645,000
Total	27,189,000
Operating Lease Agreements and Long-term Debt
Rent expense, including common area maintenance	7,100,000	$ 4,800,000	$ 5,200,000
License and royalty agreement \| DKFZ (Deutsches Krebsforschungszentrum)
License and Royalty Agreements
Commitment amount to be paid on sale of system	12,500
Royalty expense	100,000	600,000	600,000
Royalty amount accrued	25,000	300,000
License and royalty agreement \| RaySearch Laboratories AB
License and Royalty Agreements
Commitment amount to be paid on sale of system	25,000
Royalty expense	700,000	40,000
Royalty amount accrued	600,000	600,000
License and royalty agreement \| Minimum \| DKFZ (Deutsches Krebsforschungszentrum)
License and Royalty Agreements
Annual commitment amount	50,000
License and royalty agreement \| Minimum \| RaySearch Laboratories AB
License and Royalty Agreements
Annual commitment amount	750,000
License agreement \| WARF (Wisconsin Alumni Research Foundation)
License and Royalty Agreements
Royalty expense	1,000,000
Royalty amount accrued	$ 100,000	$ 300,000
Royalty as percentage of fees, royalties and other payments received under sublicenses	50.00%
License agreement \| WARF (Wisconsin Alumni Research Foundation) \| Minimum
License and Royalty Agreements
Annual commitment amount	$ 300,000
Convertible Notes
Long-term principal and interest on Convertible Note
2013	3,750,000
2014	3,750,000
2015	3,750,000
2016	3,750,000
2017	100,313,000
Thereafter
Total	$ 115,313,000

Commitments and Contingencies (Details 2)	1 Months Ended
Commitments and Contingencies (Details 2)	Jun. 30, 2011 claim counts	Apr. 30, 2011 USD ($) claim	Mar. 31, 2011 claim complaint	Aug. 31, 2009 claim	Jul. 31, 2009 claim	Apr. 28, 2011 USD ($)	Mar. 09, 2011 counts patent	Jul. 17, 2009 USD ($)	Jul. 17, 2009 JPY (¥)
Accuray Securities Litigation
Contingencies
Number of claims made in lawsuits				2	1
Number of consolidated claims				3
Legal claims settlement agreement, amount \| $						$ 13,500,000
Litigation relating to the TomoTherapy Acquisition
Contingencies
Number of claims made in lawsuits			4
Number of consolidated claims		5
Number of complaints filed that named the company and a wholly owned subsidiary \| complaint			2
Best Medical Patent Litigation
Contingencies
Number of counts of alleged willful infringement of patents \| counts							2
Number of patents against which lawsuit is not dismissed	1						2
Number of patent claims dismissed	1
TomoTherapy Former Distributor in Japan
Contingencies
Legal claims settlement agreement, amount								$ 2,300,000	¥ 190,000,000
Rotary Systems \| Minimum
Contingencies
Claim for damages \| $		$ 50,000

Stockholders' Equity (Details) $ / shares in Units, $ in Millions	1 Months Ended	12 Months Ended
	Aug. 31, 2007 USD ($)	Jun. 30, 2012 USD ($) plan $ / shares shares	Jun. 30, 2011	Jun. 30, 2010	Jun. 10, 2011 shares
Stockholders' Equity
Amount up to which common shares can be acquired under stock repurchase plan \| $	$ 25.0
Period over which common shares can be acquired under stock repurchase plan	1 year
Number of shares of common stock retired		2,140,018
Stockholders' Equity
Expected weighted average period for recognition of compensation costs			0 years
TomoTherapy
Stockholders' Equity
Stock options assumed (in shares)					1,539,255
RSAs assumed (in shares)					429,591
Incentive stock option \| Minimum
Stockholders' Equity
Exercise price of stock options as a percentage of fair value on the date of grant		100.00%
Non-qualified stock option \| Minimum
Stockholders' Equity
Exercise price of stock options as a percentage of fair value on the date of grant		85.00%
Stock option and RSUs
Stockholders' Equity
Annual vesting percentage		25.00%
RSUs
Stockholders' Equity
Percentage of the award vesting at first anniversary		10.00%
Percentage of the award vesting at second anniversary		20.00%
Percentage of the award vesting at third anniversary		30.00%
Percentage of the award vesting at fourth anniversary		40.00%
Unrecognized compensation cost , net of estimated forfeitures \| $		$ 4.5
Expected weighted average period for recognition of compensation costs		1 year 10 months 24 days
Stock options
Stockholders' Equity
Remaining contractual term		5 years 6 months 25 days	5 years 1 month 17 days
Expected weighted average period for recognition of compensation costs		2 years 8 months 12 days
Unrecognized compensation cost related to stock options \| $		$ 5.5
Weighted average assumptions used for determining fair value of options
Expected life		6 years 3 months	6 years 3 months	6 years 3 months
Stock options \| TomoTherapy
Stockholders' Equity
Remaining vesting term		0 years
Exercise price, low end of range (in dollars per share) \| $ / shares		$ 0.48
Exercise price, high end of range (in dollars per share) \| $ / shares		$ 44.24
Stock options \| Minimum
Weighted average assumptions used for determining fair value of options
Risk free interest rate (as a percent)		0.85%	1.88%	2.11%
Expected volatility (as a percent)		52.00%	52.80%	56.60%
Stock options \| Minimum \| TomoTherapy
Stockholders' Equity
Remaining contractual term		1 month 6 days
Stock options \| Minimum \| Persons with at least 10% voting rights
Stockholders' Equity
Percentage of voting rights owned by persons to whom awards granted		10.00%
Stock options \| Maximum
Stockholders' Equity
Term of award		10 years
Weighted average assumptions used for determining fair value of options
Risk free interest rate (as a percent)		1.72%	2.44%	3.04%
Expected volatility (as a percent)		52.90%	54.90%	64.70%
Stock options \| Maximum \| TomoTherapy
Stockholders' Equity
Remaining contractual term		3 years 4 months 24 days
Stock options \| Maximum \| Persons with at least 10% voting rights
Stockholders' Equity
Term of award		5 years
RSA
Stockholders' Equity
Unrecognized compensation cost , net of estimated forfeitures \| $		$ 0.5
Expected weighted average period for recognition of compensation costs		1 year 2 months 12 days
RSA \| TomoTherapy
Stockholders' Equity
Remaining vesting term		1 year 2 months 12 days
2007 Plan
Stockholders' Equity
Number of share-based compensation plans \| plan		1
Number of shares authorized under the plan		10,500,000
Number of shares available for future issuance under the plan		2,300,000
3.75% Convertible Senior Notes
Stockholders' Equity
Authorized common stock reserved for future issuance		14,700,000
Interest rate (as a percent)		3.75%

Stockholders' Equity (Details 2) - USD ($) $ in Thousands	12 Months Ended
Stockholders' Equity (Details 2) - USD ($) $ in Thousands	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Share-based compensation charges
Share-based compensation expense	$ 8,458	$ 13,365	$ 10,646
Share-based compensation expense related to accelerated vesting of stock options, RSUs and RSAs		4,400
Capitalized share-based compensation costs	400	300
Cost of revenue
Share-based compensation charges
Share-based compensation expense	1,672	1,312	1,721
Selling and marketing
Share-based compensation charges
Share-based compensation expense	729	695	1,433
Research and development
Share-based compensation charges
Share-based compensation expense	2,340	2,922	2,850
General and administrative
Share-based compensation charges
Share-based compensation expense	$ 3,717	$ 8,436	$ 4,642

- Definition

Represents the expense recognized during the period arising from equity-based compensation arrangements (for example, shares of stock, unit, stock options or other equity instruments) with employees, directors and certain consultants qualifying for treatment as employees.

+ References + Details

Stockholders' Equity (Details 3) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Stockholders' Equity
Fair value of common stock (in dollars per share)	$ 6.82
Additional disclosures
Share-based compensation expense	$ 8,458	$ 13,365	$ 10,646
Stock options
Stockholders' Equity
Total intrinsic value of options exercised	2,900	6,100	6,600
Total fair value of shares vested	$ 2,800	$ 3,400	1,100
Options Outstanding
Balance at the beginning of the period (in shares)	8,336,220
Options granted (in shares)	1,399,424
Options exercised (in shares)	(746,441)
Options forfeited/ expired (in shares)	(1,116,603)
Balance at the end of the period (in shares)	7,872,600	8,336,220
Vested or expected to vest (in shares)	7,871,741
Exercisable (in shares)	5,816,292
Weighted Average Exercise Price
Balance at the beginning of the period (in dollars per share)	$ 7.39
Options granted (in dollars per share)	4.53
Options exercised (in dollars per share)	2.50
Options forfeited/ expired (in dollars per share)	9.79
Balance at the end of the period (in dollars per share)	7.00	$ 7.39
Vested or expected to vest (in dollars per share)	7.00
Exercisable (in dollars per share)	$ 7.57
Weighted Average Remaining Contractual Life (in years)
Balance at the end of the period	5 years 6 months 25 days	5 years 1 month 17 days
Vested or expected to vest	5 years 6 months 25 days
Exercisable	4 years 5 months 16 days
Aggregate Intrinsic Value
Balance at the end of the period	$ 12,359	$ 19,131
Vested or expected to vest	12,359
Exercisable	9,242
Additional disclosures
Share-based compensation expense	$ 3,500	$ 4,700	$ 6,600
Weighted average fair value (in dollars per share)	$ 2.30	$ 3.91	$ 3.45
Realized excess tax benefits	$ 0	$ 0	$ 400
"Plans" (combined activity of 1993 Plan, 1998 Plan, and 2007 Plan)
Shares Available for Grant
Balance at the beginning of the period (in shares)	3,600,595	3,038,641	2,645,757
Additional shares reserved	1,500,000	1,500,000	1,500,000
Expirations (in shares)		(151,042)	(325,120)
Grants (in shares)	(3,400,449)	(1,389,949)	(1,686,498)
Forfeitures or cancellations (in shares)	617,864	602,945	904,502
Balance at the end of the period (in shares)	2,318,010	3,600,595	3,038,641
"Plans" (combined activity of 1993 Plan, 1998 Plan, and 2007 Plan) \| Stock options
Options Outstanding
Balance at the beginning of the period (in shares)	8,336,220	7,808,591	8,455,316
Options granted (in shares)	1,399,424	914,770	1,498,740
Options exercised (in shares)	(746,441)	(1,396,685)	(1,313,749)
Options assumed (in shares)		1,539,255
Options forfeited/ expired (in shares)	(1,116,603)	(529,711)	(831,716)
Balance at the end of the period (in shares)	7,872,600	8,336,220	7,808,591
Weighted Average Exercise Price
Balance at the beginning of the period (in dollars per share)	$ 7.39	$ 6.03	$ 5.70
Options granted (in dollars per share)	4.53	7.30	6.09
Options exercised (in dollars per share)	2.50	2.58	1.55
Options assumed (in dollars per share)		10.41
Options forfeited/ expired (in dollars per share)	9.79	8.60	9.86
Balance at the end of the period (in dollars per share)	$ 7.00	$ 7.39	$ 6.03
"Plans" (combined activity of 1993 Plan, 1998 Plan, and 2007 Plan) \| RSUs/ PSUs
Number of equity instruments other than options outstanding
Balance at the beginning of the period (in shares)	658,193	464,186	519,609
Grants (in shares)	2,001,025	475,179	187,758
Forfeitures or cancellations (in shares)	(259,107)	(79,180)	(72,786)
Releases (in shares)	(302,476)	(201,992)	(170,395)
Balance at the end of the period (in shares)	2,097,635	658,193	464,186
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share)	$ 6.97	$ 12.52	$ 18.15
Grants (in dollars per share)	4.53	6.77	6.12
Forfeitures or cancellations (in dollars per share)	5.67	9.85	18.92
Releases (in dollars per share)	4.47	7.57	6.32
Balance at the end of the period (in dollars per share)	$ 5.16	$ 6.97	$ 12.52
Vested (in shares)	296,905
Vested (in dollars per share)	$ 4.47
Non-vested (in shares)	2,097,635	652,622
Non-vested (in dollars per share)	$ 5.16	$ 6.97
2007 Plan
Shares Available for Grant
Balance at the end of the period (in shares)	2,300,000
2007 Plan \| RSUs
Additional disclosures
Share-based compensation expense	$ 2,500	$ 2,900	$ 3,000
Weighted Average Grant Date Fair Value
Grants (in dollars per share)	$ 4.53	$ 6.77	$ 6.12

Stockholders' Equity (Details 4) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010	Jun. 10, 2011
Additional disclosures
Share-based compensation expense	$ 8,458	$ 13,365	$ 10,646
TomoTherapy
Additional disclosures
Options assumed (in shares)				1,539,255
RSA
Number of equity instruments other than options outstanding
Balance at the beginning of the period (in shares)	190,522
Forfeitures or cancellations (in shares)	(10,804)
Releases (in shares)	(147,290)
Balance at the end of the period (in shares)	32,428	190,522
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share)	$ 7.39
Forfeitures or cancellations (in dollars per share)	7.39
Releases (in dollars per share)	7.39
Balance at the end of the period (in dollars per share)	$ 7.39	$ 7.39
RSA \| TomoTherapy
Additional disclosures
Share-based compensation expense	$ 1,400	$ 5,000

Stockholders' Equity (Details 5) - USD ($)	12 Months Ended
Stockholders' Equity (Details 5) - USD ($)	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Stockholders' Equity
Share-based compensation expense	$ 8,458,000	$ 13,365,000	$ 10,646,000
Other disclosures
Expected weighted average period for recognition of compensation costs		0 years
ESPP
Stockholders' Equity
Purchase price expressed as percentage of fair market value of common stock	85.00%
Number of shares per period up to which employees may purchase	2,500
Share-based compensation expense	$ 1,100,000	$ 800,000	$ 800,000
Weighted average assumptions used for determining fair value of options
Expected life	6 months	6 months	6 months
Other disclosures
Unrecognized compensation cost , net of estimated forfeitures	$ 600,000
Expected weighted average period for recognition of compensation costs	4 months 24 days
Weighted average fair value (in dollars per share)	$ 1.80	$ 2.03	$ 2.21
ESPP \| Maximum
Stockholders' Equity
Number of shares authorized	1,200,000
Payroll deductions as percentage of salaries	10.00%
Value of shares up to which employees may purchase in any calendar year	$ 25,000
Weighted average assumptions used for determining fair value of options
Risk free interest rate (as a percent)	0.12%	0.23%	0.29%
Expected volatility (as a percent)	50.60%	56.70%	78.30%
ESPP \| Minimum
Weighted average assumptions used for determining fair value of options
Risk free interest rate (as a percent)	0.05%	0.11%	0.15%
Expected volatility (as a percent)	33.60%	33.60%	56.70%

Stockholders' Equity (Details 6) - PSUs shares in Millions, $ in Millions	12 Months Ended
	Jun. 30, 2012 USD ($) shares
Performance-Based Awards
Number of awards granted to employees (in shares)	1.0
Total fair value of awards granted to employees \| $	$ 3.9
Number of awards at the end of the period	0.9

Income Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Components of income (loss) before provision for income taxes
Domestic	$ (82,494)	$ (28,621)	$ 1,169
Foreign	6,636	2,626	1,668
Income (loss) before provision for (benefit from) income taxes	(75,858)	(25,995)	2,837
Current:
Federal			(876)
State	(7)	114	265
Foreign	2,107	939	724
Total current	2,100	1,053	113
Deferred:
Foreign	495	63	(117)
Total deferred	495	63	(117)
Total provision for (benefit from) income taxes	2,595	1,116	(4)
Income tax payable	1,100	400
Reconciliation of income taxes at the statutory federal income tax rate to net income taxes
At federal statutory rate	(26,551)	(8,961)	993
State tax, net of federal benefit	(7)	114	265
Stock-based compensation expense	3,645	33	389
Change in valuation allowance	24,796	8,883	(32)
Credits	(846)	(1,373)	(877)
Federal alternative minimum tax			(873)
Meals and entertainment	335	214	178
Acquisition costs	89	2,451
Other	818	(251)	(71)
Foreign taxes	316	6	24
Total U.S. federal taxes (benefits)	2,595	1,116	$ (4)
Deferred tax assets:
Federal and state net operating losses	80,834	46,110
Accrued vacation	1,973	2,184
Accrued bonus		2,315
Deferred revenue	1,125	13,981
Deferred rent	1,165	1,355
Credits	13,985	12,500
Stock-based compensation expense	13,103	15,007
Reserves not deductible for tax purposes	4,085	9,678
Unicap	1,347	1,818
Other	689	1,642
Total deferred tax assets	118,306	106,590
Deferred tax liabilities:
Fixed assets/intangibles	(15,198)	(21,629)
Foreign currency differences	(594)	(3,034)
Total deferred tax liabilities	(15,792)	(24,663)
Valuation allowance	(102,142)	(81,800)
Net deferred tax assets	372	$ 127
Income tax uncertainties
Cumulative amount of undistributed earnings upon which no U.S. income taxes provided	$ 6,600

Income Taxes (Details 2) $ in Millions	Jun. 30, 2012 USD ($)
Operating loss carryforwards
Amount expected to be credited to additional paid-in-capital	$ 5.5
Federal
Operating loss carryforwards
Net operating loss carryforwards	209.0
State
Operating loss carryforwards
Net operating loss carryforwards	$ 43.0

Income Taxes (Details 3) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details 3) - USD ($) $ in Thousands	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Valuation allowance
Valuation allowance percentage established for domestic and foreign net deferred tax assets	100.00%
Aggregate changes in the balance of gross unrecognized tax benefits
Balance at beginning of year	$ 14,158	$ 3,669	$ 3,364
Tax positions related to current year: Additions	1,129	10,468	347
Tax positions related to prior years: Additions	40	58	6
Tax positions related to prior years: Reductions	(180)	(37)	(48)
Balance at end of year	$ 15,147	14,158	$ 3,669
Subsequent period within which no material changes in unrecognized tax benefits are expected	12 months
Reduction in uncertain tax position due to lapse of various statutes of limitation	$ 300
Uncertain tax benefits that, if realized, would affect the effective tax rate	2,500
Accrued interest and penalties related to uncertain tax positions	600	$ 400
Federal \| Research and development
Tax Credits
Tax credits	13,500
State \| Research and development
Tax Credits
Tax credits	$ 13,100

Other Income Net (Expense), (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Other Income (Expense), Net
Interest income	$ 360	$ 543	$ 1,813
Foreign currency transaction gain		2,193
Realized gain on investments		27	318
Other	170	69	270
Total interest and other income	530	2,832	2,401
Interest expense on convertible notes	(7,397)
Other interest expenses	(414)	(23)	(32)
Foreign currency transaction loss	(4,386)		(1,920)
Loss on asset disposition	(296)	(254)	(195)
State sales, use and local taxes	(877)	(267)	(226)
Fines and penalties	(31)		(27)
Total interest and other expense	(13,401)	(544)	(2,400)
Total other income, net	$ (12,871)	$ 2,288	$ 1

Acquisition (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended								12 Months Ended
	Jun. 30, 2011	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2010	Sep. 30, 2010	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010	Jun. 10, 2011
Acquisition
Revenues		$ 100,533	$ 101,816	$ 106,423	$ 100,451	$ 75,223	$ 54,747	$ 54,246	$ 38,068	$ 409,223	$ 222,284	$ 221,625
Net loss		$ 21,646	$ 16,533	$ 12,191	$ 28,083	25,409	$ 1,160	$ (4,098)	$ 4,640	$ 78,453	27,111	$ (2,841)
TomoTherapy
Acquisition
Revenues	$ 11,100
Net loss	20,600
Purchase price
Cash													$ 174,178
Common stock issued (9,112,511 shares)													67,341
Stock options assumed (1,539,255 shares)													2,234
RSAs assumed (429,591 shares)													4,270
Total purchase price	$ 248,023					248,023					248,023		$ 248,023
Common stock issued (in shares)	9,112,511
Stock options assumed (in shares)													1,539,255
RSAs assumed (in shares)													429,591
Assumptions utilized for determining the fair value of the stock options assumed
Dividend Yield (as a percent)	0.00%
Amount for each pre-adjusted RSA for fair value determination (in dollars per share)													$ 3.15
Purchase price allocation
Cash	$ 105,932					105,932					105,932
Accounts receivable	31,563					31,563					31,563
Inventories	72,383					72,383					72,383
Other assets	10,666					10,666					10,666
Property and equipment	28,878					28,878					28,878
Goodwill	49,979					49,979					49,979
Identified intangible assets	66,805					66,805					66,805		$ 66,805
Accounts payable	(14,974)					(14,974)					(14,974)
Customer advances	(13,045)					(13,045)					(13,045)
Deferred revenue	(39,856)					(39,856)					(39,856)
Other liabilities	(39,327)					(39,327)					(39,327)
Noncontrolling interest	(10,981)					(10,981)					(10,981)
Total purchase price	$ 248,023					$ 248,023					248,023		$ 248,023
Business acquisition costs
Acquisition-related costs											18,500
TomoTherapy \| Employee severance
Business acquisition costs
Acquisition-related costs											$ 10,500
TomoTherapy \| Minimum
Assumptions utilized for determining the fair value of the stock options assumed
Risk Free Rate (as a percent)	0.10%
Expected Life	5 months 8 days
Volatility (as a percent)	34.00%
TomoTherapy \| Maximum
Assumptions utilized for determining the fair value of the stock options assumed
Risk Free Rate (as a percent)	1.36%
Expected Life	4 years 5 months 8 days
Volatility (as a percent)	56.00%

Acquisition (Details 2) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010	Jun. 10, 2011
TomoTherapy
Identifiable intangible assets assumed in the acquisition
Total intangible assets subject to amortization, Fair Value				$ 54,005
Total intangible assets, Fair Value		$ 66,805		66,805
Unaudited pro forma results
Net revenue		407,963	$ 409,313
Net loss attributable to stockholders		$ (74,522)	$ (50,037)
Diluted earnings per share		$ (1.08)	$ (0.75)
In-process research and development (CPAC) \| TomoTherapy
Identifiable intangible assets assumed in the acquisition
Indefinite intangible assets, Fair Value				12,800
Developed technology
Identifiable intangible assets assumed in the acquisition
Useful Life	6 years
Developed technology \| TomoTherapy
Identifiable intangible assets assumed in the acquisition
Total intangible assets subject to amortization, Fair Value				41,645
Backlog
Identifiable intangible assets assumed in the acquisition
Useful Life	1 year 3 months
Backlog \| TomoTherapy
Identifiable intangible assets assumed in the acquisition
Total intangible assets subject to amortization, Fair Value				10,500
Distributor license
Identifiable intangible assets assumed in the acquisition
Useful Life	2 years 6 months
Distributor license \| TomoTherapy
Identifiable intangible assets assumed in the acquisition
Total intangible assets subject to amortization, Fair Value				$ 1,860

Investment in CPAC (Details) $ in Thousands	1 Months Ended		3 Months Ended	12 Months Ended	16 Months Ended
Investment in CPAC (Details) $ in Thousands	Apr. 30, 2012 USD ($)	Apr. 30, 2008 USD ($)	Jun. 30, 2012 USD ($) $ / shares shares	Jun. 30, 2012 USD ($) $ / shares shares	Mar. 31, 2012 USD ($) shares	Apr. 20, 2012 USD ($)	Dec. 31, 2011 USD ($)	Jun. 30, 2011 USD ($)	May 10, 2011 USD ($)
In-process research and development (CPAC)
Investment in CPAC
Net Amount			$ 12,800	$ 12,800				$ 12,800
TomoTherapy \| Convertible Promissory Notes
Investment in CPAC
Principal and accrued interest outstanding			1,300	1,300
Other participating investors \| Convertible Promissory Notes
Investment in CPAC
Principal and accrued interest outstanding			$ 3,600	$ 3,600
CPAC
Investment in CPAC
Ownership interest (as a percent)			15.40%
Ownership interest on fully diluted basis (as a percent)				16.30%
Total assets			$ 15,000	$ 15,000				16,000
Total liabilities			$ 600	$ 600				1,600
Exercise price of warrants \| $ / shares			0.8725	0.8725
Common shares of CPAC for which warrants received \| shares			338,839	338,839
Maximum ownership interest on conversion of revolving note (as a percent)			19.00%
CPAC \| In-process research and development (CPAC)
Investment in CPAC
Net Amount			$ 12,800	$ 12,800				$ 12,800
CPAC \| Convertible Promissory Notes
Investment in CPAC
Interest rate (as a percent)			12.00%	12.00%
Exercise price of warrants \| $ / shares			0.57	0.57
CPAC \| Revolving Promissory Note
Investment in CPAC
Interest rate (as a percent)			12.00%	12.00%
Principal and accrued interest outstanding			$ 1,900	$ 1,900			$ 2,200
Interest rate on amendment (as a percent)			8.00%	8.00%
CPAC \| TomoTherapy
Investment in CPAC
Fair market value of intellectual property investment contributed by the primary beneficiary		$ 1,900
CPAC \| TomoTherapy \| Maximum
Investment in CPAC
Ownership interest (as a percent)				50.00%
CPAC \| TomoTherapy \| Convertible Promissory Notes
Investment in CPAC
Warrants issued by VIE for consideration received \| shares					1,386,981
Consideration paid to acquire promissory notes from variable interest entity					$ 1,200
CPAC \| TomoTherapy \| Revolving Promissory Note
Investment in CPAC
Maximum amount available to borrow									$ 1,900
CPAC \| Other participating investors
Investment in CPAC
Investment in exchange for preferred stock of VIE and warrants to purchase common stock						$ 1,100
Additional investment contribution in exchange for preferred stock of VIE and warrants to purchase common stock	$ 700
CPAC \| Other participating investors \| Convertible Promissory Notes
Investment in CPAC
Warrants issued by VIE for consideration received \| shares					1,386,983
Consideration paid to acquire promissory notes from variable interest entity					$ 3,300

Debt (Details)	1 Months Ended	12 Months Ended
Debt (Details)	Aug. 31, 2011 USD ($)	Jun. 30, 2012 USD ($) shares $ / shares	Aug. 02, 2011 USD ($)
Debt
Proceeds from debt, net of costs		$ 96,100,000
Net carrying amount		79,466,000
Interest expense related to contractual interest coupon		$ 7,397,000
3.75% Convertible Senior Notes
Debt
Aggregate principal amount of debt issued	$ 100,000,000
Interest rate (as a percent)		3.75%
Proceeds from debt, net of costs	$ 96,100,000
Debt issuance costs, amortization period	5 years
Conversion rate, number of shares to be issued per $1000 of principal amount (in shares) \| shares		105.5548
Principal amount used for debt instrument conversion ratio		$ 1,000
Conversion price (in dollars per share) \| $ / shares		$ 9.47
Number of consecutive trading days during which the closing price of the entity's common stock must exceed the conversion price for at least 20 days in order for the notes to be convertible into common stock		30 days
Number of consecutive business days immediately after any five consecutive trading day period during the note measurement period		5 days
Number of consecutive trading days before five consecutive business days during the note measurement period		5 days
Number of working days preceding maturity date for delivery of shares or payment of cash		33 days
Repurchase price, as percentage of principal amount, if company undergoes change of control		100.00%
Number of consecutive trading days during which the closing price of the entity's common stock must exceed the conversion price for at least 20 days in order for the notes to be redeemable		30 days
Discount rate on liability component (as a percent)	10.00%
Debt issuance costs and discount allocated to equity conversion component			$ 900,000
Carrying amount of the equity conversion component		$ 23,189,000	24,100,000
Principal amount of the Notes		100,000,000	$ 75,900,000
Unamortized debt discount		(20,534,000)
Net carrying amount		$ 79,466,000
Amortization period	5 years	49 months
Effective interest rate (as a percent)	10.00%
Interest expense related to contractual interest coupon		$ 3,438,000
Interest expense related to amortization of debt discount		3,596,000
Total interest expense recognized		$ 7,034,000
3.75% Convertible Senior Notes \| Minimum
Debt
Number of days within 30 consecutive trading days in which the closing price of the entity's common stock must exceed the conversion price for the notes to be convertible into common stock		20 days
Percentage of the closing sales price of the entity's common stock that the conversion price must exceed in order for the notes to be convertible		130.00%
Percentage of the closing sales price of the entity's common stock that the conversion price must exceed in order for the notes to be redeemable		130.00%
Number of days within 30 consecutive trading days in which the closing price of the entity's common stock must exceed the conversion price for the notes to be redeemable		20 days
3.75% Convertible Senior Notes \| Maximum
Debt
Percentage of the trading price to the product of the sale price of the entity's common stock and the conversion rate		98.00%

Employee Benefit Plans (Details) - USD ($) $ in Millions	12 Months Ended
Employee Benefit Plans (Details) - USD ($) $ in Millions	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Employee Benefit Plans
Employer's contribution to the 401(k) Plan	$ 1.7	$ 0.7	$ 0.7

Restructuring Charges (Details) $ in Millions	3 Months Ended	12 Months Ended
Restructuring Charges (Details) $ in Millions	Dec. 31, 2011 position	Jun. 30, 2012 USD ($) employee
Restructuring Charges
Number of full-time positions expected to be affected under WFA \| position	51
Estimated restructuring-related charges associated with the WFA		$ 1.7
Number of full-time employees reduced in the global workforce under the WFA \| employee		51
Charges for severance and related benefits		$ 1.9
Charges for severance and related benefits paid		$ 1.9

- Definition

The charge against earnings in the period for known and estimated costs of termination benefits provided to current employees that are involuntarily terminated under a benefit arrangement associated with exit from or disposal of business activities or restructurings pursuant to a duly authorized plan, excluding costs or losses pertaining to an entity newly acquired in a business combination or a discontinued operation as defined by generally accepted accounting principles and costs associated with one-time termination benefits.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 420
-SubTopic 10
-Section 50
-Paragraph 1
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=6394359&loc=d3e17939-110869

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 420
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SAB TOPIC 5.P.4(b))
-URI http://asc.fasb.org/extlink&oid=6394695&loc=d3e140904-122747

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 715
-SubTopic 20
-Section 50
-Paragraph 1
-Subparagraph (a)(10)
-URI http://asc.fasb.org/extlink&oid=21915506&loc=d3e1928-114920

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 420
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SAB TOPIC 5.P.3)
-URI http://asc.fasb.org/extlink&oid=6394695&loc=d3e140864-122747

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 230
-SubTopic 10
-Section 45
-Paragraph 28
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=6943989&loc=d3e3602-108585

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 132R
-Paragraph 5-8
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 5
-Section P
-Subsection 3, 4

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 146
-Paragraph 8-13, 20
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Staff Position (FSP)
-Number FAS146-1
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 112
-Paragraph 7
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Quarterly Financial Data (unaudited) (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2010	Sep. 30, 2010	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Quarterly Financial Data (unaudited)
Net revenue	$ 100,533	$ 101,816	$ 106,423	$ 100,451	$ 75,223	$ 54,747	$ 54,246	$ 38,068	$ 409,223	$ 222,284	$ 221,625
Gross profit	36,490	36,111	40,243	24,428	32,226	27,313	29,466	18,237	137,272	107,242	104,018
Net income (loss)	(21,646)	(16,533)	(12,191)	(28,083)	(25,409)	(1,160)	4,098	(4,640)	(78,453)	(27,111)	2,841
Net income (loss) attributable to stockholders	$ (20,264)	$ (14,881)	$ (10,387)	$ (26,510)	$ (24,980)	$ (1,160)	$ 4,098	$ (4,640)	$ (72,042)	$ (26,682)	$ 2,841
Basic net (loss) per share attributable to stockholders	$ (0.28)	$ (0.21)	$ (0.15)	$ (0.38)	$ (0.40)	$ (0.02)	$ 0.07	$ (0.08)	$ (1.02)	$ (0.44)	$ 0.05
Diluted net (loss) per share attributable to stockholders	$ (0.28)	$ (0.21)	$ (0.15)	$ (0.38)	$ (0.40)	$ (0.02)	$ 0.07	$ (0.08)	$ (1.02)	$ (0.44)	$ 0.05
Shares used in basic per share calculation	71,473	71,120	70,698	70,263	62,451	59,960	59,282	58,667	70,887	60,085	57,560
Shares used in diluted per share calculation	71,473	71,120	70,698	70,263	62,451	59,960	61,376	58,667	70,887	60,085	60,191

- Definition

The amount of net income (loss) for the period per each share of common stock or unit outstanding during the reporting period.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 225
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SX 210.5-03.21)
-URI http://asc.fasb.org/extlink&oid=6880815&loc=d3e20235-122688

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6371337&loc=d3e3550-109257

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 55
-Paragraph 52
-URI http://asc.fasb.org/extlink&oid=16381557&loc=d3e4984-109258

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=7655603&loc=d3e1252-109256

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 944
-SubTopic 225
-Section S99
-Paragraph 1
-Subparagraph (SX 210.7-04.19)
-URI http://asc.fasb.org/extlink&oid=6879464&loc=d3e573970-122913

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 225
-Section S99
-Paragraph 1
-Subparagraph (SX 210.9-04.23)
-URI http://asc.fasb.org/extlink&oid=6879574&loc=d3e536633-122882

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Paragraph 18
-Article 7

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 36, 37, 38
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 07-4
-Paragraph 4
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 03
-Paragraph 20
-Article 5

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Paragraph 21
-Article 9

+ Details

- Definition

The amount of net income (loss) for the period available to each share of common stock or common unit outstanding during the reporting period and to each share or unit that would have been outstanding assuming the issuance of common shares or units for all dilutive potential common shares or units outstanding during the reporting period.

+ References + Details

- Definition

The consolidated profit or loss for the period, net of income taxes, including the portion attributable to the noncontrolling interest.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 810
-SubTopic 10
-Section 45
-Paragraph 19
-URI http://asc.fasb.org/extlink&oid=7656940&loc=SL4569616-111683

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 810
-SubTopic 10
-Section 55
-Paragraph 4K
-URI http://asc.fasb.org/extlink&oid=18733213&loc=SL4591552-111686

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 810
-SubTopic 10
-Section 50
-Paragraph 1A
-Subparagraph (a),(c)
-URI http://asc.fasb.org/extlink&oid=18733093&loc=SL4573702-111684

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 810
-SubTopic 10
-Section 55
-Paragraph 4J
-URI http://asc.fasb.org/extlink&oid=18733213&loc=SL4591551-111686

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 29
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph a
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph c(1)
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 5
-Subparagraph b
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph A1, A4, A5
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

- Definition

The average number of shares or units issued and outstanding that are used in calculating diluted EPS or earnings per unit (EPU), determined based on the timing of issuance of shares or units in the period.

+ References + Details

- Definition

Number of [basic] shares or units, after adjustment for contingently issuable shares or units and other shares or units not deemed outstanding, determined by relating the portion of time within a reporting period that common shares or units have been outstanding to the total time in that period.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 50
-Paragraph 1
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=6371337&loc=d3e3550-109257

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=7655603&loc=d3e1448-109256

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Weighted-Average Number of Common Shares Outstanding
-URI http://asc.fasb.org/extlink&oid=6528421

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 07-4
-Paragraph 4
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 8
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 171
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 40
-Subparagraph a
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Subsequent Events (Details) - Subsequent events - USD ($) $ in Millions	1 Months Ended
	Jul. 31, 2012	Jul. 15, 2012
Developed technology
Subsequent Events
Amortization period	5 years
Morphormics, Inc.
Subsequent Events
Cost to acquire remaining outstanding equity		$ 5.7

Valuation and Qualifying Accounts (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Accounts receivable
Valuation and Qualifying Accounts
Beginning Balance	$ 324	$ 115	$ 484
Additions (Deductions)	1,392	239	(358)
Write-offs/Deductions	(16)	(30)	(11)
Ending Balance	1,700	324	$ 115
Accrued warranty
Valuation and Qualifying Accounts
Beginning Balance	6,795
Additions (Deductions)	48
Write-offs/Deductions	(6,095)	(805)
Increase Due to Acquisition		7,600
Ending Balance	$ 748	$ 6,795