0001047469-13-008757 | 10-K | XBRL Viewer

Document and Entity Information - USD ($)	12 Months Ended
Document and Entity Information - USD ($)	Jun. 30, 2013	Aug. 19, 2013	Dec. 31, 2012
Document and Entity Information
Entity Registrant Name	ACCURAY INC
Entity Central Index Key	0001138723
Document Type	10-K
Document Period End Date	Jun. 30, 2013
Amendment Flag	false
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			$ 247,564,392
Entity Common Stock, Shares Outstanding		74,705,405
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	FY

Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2013	Jun. 30, 2012
Current assets:
Cash and cash equivalents	$ 73,313	$ 143,504
Restricted cash	2,728	1,560
Investments	101,084
Accounts receivable, net of allowance for doubtful accounts of $2,160 and $1,700, respectively	55,458	67,890
Inventories	81,592	81,693
Prepaid expenses and other current assets	12,595	16,715
Deferred cost of revenue - current	9,165	4,896
Total current assets	335,935	316,258
Property and equipment, net	34,733	37,458
Goodwill	59,368	59,215
Intangible assets, net	31,896	49,819
Deferred cost of revenue - noncurrent	2,149	2,433
Other assets	11,848	7,987
Total assets	475,929	473,170
Current liabilities:
Accounts payable	15,920	18,209
Accrued compensation	12,461	23,071
Other accrued liabilities	22,893	31,646
Customer advances - current	17,692	18,177
Deferred revenue - current	86,893	83,071
Total current liabilities	155,859	174,174
Long-term liabilities:
Long-term other liabilities	5,382	5,988
Deferred revenue - noncurrent	9,085	9,675
Long-term debt	198,768	79,466
Total liabilities	369,094	269,303
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: 200,000,000 and 100,000,000 shares June 30, 2013 and June 30, 2012, respectively; issued and outstanding: 74,587,231 and 71,864,268 shares at June 30, 2013 and June 30, 2012, respectively	75	72
Additional paid-in capital	424,524	409,143
Accumulated other comprehensive income	1,882	2,837
Accumulated deficit	(319,646)	(216,427)
Total stockholders' equity	106,835	195,625
Non-controlling interest		8,242
Total equity	106,835	203,867
Total liabilities and equity	$ 475,929	$ 473,170

Consolidated Balance Sheets (Parenthetical) - USD ($) $ in Thousands	Jun. 30, 2013	Jun. 30, 2012
Consolidated Balance Sheets
Accounts receivable, allowance for doubtful accounts (in dollars)	$ 2,160	$ 1,700
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	200,000,000	100,000,000
Common stock, issued shares	74,587,231	71,864,268
Common stock, outstanding shares	74,587,231	71,864,268

Consolidated Statements of Operations and Comprehensive Loss - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Net revenue:
Products	$ 137,403	$ 240,472	$ 138,595
Services	178,571	166,681	80,490
Other		2,070	3,199
Total net revenue	315,974	409,223	222,284
Cost of revenue:
Cost of products	85,498	136,180	55,524
Cost of services	132,836	134,562	56,218
Cost of other		1,209	3,300
Total cost of revenue	218,334	271,951	115,042
Gross profit	97,640	137,272	107,242
Operating expenses:
Selling and marketing	54,372	54,547	37,181
Research and development	66,197	81,287	41,301
General and administrative	57,726	57,672	56,589
Total operating expenses	178,295	193,506	135,071
Loss from operations	(80,655)	(56,234)	(27,829)
Other income (expense), net	(13,133)	(12,521)	2,288
Loss before provision for income taxes	(93,788)	(68,755)	(25,541)
Provision for income taxes	3,573	2,595	1,116
Loss from continuing operations	(97,361)	(71,350)	(26,657)
Loss from discontinued operations (Note 7):
Loss from operations of a discontinued variable interest entity	(3,505)	(7,103)	(454)
Impairment of indefinite lived intangible asset of discontinued variable interest entity	(12,200)
Loss from deconsolidation of a variable interest entity	(3,442)
Loss from discontinued operations, net of tax	(19,147)	(7,103)	(454)
Loss from discontinued operations attributable to non-controlling interest	(13,289)	(6,411)	(429)
Loss from discontinued operations attributable to stockholders	(5,858)	(692)	(25)
Net loss attributable to stockholders	$ (103,219)	$ (72,042)	$ (26,682)
Loss per share attributable to stockholders
Basic and diluted - continuing operations (in dollars per share)	$ (1.33)	$ (1.01)	$ (0.44)
Basic and diluted - discontinued operations (in dollars per share)	(0.08)	(0.01)	0.00
Basic and diluted - net loss (in dollars per share)	$ (1.41)	$ (1.02)	$ (0.44)
Weighted average common shares used in computing loss per share
Basic and diluted (in shares)	73,281	70,887	60,085
Net loss attributable to stockholders	$ (103,219)	$ (72,042)	$ (26,682)
Foreign currency translation adjustment	(498)	2,710	236
Unrealized loss on investments, net of tax	(457)		(38)
Comprehensive loss	$ (104,174)	$ (69,332)	$ (26,484)

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
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	(27,111)	(26,682)				(26,682)	(429)
Cumulative translation adjustment	236	236			236
Unrealized loss on investments, net of tax	(38)	(38)			(38)
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
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	(78,453)	(72,042)				(72,042)	(6,411)
Cumulative translation adjustment	2,710	2,710			2,710
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
Increase (Decrease) in Stockholders' Equity
Exercise of stock options, net	$ 4,201	4,201	$ 2	4,199
Exercise of stock options, net (in shares)			1,514,591
Issuance of common stock under employee stock purchase plan	3,257	3,257	$ 1	3,256
Issuance of common stock under employee stock purchase plan (in shares)			663,986
Issuance of restricted stock	1	1	$ 1
Issuance of restricted stock (in shares)			544,386
Share-based compensation	8,236	8,236		8,236
Deconsolidation of CPAC	4,737	(310)		(310)			5,047
Net loss	(116,508)	(103,219)				(103,219)	$ (13,289)
Cumulative translation adjustment	(498)	(498)			(498)
Unrealized loss on investments, net of tax	(457)	(457)			(457)
Balance at Jun. 30, 2013	$ 106,835	$ 106,835	$ 75	$ 424,524	$ 1,882	$ (319,646)
Balance (in shares) at Jun. 30, 2013	74,587,231		74,587,231

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Cash Flows From Operating Activities
Loss from continuing operations	$ (97,361)	$ (71,350)	$ (26,657)
Loss from discontinued operations	(19,147)	(7,103)	(454)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities
Depreciation and amortization	25,564	32,592	7,566
Impairment of indefinite lived intangible asset	12,200
Share-based compensation	8,216	8,458	13,365
Accretion/(amortization) of investment premiums/discounts	295		(27)
Accretion of interest on long-term debt	4,302	3,596
Provision for bad debt	787	1,392	239
Provision for write-down of inventories	5,255	2,129	1,698
Loss on disposal of property and equipment	1,013	296	312
Gain on previously held equity interest in Morphormics	(662)
Loss from deconsolidation of a variable interest entity	3,442
Provision for deferred income taxes	947	495	63
Changes in assets and liabilities:
Restricted cash	(1,163)	1,605
Accounts receivable	10,858	(9,162)	8,698
Inventories	(5,147)	11,927	(4,321)
Prepaid expenses and other assets	5,166	2,886	(1,126)
Deferred cost of revenue	(4,005)	2,080	7,586
Accounts payable	(1,140)	(21,425)	10,662
Accrued liabilities	(18,525)	(10,538)	9,768
Customer advances	(659)	(7,044)	(909)
Deferred revenue	3,587	20,887	(14,060)
Net cash provided by (used in) operating activities	(66,177)	(38,279)	12,403
Cash Flows From Investing Activities
Purchases of property and equipment , net	(15,126)	(10,769)	(4,022)
Purchases of intangible assets	(232)
Purchases of investments	(102,403)		(100,710)
Sales and maturities of investments			206,414
Acquisition of businesses, net of cash acquired	(3,861)	(1,384)	(70,265)
Net cash provided by (used in) investing activities	(121,622)	(12,153)	31,417
Cash Flows From Financing Activities
Proceeds from issuance of common stock	7,455	4,449	5,601
Proceeds from debt, net of costs	110,462	96,100
Net cash provided by financing activities	117,917	100,549	5,601
Effect of exchange rate changes on cash and cash equivalents	(309)	(2,519)	1,051
Net increase (decrease) in cash and cash equivalents	(70,191)	47,598	50,472
Cash and cash equivalents at beginning of period	143,504	95,906	45,434
Cash and cash equivalents at end of period	73,313	143,504	95,906
Supplemental Disclosure of Cash Flow Information
Cash paid for income taxes	2,000	1,198	1,392
Cash paid for interest	$ 3,750	$ 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
Description of Business	Jun. 30, 2013
Description of Business
Description of Business	1. Description of Business Organization Accuray Incorporated, together with its subsidiaries, the Company or Accuray, is incorporated in Delaware. The Company designs, develops and sells advanced radiosurgery and radiation therapy systems for the treatment of tumors throughout the body. The Company conducts its business worldwide. The Company has its headquarters in Sunnyvale, California, with additional locations in other regions in the United States, Europe and Asia.

Summary of Significant Accounting Policies

12 Months Ended

Jun. 30, 2013

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 GAAP, pursuant to the rules and regulations of the Securities and Exchange Commission, or SEC. The consolidated financial statements include the accounts of the Company, its wholly-owned subsidiaries and a variable interest entity, Compact Particle Acceleration Corporation, or CPAC until the deconsolidation of CPAC on December 21, 2012 (for further information, see Note 7, Investment in CPAC). All significant inter-company transactions and balances have been eliminated in consolidation.

Reclassification

As a result of the deconsolidation of CPAC, the results of operations of CPAC, including the loss on deconsolidation of CPAC and the losses attributable to the non-controlling interest recorded for the years ended June 30, 2013, 2012 and 2011 have been presented as discontinued operations. Accordingly, the Company revised its previously reported consolidated statements of operations and comprehensive loss and consolidated statements of cash flows for the years ended June 30, 2012 and 2011.

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 and comprehensive loss.

Fair Value Measurements

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.

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.

Investments

The Company classifies its marketable securities as available-for-sale. The cost of securities sold is based on the specific-identification method. Realized gains and losses and declines in value judged to be other-than-temporary on available-for-sale securities are included as a component of other income (expense), net. Interest on securities classified as available-for-sale is included as a component of other income (expense), net. As the Company's marketable securities are considered by the Company as available to support current operations, these securities have been classified as current assets on the consolidated balance sheets.

The Company considers highly liquid investments with original maturities of three months or less at the date of purchase to be cash equivalents. Investments with original maturities greater than three months are classified as Investments in the consolidated balance sheet. Investments include available-for-sale investment-grade debt securities that the Company carries at fair value. The Company accumulates unrealized gains and losses on the Company's available-for-sale debt securities, net of tax, in accumulated other comprehensive income in the stockholders' equity section of its consolidated balance sheets. Such an unrealized gain or loss does not reduce net income for the applicable accounting period. If the fair value of an available-for-sale debt instrument is less than its amortized cost basis, an other-than-temporary impairment is triggered in circumstances where (1) the Company intends to sell the instrument, (2) it is more likely than not that the Company will be required to sell the instrument before recovery of its amortized cost basis, or (3) the Company does not expect to recover the entire amortized cost basis of the instrument (that is, a credit loss exists). If the Company intends to sell or it is more likely than not that the Company will be required to sell the available-for-sale debt instrument before recovery of its amortized cost basis, the Company recognizes an other-than-temporary impairment in earnings equal to the entire difference between the debt instrument's amortized cost basis and its fair value. For available-for-sale debt instruments that are considered other-than-temporarily impaired due to the existence of a credit loss, if the Company does not intend to sell and it is not more likely than not that the Company will be required to sell the instrument before recovery of its remaining amortized cost basis (amortized cost basis less any current-period credit loss), the Company separates the amount of the impairment into the amount that is credit related and the amount due to all other factors. The credit loss component is recognized in earnings and is the difference between the debt instrument's amortized cost basis and the present value of its expected future cash flows. The remaining difference between the debt instrument's fair value and the present value of future expected cash flows is due to factors that are not credit related and is recognized in other comprehensive income (loss).

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. The Company does not invest an amount exceeding 5% of its combined cash, cash equivalents and investments in the securities of any one obligor or maker, except for obligations of the United States government, obligations of United States government agencies and money market accounts.

There were no customers that represented 10% or more of total net revenue for the years ended June 30, 2013, 2012 and 2011. At June 30, 2013, one customer accounted for 10% of accounts receivable. At June 30, 2012, two customers accounted for 16% and 10%, respectively, of 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.

Restricted Cash

Restricted cash primarily consists of certificates of deposit held as guarantees in connection with corporate leases as well as funds held as guarantees for Value-Added Tax, or VAT obligations in a foreign jurisdiction.

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, which approximate actual costs.

Revenue Recognition

The Company's revenue is primarily derived from sales of CyberKnife and TomoTherapy Systems, arrangements under its shared ownership program, and services, which include installation services, post-contract customer support or PCS, training and other professional services. The Company records its revenues net of any value added or sales tax. In all sales arrangements, the Company recognizes revenues when there is persuasive evidence of an arrangement, the fee is fixed or determinable, collection of the fee is reasonably assured and delivery has occurred. Payments received in advance of system 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 frequently enters into sales arrangements that contain multiple elements or deliverables. For example, a customer may purchase a system along with PCS and training. This arrangement would consist of multiple elements, with the system delivered in one reporting period and the PCS and training delivered across multiple reporting periods. For sale arrangements that contain multiple elements, the Company allocates the arrangement consideration to each element based on the relative selling price method, whereby the relative selling price of each deliverable is determined using vendor specific objective evidence, or VSOE of fair value, if it exists. VSOE of fair value for each element is based on 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 the Company is not able to establish VSOE for all deliverables in an arrangement with multiple elements, which may be due to the Company infrequently selling each element separately, not pricing products within a narrow range, or only having a limited sales history, the Company attempts to determine the selling price of each element based on third-party evidence of selling price, or TPE, as determined based on competitors' prices for similar deliverables when sold separately. TPE typically is difficult to establish due to the proprietary differences of competitive products and difficulty in obtaining reliable competitive standalone pricing information. When the Company is not able to establish selling price using VSOE or TPE, the Company uses its best estimate of selling price, or BESP in its 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 its overall go-to-market pricing strategy.

The Company has a limited number of software offerings which are not required to deliver its systems' essential functionality and can be sold separately. The Company accounts for the sale of its software products in accordance with the applicable guidance for software revenue recognition. The Company's multiple-element arrangements may also include software deliverables that are subject to the software revenue recognition guidance; and in these cases, the revenue for these multiple-element arrangements is allocated to the software deliverable and the nonsoftware deliverables based on the relative selling prices of all of the deliverables in the arrangement using VSOE, TPE or BESP.

The Company regularly reviews VSOE, TPE and BESP for all of its products and services and maintains internal controls over the establishment and updates of these estimates. As the Company's go-to-market strategies and other factors change, the Company may modify its pricing practices in the future, which may impact the selling prices of systems and services as well as VSOE, TPE and BESP of systems and services. As a result, the Company's future revenue recognition for multiple element arrangements could differ materially from that recorded in the current period.

Product Revenue

The majority of product revenue is generated from sales of CyberKnife and TomoTherapy systems. The Company sells its systems with PCS contracts, installation services, training, 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.

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, including evidence of an end-user order. 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, including evidence of an end-user order.

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.

Service Revenue

Service revenue is generated primarily from PCS (warranty period services and post warranty services), installation services, training, and professional services. PCS revenue is deferred and recognized over the service period. Installation service revenue is recognized concurrent with system revenue. Training and professional service revenues that are not deemed essential to the functionality of the systems are recognized as such services are performed.

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 incremental costs are deferred and are recognized over the period of revenue recognition.

Shared ownership program

The Company enters into arrangements under its shared ownership program with certain customers. These arrangements typically have a term of five years and provide the customer an option to purchase the system during the contractual term 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 which are included in product revenue in the consolidated statements of operations and comprehensive loss. Revenues from shared ownership arrangements were $1.5 million, $1.2 million and $1.4 million for the years ended June 30, 2013, 2012 and 2011, respectively.

Other revenue

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

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 revenue in the consolidated statements of operations and comprehensive loss. Any loss provision identified from the total contract in the period is recorded as an increase to cost of revenue. Historically, such loss provisions have not been significant.

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 3, 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.

Business Combinations

The Company allocates the fair value of the purchase consideration of its acquisitions to the tangible assets, liabilities, and intangible assets acquired, including in-process research and development, or IPR&D, based on their estimated fair values. Goodwill represents the excess of acquisition cost over the fair value of tangible and identified intangible net assets of businesses acquired. 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 and comprehensive loss. 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 closing date of the merger or acquisition.

Goodwill and Purchased Intangible Assets

Goodwill is not amortized, but is evaluated for impairment on an annual basis and 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, 2013, 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. IPR&D is initially capitalized at fair value as an intangible asset with an indefinite life and assessed for impairment thereafter. When a project underlying reported IPR&D is completed, the corresponding amount of IPR&D is reclassified as an amortizable purchased intangible asset and is amortized over the asset's estimated useful life. During the year ended June 30, 2013, the Company recorded an impairment charge of approximately $12.2 million related to IPR&D (see Note 6, Goodwill and Purchased Intangible Assets).

Acquisition-related expenses and restructuring costs are recognized separately from the business combination and are expensed as incurred.

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 $0.7 million, $0.5 million and $0.4 million for the years ended June 30, 2013, 2012 and 2011, 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 the fair value of all share-based payment awards based on the estimated grant date fair values and recognizing the related expense over the requisite service periods. Such share-based payment awards include employee stock options, restricted stock units, or RSUs, restricted stock awards, or RSAs, performance stock units, or PSUs, market stock units, or MSUs and the employee stock purchase plan, or ESPP. For some awards, the determination of fair value involves a number of significant estimates. The Company uses the Black-Scholes option valuation model to estimate the fair value of stock options and ESPP shares, 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. Expected volatility is derived from the historical volatilities of the Company's common stock. Prior to the second quarter of fiscal 2013, the Company used expected volatility derived from the historical volatilities of several unrelated public companies within industries related to its business. The Company estimates the expected term of stock options by taking the average of the vesting term and the contractual term of the option, as illustrated by the simplified method. 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 10, Stock Incentive Plan and Employee Stock Purchase Plan, for additional information.

The Company uses the Monte-Carlo simulation model to estimate the fair value of MSUs and recognizes the related expense over the requisite service period.

Loss Contingencies

The Company is involved in various lawsuits, claims and proceedings that arise in the ordinary course of business. The Company records a provision for a liability when it believes that it is both probable that a liability has been incurred and the amount can be reasonably estimated. Significant judgment is required to determine both probability and the estimated amount. The Company reviews these provisions at least quarterly and adjusts these provisions to reflect the impact of negotiations, settlements, rulings, advice of legal counsel, and updated information. 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.

Corporate Bonus Expense and Accruals

The Company records accruals for estimated corporate bonus expense each quarter which is paid out in the first quarter of the subsequent fiscal year. The Company's expense accrual for each quarter is based on its performance against Company defined metrics: net revenue, gross margin and orders to backlog. If the Company underestimates or overestimates any of these metrics during any quarter, adjustments to bonus expense and accruals may be necessary in subsequent periods during the year.

Net Loss Per Common Share

Basic and diluted loss per share is computed by dividing loss attributable to stockholders by the weighted average number of 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, PSUs and MSUs, and the purchase of shares under the ESPP, as determined under the treasury stock method, are excluded from the computation of diluted loss per share because their effect would have been anti-dilutive. The 3.75% Convertible Senior Notes due August 1, 2016, or the "3.75% Convertible Notes," and the 3.50% Convertible Senior Notes due February 1, 2018, or the "3.50% Convertible Notes" are included in the calculation of diluted loss per share if their inclusion is dilutive under the if-converted method.

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

	Years ended June 30,

	2013			2012			2011
Numerator:
Loss from operations used in computing loss per share from continuing operations	$	(97,361	)	$	(71,350	)	$	(26,657	)

Loss from discontinued operations used in computing loss per share from discontinued operations		(5,858	)		(692	)		(25	)

Net loss used in computing net loss per share	$	(103,219	)	$	(72,042	)	$	(26,682	)

Denominator:
Weighted average shares used in computing basic net loss per share		73,281			70,887			60,085
Add: Dilutive stock options and awards outstanding		—			—			—

Weighted average shares used in computing diluted net loss per share		73,281			70,887			60,085

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,

	2013		2012		2011
Stock options		4,844		7,873		8,337
RSUs, PSUs and MSUs		3,387		2,097		658
3.50% Convertible Notes		21,576		—		—
3.75% Convertible Notes		10,560		10,560

		40,367		20,530		8,995

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.

Comprehensive Loss

Comprehensive loss is comprised of net loss and other comprehensive income (loss). Other comprehensive income (loss) consists of foreign currency translation adjustments for the years ended June 30, 2013, 2012 and 2011, and unrealized losses on investments for the year ended June 30, 2013.

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,

	2013		2012		2011
Americas (including Puerto Rico)	$	143,613	$	189,072	$	122,636
Europe, Middle East, India and Africa		101,172		110,331		67,244
Asia (excluding Japan)		37,829		64,026		16,158
Japan		33,360		45,794		16,246

Total	$	315,974	$	409,223	$	222,284

Recent Accounting Pronouncements

In October 2012, the Financial Accounting Standards Board, or FASB, issued ASU No. 2012-04—Technical Corrections and Improvements. The amendments in this ASU cover a wide range of topics in the ASC. These amendments include technical corrections and improvements to the ASC and conforming amendments related to fair value measurements. The amendments in this update will be effective for annual periods beginning after December 15, 2012. The Company does not expect this to have a material impact on its consolidated financial statements.

In February 2013, the FASB issued Accounting Standards Update No. 2013-02, Comprehensive Income (Topic 220)—Reporting of Amounts Reclassified Out of Accumulated Other Comprehensive Income, or ASU 2013-02, to improve the reporting of reclassifications out of accumulated other comprehensive income. ASU 2013-02 requires an entity to report the effect of significant reclassifications out of accumulated other comprehensive income on the respective line items in net income if the amount being reclassified is required under GAAP to be reclassified in its entirety to net income. For other amounts that are not required under GAAP to be reclassified in their entirety from accumulated other comprehensive income to net income in the same reporting period, an entity is required to cross-reference other disclosures required under GAAP that provide additional detail about those amounts. ASU 2013-02 is effective for the Company in its first quarter of fiscal 2014 and will be applied prospectively. The Company does not expect that adoption of this guidance during fiscal 2014 will have a material impact on the Company's consolidated financial position, results of operations or cash flows.

Balance Sheet Components

12 Months Ended

Jun. 30, 2013

Balance Sheet Components

Balance Sheet Components

3. Balance Sheet Components

Cash and Cash Equivalents

The following is a summary of cash and cash equivalents (in thousands):

	June 30, 2013		June 30, 2012

Cash	$	60,082	$	96,694
Certificates of deposit		12,758		6,742
Money market funds		473		40,068

	$	73,313	$	143,504

Investments

The following is a summary of investments (in thousands):

	June 30, 2013

	Amortized Cost		Gross Unrealized Loss			Fair Value
Certificates of deposit	$	2,607	$	—		$	2,607
Commercial paper		3,993		(1	)		3,992
Corporate notes		94,941		(456	)		94,485

	$	101,541	$	(457	)	$	101,084

Investments classified as available-for-sale are carried at fair value as of June 30, 2013. The Company did not have such investments June 30, 2012. The aggregate fair value of available-for-sale securities with unrealized losses as of June 30, 2013 was $98.5 million. The Company did not have realized gains and losses from sales and/or maturities of investments during the year ended June 30, 2013. Gross unrealized loss on available-for-sale securities as of June 30, 2013 was $0.5 million, which the Company believes to be temporary losses. In determining that the decline in fair value of these securities was temporary, the Company considered the length of time each security was in an unrealized loss position, the extent to which the fair value was less than cost, and the fact that it does not intend to sell these securities and it is more likely than not that it will not be required to sell these securities before the recovery of their amortized cost basis.

The Company did not have any investments that were in an unrealized loss position for 12 months or greater as of June 30, 2013. The aggregate fair value and unrealized loss of investments in an unrealized loss position for less than 12 months was $98.5 million and $0.5 million, respectively, as of June 30, 2013.

The following table summarizes the estimated fair value of our investments in marketable securities designated as available-for-sale classified by the contractual maturity date of the security (in thousands):

	June 30, 2013

	Amortized Cost		Fair Value
Due in 1 year or less	$	40,235	$	40,188
Due in 1 - 2 years		35,428		35,256
Due in 2 - 3 years		25,878		25,640

	$	101,541	$	101,084

Accounts receivable, net

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

	June 30,

	2013			2012
Accounts receivable	$	56,830		$	69,285
Unbilled fees and services		788			305

		57,618			69,590
Less: Allowance for doubtful accounts		(2,160	)		(1,700	)

Accounts receivable, net	$	55,458		$	67,890

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 totaled $2.9 million and $2.5 million at June 30, 2013 and June 30, 2012, respectively and are included in Other Assets in the consolidated balance sheets. There was no balance in the allowance for doubtful accounts related to such financing receivables as of June 30, 2013 and June 30, 2012, respectively.

Inventories

Inventories consisted of the following (in thousands):

	June 30,

	2013		2012
Raw materials	$	33,721	$	42,951
Work-in-process		20,564		16,932
Finished goods		27,307		21,810

Inventories	$	81,592	$	81,693

Property and Equipment, net

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

	June 30,

	2013			2012
Furniture and fixtures	$	6,506		$	5,921
Computer and office equipment		9,481			9,126
Software		9,586			9,429
Leasehold improvements		19,199			16,065
Machinery and equipment		37,371			33,493
Shared ownership systems		4,979			4,979
Construction in progress		3,084			3,787

		90,206			82,800
Less: Accumulated depreciation and amortization		(55,473	)		(45,342	)

Property and equipment, net	$	34,733		$	37,458

Depreciation and amortization expense related to property and equipment for the years ended June 30, 2013, 2012 and 2011 was $15.2 million, $16.4 million and $6.4 million, respectively.

Financial Instruments

12 Months Ended

Jun. 30, 2013

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.

The following tables summarize the fair value of financial instruments measured on a recurring basis as of June 30, 2013 and June 30, 2012 (in thousands):

	Fair value measurement using

Type of instrument and line item in consolidated balance sheets	Quoted Prices in Active Markets for Identical Instruments (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Fair Value
Assets at June 30, 2013
Certificates of deposit—included in cash and cash equivalents and investments(1)	$	15,365	$	—	$	—	$	15,365
Money market funds—included in cash and cash equivalents		473		—		—		473
Commercial paper—included in investments		—		3,992		—		3,992
Corporate notes—included in investments		—		94,485		—		94,485

Total assets measured and recorded at fair value	$	15,838	$	98,477	$	—	$	114,315

Assets at June 30, 2012
Money market funds—included in cash and cash equivalents	$	40,068	$	—	$	—	$	40,068
Certificates of deposit—included in cash and cash equivalents		6,742		—		—		6,742

Total assets measured and recorded at fair value	$	46,810	$	—	$	—	$	46,810

(1): Includes $2.6 million of certificates of deposit, which were included in investments in the consolidated balance sheet at June 30, 2013.

The following tables summarize the fair value of financial instruments that are not measured on a recurring basis as of June 30, 2013 and June 30, 2012 (in thousands):

	Fair value measurement using

Type of instrument and line item in consolidated balance sheets	Quoted Prices in Active Markets for Identical Instruments (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Fair Value
At June 30, 2013
3.75% Convertible Notes—included in long term debt	$	—	$	96,560	$	—	$	96,560
3.50% Convertible Notes—included in long term debt		—		144,302		—		144,302

Total liabilities measured on a non-recurring basis	$	—	$	240,862	$	—	$	240,862

At June 30, 2012
3.75% Convertible Notes—included in long term debt	$	—	$	101,400	$	—	$	101,400

Total liabilities measured on a non-recurring basis	$	—	$	101,400	$	—	$	101,400

The Company's Level 2 investments in the table above are classified as Level 2 items because quoted prices in an active market are not readily accessible for those specific financial assets, or the Company may have relied on alternative pricing methods that do not rely exclusively on quoted prices to determine the fair value of the investments.

Long-term debt 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 observable quoted prices of the 3.75% Convertible Notes and the 3.50% Convertible Notes are not readily available.

- 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

Business Combinations

12 Months Ended

Jun. 30, 2013

Business Combinations

Business Combinations

5. Business Combinations

Fiscal 2013 Acquisition

On July 16, 2012, the Company acquired the remaining 90% of the outstanding shares of Morphormics, Inc., or Morphormics, a privately-held developer of medical imaging software based in North Carolina. This acquisition enables the Company to extend auto-contouring capabilities for both the CyberKnife and TomoTherapy systems to improve disease specific workflows. The Company previously held 10% of the outstanding shares of Morphormics, which had a carrying value of zero prior to the acquisition date and was valued at $0.7 million as of the acquisition date based on the fair value of the consideration paid. The acquisition was accounted for as a business combination, and accordingly, Morphormics' results of operations were included in the consolidated financial statements from July 16, 2012. This transaction was not considered a material business combination, and Company did not incur significant severance or acquisition-related costs in connection with the transaction.

The fair value of total purchase consideration paid and payable for 100% of Morphormics' equity interest as of the acquisition date was as follows (in thousands):


Cash paid and payable	$	5,385
Fair value of pre-existing investment in Morphormics		662

Total	$	6,047

The total purchase price was allocated to the net tangible and intangible assets acquired and liabilities assumed based on their fair values as of the acquisition date as follows (in thousands):


Cash and cash equivalents	$	668
Accounts receivable		283
Other current assets		7
Amortizable intangible assets—developed technology		5,100
Goodwill		77
Accrued compensation		(88	)

Total purchase price	$	6,047

Pro forma results of operations for the acquisition have not been presented because they are not material to the Company's consolidated statements of operations and comprehensive loss, balance sheets, or cash flows.

Fiscal 2011 Acquisition

On June 10, 2011, the Company completed the acquisition of TomoTherapy for a total purchase price of $248.0 million. TomoTherapy is a creator of advanced radiation therapy solutions for cancer care. The acquisition of TomoTherapy enables the Company to provide patients with radiation treatments tailored to their specific needs, from high-precision radiosurgery to image-guided, intensity-modulated radiation therapy. The purchase price allocation was as follows:


Net tangible assets	$	142,220
Purchased intangible assets		66,805
Goodwill		49,979
Noncontrolling interest		(10,981	)

Total purchase price	$	248,023

The Company incurred $18.5 million of acquisition-related costs in connection with the TomoTherapy acquisition, including $10.5 million of severance payments to certain employees of TomoTherapy. These costs were included in operating expenses in the consolidated statements of operations and comprehensive loss for the year ended June 30, 2011.

- 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
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+ Details

Goodwill and Purchased Intangible Assets

12 Months Ended

Jun. 30, 2013

Goodwill and Purchased Intangible Assets

Goodwill and Purchased Intangible Assets

6. Goodwill and Purchased Intangible Assets

Goodwill

Goodwill as of June 30, 2013 and 2012 and changes in the carrying amount of goodwill for the respective periods are as follows (in thousands):

	Year Ended June 30, 2013		Year Ended June 30, 2012

Balance at the beginning of the period	$	59,215	$	54,474
Addition related to acquisition		77		—
Currency translation and other adjustments		76		—
Adjustments related to prior year acquisition(1)		—		4,741

Balance at the end of the period	$	59,368	$	59,215

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

Purchased Intangible Assets

The Company's intangible assets associated with completed acquisitions are as follows:

(in thousands):

		June 30, 2013							June 30, 2012

	Useful Lives	Gross Carrying Amount		Accumulated Amortization			Net Amount		Gross Carrying Amount		Accumulated Amortization			Net Amount
	(in years)
Developed technology	5 - 6	$	46,747	$	(15,276	)	$	31,471	$	43,455	$	(9,161	)	$	34,294
Backlog	1.25		10,500		(10,500	)		—		10,500		(8,867	)		1,633
Distributor license	1.5 - 2.5		2,043		(1,618	)		425		1,860		(768	)		1,092
In-process research and development (CPAC)	Indefinite		—		—			—		12,800		—			12,800

		$	59,290	$	(27,394	)	$	31,896	$	68,615	$	(18,796	)	$	49,819

During the year ended June 30, 2013, the Company recorded an impairment charge of approximately $12.2 million related to IPR&D technology due to a decrease in projected future usage of the technology. The Company did not have an impairment of goodwill during the years ended June 30, 2013, 2012 and 2011.

Amortization expense, excluding impairment charges related to purchased intangible assets was $10.4 million, $16.2 million and $1.2 million for the years ended June 30, 2013, 2012 and 2011, respectively.

The estimated future amortization expense of purchased intangible assets as of June 30, 2013 is as follows (in thousands):

Year Ending June 30,	Amount

2014	$	8,380
2015		7,953
2016		7,953
2017		7,568
2018		42

	$	31,896

- 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

Investment in CPAC	12 Months Ended
Investment in CPAC	Jun. 30, 2013
Investment in CPAC
Investment in CPAC	7. Investment in CPAC In April 2008, TomoTherapy established a new affiliate, CPAC, to develop a compact proton therapy system for the treatment of cancer. From the formation of CPAC through December 2012, the Company and TomoTherapy contributed both cash and intellectual property to CPAC, resulting in a combined equity interest of approximately 15.4% of the outstanding stock of CPAC and approximately 16.3% on a fully diluted basis. The Company determined that CPAC was a variable interest entity or VIE, as CPAC depended on the Company, TomoTherapy and other investors to fund its operations. Under the accounting standards for consolidating variable interest entities, the consolidating investor is the entity with the power to direct the activities of the venture that most significantly impact the venture's economic performance and with the obligation to absorb losses or the right to receive benefits from the venture that could potentially be significant to the venture. Although the Company and its subsidiary held less than a 50% ownership interest in CPAC, it was determined that the Company met these two characteristics, and therefore, was the primary beneficiary of CPAC. The Company consolidated the results of operations of CPAC from June 10, 2011 (the date the Company acquired TomoTherapy) to December 21, 2012. On December 21, 2012, the Company and CPAC entered into a Purchase Agreement and Release, or Purchase Agreement, which provided for all the equity and debt investments held by the Company in CPAC to be purchased by CPAC for a nominal consideration. In addition, the Company assigned all its rights to the Dielectric Wall Accelerator, or DWA technology licensed from Lawrence Livermore National Security, LLC to CPAC. As a result of the Purchase Agreement, the Company concluded that it was no longer the primary beneficiary of CPAC since it did not have any variable interest in CPAC. In the second quarter of fiscal 2013, the Company deconsolidated CPAC and recorded a loss of $3.4 million, resulting from the write-down of the carrying value of CPAC's net liabilities, the write-off of receivables from CPAC and the non-controlling interest in CPAC, net of cash consideration received. The results of operations of CPAC, including the loss on deconsolidation of CPAC and the losses attributable to the non-controlling interest recorded for the years ended June 30, 2013, 2012 and 2011 have been presented as discontinued operations in the consolidated statements of operations and comprehensive loss. The results of operations of CPAC during the years ended June 30, 2013, 2012 and 2011 comprised of research and development expenses of $2.8 million, $5.8 million and $0.4 million, respectively, general and administrative expenses of $0.6 million, $0.9 million and $0.1 million, respectively and other expense, net of $0.1 million, $0.4 million and nil, respectively.

Commitments and Contingencies

12 Months Ended

Jun. 30, 2013

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 $8.7 million, $7.1 million and $4.8 million for the years ended June 30, 2013, 2012 and 2011, 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 13, Debt, for details.

Future minimum lease payments under non-cancelable operating lease agreements and long-term principal and interest on the Convertible Notes as of June 30, 2013 are as follows (in thousands):

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

2014	$	7,602	$	7,775
2015		6,067		7,775
2016		3,727		7,775
2017		3,735		104,338
2018		3,536		117,348
Thereafter		435		—

Total	$	25,102	$	245,011

(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 noted in the preceding table.

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, 2013.

Royalty Agreements

The Company has a license and royalty agreement with RaySearch Laboratories AB, or RaySearch, a Swedish provider of treatment planning software, which provides the Company with a non-exclusive license to use certain technology owned by RaySearch until September 2013. Under the agreement, 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 to RaySearch for the remainder of the licensing term. The Company recorded royalty costs of $0.7 million, $0.7 million and $40,000 during the years ended June 30, 2013, 2012 and 2011, respectively, which were recorded in cost of revenue or deferred cost of revenue. The Company had accrued liabilities of approximately $0.6 million at June 30, 2013 and 2012 related to this agreement. The Company does not intend to renew this license and royalty agreement.

The Company has an exclusive license agreement with the Wisconsin Alumni Research Foundation, or 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 TomoTherapy System sold that includes the licensed technology. The license agreement expires upon expiration of the patents and may be terminated earlier if the Company so elects. WARF has the right to terminate the license agreement if the Company does not meet the minimum royalty obligation of $0.3 million per year, or if the Company commits any breach of the license agreement's covenants. The Company recorded royalty costs of $0.6 million, $1.0 million and zero for the years ended June 30, 2013, 2012 and 2011, respectively, which were recorded in cost of revenue or deferred cost of revenue. The Company had accrued liabilities of approximately $0.1 million at June 30, 2013 and 2012 related to this agreement.

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 not recorded any liability associated with this indemnification, as it is not aware of any pending or threatened actions that represent probable losses as of June 30, 2013.

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 losses related to any current legal proceedings and claims that would individually or in the aggregate materially adversely affect its financial condition or operating results. For certain legal proceedings, management believes that there is a reasonable possibility that losses may be incurred. Management currently estimates a range of loss between zero and $3 million in the aggregate for such legal proceedings, where it is possible to make such estimates in excess of amounts accrued. 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 that could have a material impact on its results of operations, financial position and cash flows.

Best Medical Trade Secret Litigation

On September 3, 2009, Best Medical International, Inc., or 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. On October 25, 2011, the court presiding over the case granted summary judgment in favor of the Company on all counts. On November 21, 2011 Best Medical filed a notice of appeal. On December 22, 2011 the Court awarded attorney fees and costs to the Company and ordered the Company to file an accounting of its fees and costs. Following the filing of the accounting of the Company's fees and costs, the magistrate judge presiding over the case issued a report on the Company's accounting and recommended an award to the Company in the amount of $512,090 in attorney fees and costs. Best Medical filed objections to the report. On July 3, 2013, the Court of Appeals for the Third Circuit issued a briefing schedule for the appeal of this case. Best Medical's brief was due on August 26, 2013 with the Company's brief due 30 days thereafter. Best Medical has filed for an extension but the Court has not yet ruled on the extension request.

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. In December 2010 Best Medical amended its complaint by 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. In March 2011, the Court dismissed with prejudice all counts against the Company, except for two counts of alleged willful infringement of two of the patents. Following several procedural rulings by the court, 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 parties failed to a reach settlement during the mandatory hearings held in March and May 2013. Best Medical is seeking declaratory and injunctive relief, as well as unspecified compensatory and treble damages and other relief. The Company will continue to litigate this case, and discovery is expected to be completed by January 2014.

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 on May 19, 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. On May 21, 2012, the court granted the Company's motion for sanctions, in part, and gave Rotary Systems sixty days to identify the alleged trade secrets with specificity or face dismissal of its claim with prejudice. The court held a hearing on September 20, 2012 to review Rotary System's amended complaint and set a calendar for discovery. The court ruled on the amended complaint, and the parties have started discovery, which is expected to be completed by October 2013.

Radiation Stabilization Solutions Patent Litigation

On September 15, 2011, Radiation Stabilization Solutions LLC, or RSS 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, RSS 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. RSS also filed individual suits against each of Varian and Elekta and several of their respective customers. RSS 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. On August 21, 2012, the court granted the Company's motion in part and gave RSS leave to amend the complaint. On September 21, 2012, RSS filed an amended complaint. On November 2, 2012, the Company and RSS entered into a settlement agreement, under which the Company paid $150,000 to resolve all outstanding claims.

Accuray Securities Complaint

On November 1, 2012, a complaint was filed in Santa Clara County Superior Court purportedly on behalf of a class of shareholders seeking to enjoin the shareholder vote to be held at our annual meeting scheduled for November 30, 2012. The complaint named as defendants the Company and the members of the board of directors and alleged that the disclosures in the proxy statement for the annual meeting concerning the advisory vote on executive compensation and the proposal to amend the certificate of incorporation to increase the number of authorized shares were inadequate and constituted a breach of fiduciary duty. In addition to an injunction, the complaint sought unspecified monetary damages and other relief. The annual meeting was held on November 30, 2012. On December 28, 2012, the plaintiffs requested dismissal of the case from the court without prejudice, which was granted on January 3, 2013.

Sarif Biomedical Patent Litigation

On January 28, 2013, Sarif Biomedical filed a patent infringement complaint against the Company in the United States District Court for Delaware. The complaint alleges the Company's CyberKnife System directly infringes U.S. Patent No. 5,755,725 and seeks unspecified monetary damages for the alleged infringement. Accuray filed an answer to the complaint in March 2013.

- 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
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-URI http://asc.fasb.org/extlink&oid=6398077&loc=d3e12565-110249

Reference 3: http://www.xbrl.org/2003/role/presentationRef
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Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.25)
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

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-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
Stockholders' Equity	Jun. 30, 2013
Stockholders' Equity
Stockholders' Equity	9. Stockholders' Equity In fiscal 2012, the Company retired 2,140,018 shares of its common stock that were repurchased in prior years and accounted for as treasury stock. The Company did not have an active stock repurchase program at June 30, 2013. At June 30, 2013, the Company had 13.2 million and 21.6 million shares of common stock reserved for future issuance to the holders of the 3.75% Convertible Senior Note and the 3.50% Convertible Senior Note, respectively, and had 14.2 million shares of common stock reserved for issuance under the stock incentive plans and the employee stock purchase plan.

- Definition

The entire disclosure for shareholders' equity, comprised of portions attributable to the parent entity and noncontrolling interest, if any, including other comprehensive income (as applicable). Including, but not limited to: (1) balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings; (2) accumulated balance for each classification of other comprehensive income and total amount of comprehensive income; (3) amount and nature of changes in separate accounts, including the number of shares authorized and outstanding, number of shares issued upon exercise and conversion, and for other comprehensive income, the adjustments for reclassifications to net income; (4) rights and privileges of each class of stock authorized; (5) basis of treasury stock, if other than cost, and amounts paid and accounting treatment for treasury stock purchased significantly in excess of market; (6) dividends paid or payable per share and in the aggregate for each class of stock for each period presented; (7) dividend restrictions and accumulated preferred dividends in arrears (in aggregate and per share amount); (8) retained earnings appropriations or restrictions, such as dividend restrictions; (9) impact of change in accounting principle, initial adoption of new accounting principle and correction of an error in previously issued financial statements; (10) shares held in trust for Employee Stock Ownership Plan (ESOP); (11) deferred compensation related to issuance of capital stock; (12) note received for issuance of stock; (13) unamortized discount on shares; (14) description, terms, and number of warrants or rights outstanding; (15) shares under subscription and subscription receivables, effective date of new retained earnings after quasi-reorganization and deficit eliminated by quasi-reorganization and, for a period of at least ten years after the effective date, the point in time from which the new retained dates; and (16) retroactive effective of subsequent change in capital structure.

+ 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.(d),(e))
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Reference 8: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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Reference 10: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Preferred Stock
-URI http://asc.fasb.org/extlink&oid=6521494

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 43
-Section B
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-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 15: http://www.xbrl.org/2003/role/presentationRef
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-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 16: http://www.xbrl.org/2003/role/presentationRef
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-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 SEC
-Name Regulation S-X (SX)
-Number 210
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Reference 18: http://www.xbrl.org/2003/role/presentationRef
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-Number 210
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Reference 19: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
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Reference 20: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
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Reference 21: http://www.xbrl.org/2003/role/presentationRef
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Reference 22: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
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-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 23: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Article 3

+ Details

Stock Incentive Plan and Employee Stock Purchase Plan

12 Months Ended

Jun. 30, 2013

Stock Incentive Plan and Employee Stock Purchase Plan

Stock Incentive Plan and Employee Stock Purchase Plan

10. Stock Incentive Plan and Employee Stock Purchase Plan

As of June 30, 2013, the Company had three stock incentive plans: the 2007 Stock Incentive Plan, or the 2007 Plan; the 1998 Stock Incentive Plan, or the1998 Plan; and the 1993 Stock Incentive Plan, or the1993 Plan. The 2007 Plan permits the granting of stock options, restricted stock awards, or RSA and restricted stock units, or RSU. The vesting of RSUs under the 2007 Plan may be time-based (over the requisite service period), performance-based, or PSU or market-based, orMSU. Only employees of the Company are eligible to receive incentive stock options. Non-employees may be granted non-qualified options.

Stock options granted under the 2007 Plan have an exercise price of at least 100% of the fair market value of the underlying stock on the grant date and no less than 85% of the fair value for non-qualified stock options. The stock options have 10 year contractual terms and generally become exercisable for 25% of the option shares one year from the date of grant and then ratably over the following 36 months. Time-based RSUs generally vest 25% of the share units covered by the grant on each of the first through fourth anniversaries of the date of the grant. However, certain of the outstanding RSUs 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. The Board of Directors has the discretion to use different vesting schedules.

As of June 30, 2013, the 1998 Plan and the 1993 Plan continued to remain in effect; however, the Company can no longer make equity awards under the 1998 Plan and 1993 Plan.

In connection with the acquisition of TomoTherapy in June 2011, the Company assumed 1,539,255 outstanding stock options and 429,591 Restricted Stock Awards, or RSAs under TomoTherapy's stock plans. The stock options had exercise prices ranging from $0.48 to $44.24. As of the acquisition date, the options were fully vested and had remaining contractual terms of 0.1 to 3.4 years. The RSAs had remaining vesting terms of 1.2 years as of the acquisition date.

The Company uses the Black-Scholes option pricing model to measure the fair value of stock option grants. During the years ended June 30, 2013, 2012 and 2011, the following weighted average assumptions were used:

	Years Ended June 30,

	2013			2012			2011
Risk-free interest rate		0.87% - 1.15	%		0.85% - 1.72	%		1.88% - 2.44	%
Dividend yield		—			—			—
Expected life		6.25			6.25			6.25
Expected volatility		52.7% - 63.2	%		52.0% - 52.9	%		52.8% - 54.9	%

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

	Years ended June 30,

	2013		2012		2011
Cost of revenue	$	1,498	$	1,672	$	1,312
Selling and marketing		1,121		729		695
Research and development		1,949		2,340		2,922
General and administrative		3,648		3,717		8,436

	$	8,216	$	8,458	$	13,365

In fiscal 2011, the Company recognized $4.4 million of share-based compensation expense related to accelerated vesting of stock options, RSUs and RSAs in connection with employee separation costs. The Company did not have such expenses in the years ended June 30, 2013 and 2012. For the years ended June 30, 2013, 2012 and 2011, the Company capitalized share-based compensation costs of $0.6 million, $0.4 million and $0.3 million, respectively, as components of inventory.

Option activity during the years ended June 30, 2011, 2012 and 2013 was as follows:

			Weighted Average Exercise Price			Aggregate Intrinsic Value (in thousands)

Balance at June 30, 2010	7,809		$	6.03	5.94	$	16,651
Options granted	915		$	7.30
Options assumed	1,539		$	10.41
Options exercised	(1,397	)	$	2.58
Options forfeited/expired	(530	)	$	8.60

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

Balance at June 30, 2012	7,873		$	7.00	5.57	$	12,359
Options granted	1,250		$	6.54
Options exercised	(1,515	)	$	2.77
Options forfeited/expired	(2,764	)	$	8.86

Balance at June 30, 2013	4,844		$	7.15	6.17	$	2,771

Vested or Expected to vest at June 30, 2013	4,843		$	7.15	6.17	$	2,771

Exercisable at June 30, 2013	3,205		$	7.77	4.81	$	1,996

The aggregate intrinsic value in the table above represents the total pre-tax intrinsic value (the difference between the fair value of the Company's common stock on June 28, 2013 of $5.74 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, 2013. The total intrinsic value of options exercised in the years ended June 30, 2013, 2012, and 2011 was approximately $4.5 million, $2.9 million and $6.1 million, respectively.

During the years ended June 30, 2013, 2012 and 2011, the Company recognized $2.9 million, $3.5 million and $4.7 million, respectively, of share-based compensation expense for stock options granted to employees. The weighted average fair value of options granted was $3.48, $2.30 and $3.91 per share for the years ended June 30, 2013, 2012 and 2011, 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 related to stock options exercises was zero for each of the years ended June 30, 2013, 2012 and 2011.

As of June 30, 2013, there was approximately $4.9 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 2.84 years.

The following table summarizes the activity of RSUs, PSUs and MSU during the years ended June 30, 2011, 2012 and 2013:

			Weighted Average Grant Date Fair Value Per Share

Balance at June 30, 2010	464		$	12.52
Granted	475		$	6.77
Vested	(202	)	$	7.57
Cancelled/Forfeited	(79	)	$	9.85

Balance at June 30, 2011	658		$	6.97
Granted	2,001		$	4.53
Vested	(302	)	$	4.47
Cancelled/Forfeited	(259	)	$	5.67

Balance at June 30, 2012	2,098		$	5.16
Granted	2,662		$	5.52
Vested	(544	)	$	5.18
Cancelled/Forfeited	(829	)	$	5.18

Balance at June 30, 2013	3,387		$	5.66

Restricted Stock Units

The Company recognized $3.6 million, $2.5 million and $2.9 million of share-based compensation expense, net of estimated forfeitures, related to RSUs during the years ended June 30, 2013, 2012 and 2011. The weighted average grant date fair value per share of RSUs was $5.89, $4.80 and $6.77 for the years ended June 30, 2013, 2012 and 2011, respectively. As of June 30, 2013, there was approximately $11.1 million of unrecognized compensation cost, net of estimated forfeitures, related to RSUs, which is expected to be recognized over a weighted average period of 2.08 years. The aggregate fair market value of RSUs that vested during the year ended June 30, 2013 was $3.5 million.

The Company recognized $0.3 million, $1.4 million and $5.0 million of share-based compensation expense during the years ended June 30, 2013 and 2012 and 2011 respectively, related to RSAs assumed in connection with the acquisition of TomoTherapy. As of June 30, 2013, unrecognized compensation cost related to RSAs was immaterial.

Performance-Based Awards

During fiscal 2012, the Compensation Committee approved the grant of 1.0 million PSUs to certain employees of the Company. The PSUs had a grant date fair value of $3.9 million and would vest 100% if the Company met certain financial performance targets during the performance period, commencing on the first day of the Company's 2012 fiscal year (July, 1 2011) and ending on the last day of the Company's 2013 fiscal year. As of June 30, 2013, the last day of the performance period, it was determined that the Company did not achieve the requisite performance targets. The Company did not recognize any associated stock-based compensation expense during the years ended June 30, 2013 and 2012.

Market Stock Units

In October 2012, the Compensation Committee approved a new performance equity program, referred to as the market stock unit program, or MSU Program. The MSU Program uses the Russell 2000 index as a performance benchmark and requires that the Company's total stockholder return exceeds that of the Russell 2000. Based on a sliding scale of by how much the Company's total stockholder return outperforms the Russell 2000 benchmark, the participating executives can earn up to a maximum of 150% of the target number of shares over two measurement periods (at June 30, 2014 and June 30, 2015). The MSUs were valued at approximately $1.5 million based on a Monte-Carlo simulation on the grant date and the related stock-based compensation expense is being recognized over a weighted average period of 1.8 years. During the year ended June 30, 2013, the Company granted approximately 0.5 million MSUs, at a weighted average grant date fair value per share of $5.39. The Company recognized $0.3 million of share-based compensation expense, net of estimated forfeitures, related to MSUs during the year ended June 30, 2013. As of June 30, 2013, there was approximately $1.0 million of unrecognized compensation cost, net of estimated forfeitures, related to MSUs, which is expected to be recognized over a weighted average period of 1.6 years.

Employee Stock Purchase Plan

Under the Company's 2007 Employee Stock Purchase Plan, or 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 Company estimates the fair value of ESPP shares at the date of grant using the Black-Scholes option pricing model. The weighted average assumptions were as follows:

	Years Ended June 30,

	2013			2012			2011
Risk-free interest rate		0.07% - 0.14	%		0.05% - 0.12	%		0.11% - 0.23	%
Dividend yield		—			—			—
Expected life		0.50			0.50			0.50
Expected volatility		40.3% - 53.7	%		33.6% - 50.6	%		33.6% - 56.7	%

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; expected volatility was based on the historical volatility of the Company's common stock; and the expected term of six months was based upon the offering period of the ESPP. For the years ended June 30, 2013, 2012 and 2011, the Company recognized $1.3 million, $1.1 million and $0.8 million, respectively, of compensation expense related to its ESPP.

The weighted average fair value of ESPP options was $2.06, $1.80 and $2.03 per share for the years ended June 30, 2013, 2012 and 2011, respectively. As of June 30, 2013, 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.

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 50
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6406099&loc=d3e25284-112666

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 40
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6418621&loc=d3e17540-113929

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5070-113901

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5047-113901

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5444-113901

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 14

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 123R
-Paragraph 64, 65, A240
-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 Statement of Position (SOP)
-Number 93-6
-Paragraph 53
-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

Income Taxes

12 Months Ended

Jun. 30, 2013

Income Taxes

Income Taxes

11. Income Taxes

Loss before provision for income taxes on the accompanying statements of operations and comprehensive loss included the following components (in thousands):

	Years Ended June 30,

	2013			2012			2011
Domestic	$	(103,964	)	$	(75,391	)	$	(28,167	)
Foreign		10,176			6,636			2,626

Total worldwide	$	(93,788	)	$	(68,755	)	$	(25,541	)

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

	Years Ended June 30,

	2013			2012			2011
Current:
Federal	$	—		$	—		$	—
State		(21	)		(7	)		114
Foreign		2,647			2,107			939

Total current		2,626			2,100			1,053
Deferred:
Federal		—			—			—
State		—			—			—
Foreign		947			495			63

Total deferred		947			495			63

Total provision for income taxes	$	3,573		$	2,595		$	1,116

Income tax payable was $1.2 million and $1.1 million at June 30, 2013 and 2012 respectively. A reconciliation of income taxes at the statutory federal income tax rate to the provision for income taxes included in the accompanying consolidated statements of operations and comprehensive loss is as follows (in thousands):

	Years Ended June 30,

	2013			2012			2011
U.S. federal taxes (benefit):
At federal statutory rate	$	(32,826	)	$	(24,064	)	$	(8,939	)
State tax, net of federal benefit		(21	)		(7	)		114
Stock-based compensation expense		4,061			3,645			33
Change in valuation allowance		33,454			24,796			8,883
Credits		(1,272	)		(846	)		(1,373	)
Meals and entertainment		246			335			214
Acquisition costs		—			89			2,451
Other		(177	)		(1,669	)		(273	)
Foreign taxes		108			316			6

Total	$	3,573		$	2,595		$	1,116

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 are as follows (in thousands):

	June 30,

	2013			2012
Deferred tax assets:
Federal and state net operating losses	$	105,110		$	80,834
Accrued vacation and bonus		1,503			1,973
Deferred revenue		1,913			1,125
Deferred rent		710			1,165
Credits		16,636			13,985
Share-based compensation expense		10,691			13,103
Reserves not deductible for tax purposes		(76	)		4,085
Unicap		1,540			1,347
Other		623			689

Total deferred tax assets		138,650			118,306
Deferred tax liabilities:
Fixed assets/intangibles		(11,740	)		(15,198	)
Foreign currency differences		(1,697	)		(594	)

Total deferred tax liabilities		(13,437	)		(15,792	)
Valuation allowance		(124,781	)		(102,142	)

Net deferred tax assets	$	432		$	372

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, 2013 was $9.8 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, 2013 the Company had approximately $288.1 million and $114.5 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 $3.4 million as a credit to additional paid-in capital as and when such excess benefits are ultimately realized.

In addition, as of June 30, 2013, the Company had federal and state research and development tax credits of approximately $9.8 million and $6.8 million, respectively. The federal research credits will begin to expire in 2019, the California research credits have no expiration date, and the other state research credits will begin to expire in 2014.

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 the combined domestic net deferred tax assets of Accuray and TomoTherapy due to uncertainty surrounding the realization of such deferred tax assets.

The aggregate changes in the balance of gross unrecognized tax benefits were as follows (in thousands):

	Years Ended June 30,

	2013			2012			2011
Balance at beginning of year	$	15,147		$	14,158		$	3,669
Tax positions related to current year:
Additions		1,781			1,129			10,468
Tax positions related to prior years:
Additions		564			40			58
Reductions		(743	)		(180	)		(37	)

Balance at end of year	$	16,749		$	15,147		$	14,158

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 reduction in prior years tax positions primarily relates to lapses of applicable statutes of limitations. 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, 2013, the amount of gross unrecognized tax benefits was $16.7 million of which $3.6 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, 2013 and 2012, respectively, the Company had approximately $0.7 million and $0.6 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 material foreign jurisdictions are France, Switzerland, and Japan, whose tax years remain open from 2011, 2006, and 2006, respectively.

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 state tax returns for New York and Tennessee. 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

+ Details

Other Income (Expense), Net

12 Months Ended

Jun. 30, 2013

Other Income (Expense), Net

Other Income (Expense), Net

12. Other Income (Expense), Net

Other income (expense), net consisted of the following (in thousands):

	Years Ended June 30,

	2013			2012			2011
Interest expense on convertible notes	$	(10,378	)	$	(7,397	)	$	—
Foreign currrency transaction gain (loss)		(2,503	)		(4,386	)		2,193
Other		(252	)		(738	)		95

Total other income (expense), net	$	(13,133	)	$	(12,521	)	$	2,288

Debt

12 Months Ended

Jun. 30, 2013

Debt

Debt

13. Debt

3.75% Convertible Senior Notes due August 2016

On August 1, 2011, the Company issued the 3.75% Convertible Notes to certain qualified institutional buyers or QIBs. The 3.75% Convertible Notes were offered and sold to the QIBs pursuant to Rule 144A under the Securities Act of 1933, as amended or Rule 144A. The net proceeds from the $100 million 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 3.75% 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 3.75% Convertible Notes will mature on August 1, 2016, unless earlier repurchased, redeemed or converted.

The 3.75% 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 3.75% Convertible Notes may convert their 3.75% 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 3.75% Convertible Notes may convert their 3.75% 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 3.75% 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 3.75% 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 3.75% 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 3.75% 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 3.75% Convertible Notes being converted. The initial conversion rate is 105.5548 shares of the Company's common stock per $1,000 principal amount of 3.75% 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, are subject to adjustment as further described below.

Holders of the 3.75% Convertible Notes who convert their 3.75% 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 3.75% Convertible Notes may require the Company to purchase all or a portion of their 3.75% Convertible Notes at a fundamental change repurchase price equal to 100% of the principal amount of 3.75% 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 3.75% 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 3.75% 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 Accounting Standards Codification, or ASC 470-20, Debt with Conversion and Other Options, the Company separately accounts for the liability and equity conversion components of the 3.75% Convertible Notes. The principal amount of the liability component of the 3.75% Convertible Notes was $75.9 million as of the 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 is being accreted to the principal amount of the 3.75% Convertible Notes using the effective interest method over five years.

The following table presents the carrying value of the 3.75% Convertible Notes as of June 30, 2013 (in thousands):


Carrying amount of the equity conversion component	$	23,189

Principal amount of the Convertible Notes	$	100,000
Unamortized debt discount(1)		(16,232	)

Net carrying amount	$	83,768

(1): As of June 30, 2013, the remaining period over which the unamortized debt discount will be amortized is 37 months using an effective interest rate of 10.9%.

3.50% Convertible Senior Notes due February 2018

In February 2013, the Company issued $115.0 million aggregate principal amount of its 3.50% Convertible Notes to certain QIBs. The 3.50% Convertible Notes were offered and sold to the QIBs pursuant to Rule 144A. The net proceeds from the offering, after deducting the initial purchaser's discount and commission and the related offering costs, were approximately $110.5 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 3.50% Convertible Notes bear interest at a rate of 3.50% per year, payable semi-annually in arrears in cash on February 1 and August 1 of each year, beginning on August 1, 2013. The 3.50% Convertible Notes will mature on February 1, 2018, unless earlier repurchased, redeemed or converted.

The 3.50% 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 3.50% Convertible Notes may convert their 3.50% Convertible Notes at any time until the close of business on the business day immediately preceding the maturity date. The 3.50% Convertible Notes are convertible, as described below into common stock of Accuray at an initial conversion rate equal to 187.6877 shares of common stock per $1,000 principal amount of the 3.50% Convertible Notes, which is equivalent to a conversion price of approximately $5.33 per share of common stock, subject to adjustment.

Holders of the 3.50% Convertible Notes who convert their 3.50% 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 3.50% Convertible Notes may require the Company to purchase all or a portion of their 3.50% Convertible Notes at a fundamental change repurchase price equal to 100% of the principal amount of 3.50% Convertible Notes, plus accrued and unpaid interest, if any, to, but not including, the fundamental change repurchase date.

In accordance with guidance in ASC 470-20, Debt with Conversion and Other Options and ASC 815-15, Embedded Derivatives, the Company determined that the embedded conversion components of the 3.50% Convertible Note do not require bifurcation and separate accounting. The $115.0 million principal amount of the 3.50% Convertible Note has been recorded in Long-term Debt on the consolidated balance sheet as of June 30, 2013.

A summary of interest expense on the 3.75% Convertible Note and the 3.50% Convertible Note is as follows (in thousands):

	Year ended June 30,

	2013		2012
Interest expense related to contractual interest coupon	$	5,292	$	3,438
Interest expense related to amortization of debt discount		4,302		3,596
Interest expense related to amortization of debt issuance costs		784		363

	$	10,378	$	7,397

The remaining debt discount will be amortized over 37 months as of June 30, 2013. The Company did not have debt at June 30, 2011.

- 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
Employee Benefit Plans	Jun. 30, 2013
Employee Benefit Plans
Employee Benefit Plans	14. 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 $2.3 million, $2.2 million and $0.7 million to the 401(k) Plan during the years ended June 30, 2013, 2012 and 2011, 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
Restructuring Charges	Jun. 30, 2013
Restructuring Charges
Restructuring Charges	15. Restructuring Charges Fiscal 2013 Restructuring During fiscal 2013, the Company initiated a number of restructuring activities to address various areas of its business, including changes in the executive management team and increased focus on improving its commercial execution, revenue growth and profitability. In the year ended June 30, 2013, the Company recorded restructuring charges of $9.1 million, included in general and administrative expenses in the consolidated statements of operations and comprehensive loss. Restructuring expenses during the year ended June 30, 2013 were comprised of the following: • Lease termination charge of $1.4 million, net of estimated sub-lease income, for the remaining lease obligations on an office facility that the Company vacated, and a charge of $0.3 million related to the disposition of certain fixed assets and the write-down of leasehold improvements at this office facility. • Severance-related charges of $7.4 million primarily related to the terminations of the Company's former Chief Executive Officer and Chief Operating Officer and a 13% reduction in its worldwide headcount. As of June 30, 2013, the Company had approximately $1.0 million of accrued liabilities related to the lease termination, which it will continue to pay through June 2014. Also, at June 30, 2013, the Company had approximately $1.0 million of other accrued restructuring expenses, primarily comprised of severance-related expenses, which it expects to fully pay in the first two quarters of fiscal 2014. Fiscal 2012 Restructuring In fiscal 2012, the Company initiated a restructuring plan to reposition its workforce to appropriately support its growth strategy and to help achieve cost synergies associated with its acquisition of TomoTherapy. In connection with this restructuring plan, the Company eliminated approximately 51 full-time positions worldwide, across various functions, and recorded an associated restructuring charge of approximately $1.7 million, primarily comprised of severance and related benefits. For the year ended June 30, 2012, the Company recorded total restructuring charges of $1.9 million, including the $1.7 million of restructuring expenses discussed above. Fiscal 2011 Restructuring The Company had no restructuring activities during the year ended June 30, 2011.

- 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, 2013

Quarterly Financial Data (unaudited)

Quarterly Financial Data (unaudited)

16. Quarterly Financial Data (unaudited)

The following table provides the selected quarterly financial data for fiscal 2013 and 2012 (in thousands, except per share amounts):

	Quarters ended

	September 30, 2012			December 31, 2012			March 31, 2013			June 30, 2013
Net revenue	$	82,748		$	77,779		$	70,547		$	84,900
Gross profit	$	23,676		$	26,626		$	20,053		$	27,285
Loss from continuing operations	$	(21,930	)	$	(25,513	)	$	(31,203	)	$	(18,715	)
Loss from discontinued operations	$	(2,200	)	$	(3,658	)	$	—		$	—
Net loss	$	(24,130	)	$	(29,171	)	$	(31,203	)	$	(18,715	)
Basic and diluted—continuing operations	$	(0.31	)	$	(0.35	)	$	(0.42	)	$	(0.25	)
Basic and diluted—discontinued operations	$	(0.03	)	$	(0.05	)	$	—		$	—
Basic and diluted—net loss	$	(0.34	)	$	(0.40	)	$	(0.42	)	$	(0.25	)
Shares used in basic per share calculation		71,995			72,870			74,016			74,270
Shares used in diluted per share calculation		71,995			72,870			74,016			74,270

	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
Loss from continuing operations	$	(26,269	)	$	(10,283	)	$	(14,785	)	$	(20,013	)
Loss from discontinued operations	$	(241	)	$	(104	)	$	(96	)	$	(251	)
Net loss	$	(26,510	)	$	(10,387	)	$	(14,881	)	$	(20,264	)
Basic and diluted—continuing operations	$	(0.38	)	$	(0.15	)	$	(0.21	)	$	(0.28	)
Basic and diluted—discontinued operations	$	(0.00	)	$	(0.00	)	$	(0.00	)	$	(0.00	)
Basic and diluted—net loss	$	(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

- 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

SCHEDULE II Valuation and Qualifying Accounts

12 Months Ended

Jun. 30, 2013

SCHEDULE II Valuation and Qualifying Accounts

SCHEDULE II Valuation and Qualifying Accounts

SCHEDULE II
Valuation and Qualifying Accounts
(in thousands)

	Beginning Balance		Additions (Deductions)		Write-offs			Ending Balance

Accounts receivable allowances
Year ended June 30, 2011	$	115	$	239	$	(30	)	$	324
Year ended June 30, 2012	$	324	$	1,392	$	(16	)	$	1,700
Year ended June 30, 2013	$	1,700	$	787	$	(327	)	$	2,160

	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
Year ended June 30, 2013	$	748	$	—	$	57	$	(775	)	$	30

Summary of Significant Accounting Policies (Policies)

12 Months Ended

Jun. 30, 2013

Summary of Significant Accounting Policies

Basis of Presentation and Principles of Consolidation

Basis of Presentation and Principles of Consolidation

Reclassification

Reclassification

Use of Estimates

Use of Estimates

Foreign Currency

Foreign Currency

Fair Value Measurements

Fair Value Measurements

Cash and Cash Equivalents

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.

Investments

Investments

Concentration of Credit Risk and Other Risks and Uncertainties

Concentration of Credit Risk and Other Risks and Uncertainties

Restricted Cash

Restricted Cash

Inventories

Inventories

Revenue Recognition

Revenue Recognition

Product Revenue

Service Revenue

Shared ownership program

Other revenue

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

Long-term construction and manufacturing contracts

Deferred Revenue and Deferred Cost of Revenue

Deferred Revenue and Deferred Cost of Revenue

Customer Advances

Customer Advances

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

Property and Equipment

Property and Equipment

Software Capitalization Costs

Software Capitalization Costs

Impairment of Long-Lived Assets

Impairment of Long-Lived Assets

Business Combinations

Business Combinations

Goodwill and Purchased Intangible Assets

Goodwill and Purchased Intangible Assets

Acquisition-related expenses and restructuring costs are recognized separately from the business combination and are expensed as incurred.

Shipping and Handling

Shipping and Handling

Advertising Expenses

Advertising Expenses

Research and Development Costs

Research and Development Costs

Share-Based Compensation

Share-Based Compensation

The Company uses the Monte-Carlo simulation model to estimate the fair value of MSUs and recognizes the related expense over the requisite service period.

Loss Contingencies

Loss Contingencies

Corporate Bonus Expense and Accruals

Corporate Bonus Expense and Accruals

Net Loss Per Common Share

Net Loss Per Common Share

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

	Years ended June 30,

	2013			2012			2011
Numerator:
Loss from operations used in computing loss per share from continuing operations	$	(97,361	)	$	(71,350	)	$	(26,657	)

Loss from discontinued operations used in computing loss per share from discontinued operations		(5,858	)		(692	)		(25	)

Net loss used in computing net loss per share	$	(103,219	)	$	(72,042	)	$	(26,682	)

Denominator:
Weighted average shares used in computing basic net loss per share		73,281			70,887			60,085
Add: Dilutive stock options and awards outstanding		—			—			—

Weighted average shares used in computing diluted net loss per share		73,281			70,887			60,085

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,

	2013		2012		2011
Stock options		4,844		7,873		8,337
RSUs, PSUs and MSUs		3,387		2,097		658
3.50% Convertible Notes		21,576		—		—
3.75% Convertible Notes		10,560		10,560

		40,367		20,530		8,995

Income Taxes

Income Taxes

Comprehensive Loss

Comprehensive Loss

Segment Information

Segment Information

	Years ended June 30,

	2013		2012		2011
Americas (including Puerto Rico)	$	143,613	$	189,072	$	122,636
Europe, Middle East, India and Africa		101,172		110,331		67,244
Asia (excluding Japan)		37,829		64,026		16,158
Japan		33,360		45,794		16,246

Total	$	315,974	$	409,223	$	222,284

Recent Accounting Pronouncements

Recent Accounting Pronouncements

Summary of Significant Accounting Policies (Tables)

12 Months Ended

Jun. 30, 2013

Summary of Significant Accounting Policies

Schedule of reconciliation of the numerator and denominator used in the calculation of basic and diluted loss per share

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

	Years ended June 30,

	2013			2012			2011
Numerator:
Loss from operations used in computing loss per share from continuing operations	$	(97,361	)	$	(71,350	)	$	(26,657	)

Loss from discontinued operations used in computing loss per share from discontinued operations		(5,858	)		(692	)		(25	)

Net loss used in computing net loss per share	$	(103,219	)	$	(72,042	)	$	(26,682	)

Denominator:
Weighted average shares used in computing basic net loss per share		73,281			70,887			60,085
Add: Dilutive stock options and awards outstanding		—			—			—

Weighted average shares used in computing diluted net loss per share		73,281			70,887			60,085

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

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,

	2013		2012		2011
Stock options		4,844		7,873		8,337
RSUs, PSUs and MSUs		3,387		2,097		658
3.50% Convertible Notes		21,576		—		—
3.75% Convertible Notes		10,560		10,560

		40,367		20,530		8,995

Schedule of revenue by geographic region

The following summarizes revenue by geographic region (in thousands):

	Years ended June 30,

	2013		2012		2011
Americas (including Puerto Rico)	$	143,613	$	189,072	$	122,636
Europe, Middle East, India and Africa		101,172		110,331		67,244
Asia (excluding Japan)		37,829		64,026		16,158
Japan		33,360		45,794		16,246

Total	$	315,974	$	409,223	$	222,284

Balance Sheet Components (Tables)

12 Months Ended

Jun. 30, 2013

Balance Sheet Components

Summary of cash and cash equivalents

The following is a summary of cash and cash equivalents (in thousands):

	June 30, 2013		June 30, 2012

Cash	$	60,082	$	96,694
Certificates of deposit		12,758		6,742
Money market funds		473		40,068

	$	73,313	$	143,504

Summary of investments

The following is a summary of investments (in thousands):

	June 30, 2013

	Amortized Cost		Gross Unrealized Loss			Fair Value
Certificates of deposit	$	2,607	$	—		$	2,607
Commercial paper		3,993		(1	)		3,992
Corporate notes		94,941		(456	)		94,485

	$	101,541	$	(457	)	$	101,084

Summary of the estimated fair value of investments in marketable securities designated as available-for-sale classified by the contractual maturity date of the security

	June 30, 2013

	Amortized Cost		Fair Value
Due in 1 year or less	$	40,235	$	40,188
Due in 1 - 2 years		35,428		35,256
Due in 2 - 3 years		25,878		25,640

	$	101,541	$	101,084

Schedule of accounts receivable, net

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

	June 30,

	2013			2012
Accounts receivable	$	56,830		$	69,285
Unbilled fees and services		788			305

		57,618			69,590
Less: Allowance for doubtful accounts		(2,160	)		(1,700	)

Accounts receivable, net	$	55,458		$	67,890

Schedule of inventories

Inventories consisted of the following (in thousands):

	June 30,

	2013		2012
Raw materials	$	33,721	$	42,951
Work-in-process		20,564		16,932
Finished goods		27,307		21,810

Inventories	$	81,592	$	81,693

Schedule of property and equipment, net

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

	June 30,

	2013			2012
Furniture and fixtures	$	6,506		$	5,921
Computer and office equipment		9,481			9,126
Software		9,586			9,429
Leasehold improvements		19,199			16,065
Machinery and equipment		37,371			33,493
Shared ownership systems		4,979			4,979
Construction in progress		3,084			3,787

		90,206			82,800
Less: Accumulated depreciation and amortization		(55,473	)		(45,342	)

Property and equipment, net	$	34,733		$	37,458

Financial Instruments (Tables)

12 Months Ended

Jun. 30, 2013

Financial Instruments

Schedule of fair value of financial instruments measured on a recurring basis

The following tables summarize the fair value of financial instruments measured on a recurring basis as of June 30, 2013 and June 30, 2012 (in thousands):

	Fair value measurement using

Type of instrument and line item in consolidated balance sheets	Quoted Prices in Active Markets for Identical Instruments (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Fair Value
Assets at June 30, 2013
Certificates of deposit—included in cash and cash equivalents and investments(1)	$	15,365	$	—	$	—	$	15,365
Money market funds—included in cash and cash equivalents		473		—		—		473
Commercial paper—included in investments		—		3,992		—		3,992
Corporate notes—included in investments		—		94,485		—		94,485

Total assets measured and recorded at fair value	$	15,838	$	98,477	$	—	$	114,315

Assets at June 30, 2012
Money market funds—included in cash and cash equivalents	$	40,068	$	—	$	—	$	40,068
Certificates of deposit—included in cash and cash equivalents		6,742		—		—		6,742

Total assets measured and recorded at fair value	$	46,810	$	—	$	—	$	46,810

(1): Includes $2.6 million of certificates of deposit, which were included in investments in the consolidated balance sheet at June 30, 2013.

Schedule of fair value of financial instruments that are not measured on a recurring basis

The following tables summarize the fair value of financial instruments that are not measured on a recurring basis as of June 30, 2013 and June 30, 2012 (in thousands):

	Fair value measurement using

Type of instrument and line item in consolidated balance sheets	Quoted Prices in Active Markets for Identical Instruments (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Fair Value
At June 30, 2013
3.75% Convertible Notes—included in long term debt	$	—	$	96,560	$	—	$	96,560
3.50% Convertible Notes—included in long term debt		—		144,302		—		144,302

Total liabilities measured on a non-recurring basis	$	—	$	240,862	$	—	$	240,862

At June 30, 2012
3.75% Convertible Notes—included in long term debt	$	—	$	101,400	$	—	$	101,400

Total liabilities measured on a non-recurring basis	$	—	$	101,400	$	—	$	101,400

- Definition

Tabular disclosure of assets, including [financial] instruments measured at fair value that are classified in stockholders' equity, if any, by class that are measured at fair value on a recurring basis. The disclosures contemplated herein include the fair value measurements at the reporting date by the level within the fair value hierarchy in which the fair value measurements in their entirety fall, segregating fair value measurements using quoted prices in active markets for identical assets (Level 1), significant other observable inputs (Level 2), and significant unobservable inputs (Level 3).

+ References + Details

Business Combinations (Tables)

12 Months Ended

Jun. 30, 2013

Acquisition

Schedule of components of purchase price

The total purchase price was allocated to the net tangible and intangible assets acquired and liabilities assumed based on their fair values as of the acquisition date as follows (in thousands):


Cash and cash equivalents	$	668
Accounts receivable		283
Other current assets		7
Amortizable intangible assets—developed technology		5,100
Goodwill		77
Accrued compensation		(88	)

Total purchase price	$	6,047

Morphormics

Acquisition

Schedule of purchase price allocation

The fair value of total purchase consideration paid and payable for 100% of Morphormics' equity interest as of the acquisition date was as follows (in thousands):


Cash paid and payable	$	5,385
Fair value of pre-existing investment in Morphormics		662

Total	$	6,047

TomoTherapy

Acquisition

Schedule of purchase price allocation


Net tangible assets	$	142,220
Purchased intangible assets		66,805
Goodwill		49,979
Noncontrolling interest		(10,981	)

Total purchase price	$	248,023

Goodwill and Purchased Intangible Assets (Tables)

12 Months Ended

Jun. 30, 2013

Goodwill and Purchased Intangible Assets

Schedule of goodwill

Goodwill as of June 30, 2013 and 2012 and changes in the carrying amount of goodwill for the respective periods are as follows (in thousands):

	Year Ended June 30, 2013		Year Ended June 30, 2012

Balance at the beginning of the period	$	59,215	$	54,474
Addition related to acquisition		77		—
Currency translation and other adjustments		76		—
Adjustments related to prior year acquisition(1)		—		4,741

Balance at the end of the period	$	59,368	$	59,215

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

Schedule of intangible assets associated with completed acquisitions

The Company's intangible assets associated with completed acquisitions are as follows:

(in thousands):

		June 30, 2013							June 30, 2012

	Useful Lives	Gross Carrying Amount		Accumulated Amortization			Net Amount		Gross Carrying Amount		Accumulated Amortization			Net Amount
	(in years)
Developed technology	5 - 6	$	46,747	$	(15,276	)	$	31,471	$	43,455	$	(9,161	)	$	34,294
Backlog	1.25		10,500		(10,500	)		—		10,500		(8,867	)		1,633
Distributor license	1.5 - 2.5		2,043		(1,618	)		425		1,860		(768	)		1,092
In-process research and development (CPAC)	Indefinite		—		—			—		12,800		—			12,800

		$	59,290	$	(27,394	)	$	31,896	$	68,615	$	(18,796	)	$	49,819

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

The estimated future amortization expense of purchased intangible assets as of June 30, 2013 is as follows (in thousands):

Year Ending June 30,	Amount

2014	$	8,380
2015		7,953
2016		7,953
2017		7,568
2018		42

	$	31,896

- 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, 2013

Commitments and Contingencies

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

Future minimum lease payments under non-cancelable operating lease agreements and long-term principal and interest on the Convertible Notes as of June 30, 2013 are as follows (in thousands):

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

2014	$	7,602	$	7,775
2015		6,067		7,775
2016		3,727		7,775
2017		3,735		104,338
2018		3,536		117,348
Thereafter		435		—

Total	$	25,102	$	245,011

(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 noted in the preceding table.

Stock Incentive Plan and Employee Stock Purchase Plan (Tables)

12 Months Ended

Jun. 30, 2013

Stock Incentive Plan and Employee Stock Purchase Plan

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

	Years Ended June 30,

	2013			2012			2011
Risk-free interest rate		0.87% - 1.15	%		0.85% - 1.72	%		1.88% - 2.44	%
Dividend yield		—			—			—
Expected life		6.25			6.25			6.25
Expected volatility		52.7% - 63.2	%		52.0% - 52.9	%		52.8% - 54.9	%

Summary of share-based compensation charges

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

	Years ended June 30,

	2013		2012		2011
Cost of revenue	$	1,498	$	1,672	$	1,312
Selling and marketing		1,121		729		695
Research and development		1,949		2,340		2,922
General and administrative		3,648		3,717		8,436

	$	8,216	$	8,458	$	13,365

Schedule of option activity

			Weighted Average Exercise Price			Aggregate Intrinsic Value (in thousands)

Balance at June 30, 2010	7,809		$	6.03	5.94	$	16,651
Options granted	915		$	7.30
Options assumed	1,539		$	10.41
Options exercised	(1,397	)	$	2.58
Options forfeited/expired	(530	)	$	8.60

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

Balance at June 30, 2012	7,873		$	7.00	5.57	$	12,359
Options granted	1,250		$	6.54
Options exercised	(1,515	)	$	2.77
Options forfeited/expired	(2,764	)	$	8.86

Balance at June 30, 2013	4,844		$	7.15	6.17	$	2,771

Vested or Expected to vest at June 30, 2013	4,843		$	7.15	6.17	$	2,771

Exercisable at June 30, 2013	3,205		$	7.77	4.81	$	1,996

Schedule of activity of RSUs, PSUs and MSUs

			Weighted Average Grant Date Fair Value Per Share

Balance at June 30, 2010	464		$	12.52
Granted	475		$	6.77
Vested	(202	)	$	7.57
Cancelled/Forfeited	(79	)	$	9.85

Balance at June 30, 2011	658		$	6.97
Granted	2,001		$	4.53
Vested	(302	)	$	4.47
Cancelled/Forfeited	(259	)	$	5.67

Balance at June 30, 2012	2,098		$	5.16
Granted	2,662		$	5.52
Vested	(544	)	$	5.18
Cancelled/Forfeited	(829	)	$	5.18

Balance at June 30, 2013	3,387		$	5.66

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

	Years Ended June 30,

	2013			2012			2011
Risk-free interest rate		0.07% - 0.14	%		0.05% - 0.12	%		0.11% - 0.23	%
Dividend yield		—			—			—
Expected life		0.50			0.50			0.50
Expected volatility		40.3% - 53.7	%		33.6% - 50.6	%		33.6% - 56.7	%

- 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, 2013

Income Taxes

Schedule of components of loss before provision for income taxes on the accompanying statements of operations and comprehensive loss

Loss before provision for income taxes on the accompanying statements of operations and comprehensive loss included the following components (in thousands):

	Years Ended June 30,

	2013			2012			2011
Domestic	$	(103,964	)	$	(75,391	)	$	(28,167	)
Foreign		10,176			6,636			2,626

Total worldwide	$	(93,788	)	$	(68,755	)	$	(25,541	)

Schedule of provision for income taxes

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

	Years Ended June 30,

	2013			2012			2011
Current:
Federal	$	—		$	—		$	—
State		(21	)		(7	)		114
Foreign		2,647			2,107			939

Total current		2,626			2,100			1,053
Deferred:
Federal		—			—			—
State		—			—			—
Foreign		947			495			63

Total deferred		947			495			63

Total provision for income taxes	$	3,573		$	2,595		$	1,116

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

A reconciliation of income taxes at the statutory federal income tax rate to the provision for income taxes included in the accompanying consolidated statements of operations and comprehensive loss is as follows (in thousands):

	Years Ended June 30,

	2013			2012			2011
U.S. federal taxes (benefit):
At federal statutory rate	$	(32,826	)	$	(24,064	)	$	(8,939	)
State tax, net of federal benefit		(21	)		(7	)		114
Stock-based compensation expense		4,061			3,645			33
Change in valuation allowance		33,454			24,796			8,883
Credits		(1,272	)		(846	)		(1,373	)
Meals and entertainment		246			335			214
Acquisition costs		—			89			2,451
Other		(177	)		(1,669	)		(273	)
Foreign taxes		108			316			6

Total	$	3,573		$	2,595		$	1,116

Schedule of significant components of deferred tax assets

Significant components of the Company's net deferred tax assets are as follows (in thousands):

	June 30,

	2013			2012
Deferred tax assets:
Federal and state net operating losses	$	105,110		$	80,834
Accrued vacation and bonus		1,503			1,973
Deferred revenue		1,913			1,125
Deferred rent		710			1,165
Credits		16,636			13,985
Share-based compensation expense		10,691			13,103
Reserves not deductible for tax purposes		(76	)		4,085
Unicap		1,540			1,347
Other		623			689

Total deferred tax assets		138,650			118,306
Deferred tax liabilities:
Fixed assets/intangibles		(11,740	)		(15,198	)
Foreign currency differences		(1,697	)		(594	)

Total deferred tax liabilities		(13,437	)		(15,792	)
Valuation allowance		(124,781	)		(102,142	)

Net deferred tax assets	$	432		$	372

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

The aggregate changes in the balance of gross unrecognized tax benefits were as follows (in thousands):

	Years Ended June 30,

	2013			2012			2011
Balance at beginning of year	$	15,147		$	14,158		$	3,669
Tax positions related to current year:
Additions		1,781			1,129			10,468
Tax positions related to prior years:
Additions		564			40			58
Reductions		(743	)		(180	)		(37	)

Balance at end of year	$	16,749		$	15,147		$	14,158

Other Income (Expense), Net (Tables)

12 Months Ended

Jun. 30, 2013

Other Income (Expense), Net

Schedule of other income (expense), net

Other income (expense), net consisted of the following (in thousands):

	Years Ended June 30,

	2013			2012			2011
Interest expense on convertible notes	$	(10,378	)	$	(7,397	)	$	—
Foreign currrency transaction gain (loss)		(2,503	)		(4,386	)		2,193
Other		(252	)		(738	)		95

Total other income (expense), net	$	(13,133	)	$	(12,521	)	$	2,288

Debt (Tables)

12 Months Ended

Jun. 30, 2013

Debt

Schedule of carrying value of the 3.75% Convertible Notes

The following table presents the carrying value of the 3.75% Convertible Notes as of June 30, 2013 (in thousands):


Carrying amount of the equity conversion component	$	23,189

Principal amount of the Convertible Notes	$	100,000
Unamortized debt discount(1)		(16,232	)

Net carrying amount	$	83,768

(1): As of June 30, 2013, the remaining period over which the unamortized debt discount will be amortized is 37 months using an effective interest rate of 10.9%.

Summary of interest expense on the 3.75% Convertible Note and the 3.50% Convertible Note

A summary of interest expense on the 3.75% Convertible Note and the 3.50% Convertible Note is as follows (in thousands):

	Year ended June 30,

	2013		2012
Interest expense related to contractual interest coupon	$	5,292	$	3,438
Interest expense related to amortization of debt discount		4,302		3,596
Interest expense related to amortization of debt issuance costs		784		363

	$	10,378	$	7,397

Quarterly Financial Data (unaudited) (Tables)

12 Months Ended

Jun. 30, 2013

Quarterly Financial Data (unaudited)

Schedule of quarterly financial data (unaudited)

The following table provides the selected quarterly financial data for fiscal 2013 and 2012 (in thousands, except per share amounts):

	Quarters ended

	September 30, 2012			December 31, 2012			March 31, 2013			June 30, 2013
Net revenue	$	82,748		$	77,779		$	70,547		$	84,900
Gross profit	$	23,676		$	26,626		$	20,053		$	27,285
Loss from continuing operations	$	(21,930	)	$	(25,513	)	$	(31,203	)	$	(18,715	)
Loss from discontinued operations	$	(2,200	)	$	(3,658	)	$	—		$	—
Net loss	$	(24,130	)	$	(29,171	)	$	(31,203	)	$	(18,715	)
Basic and diluted—continuing operations	$	(0.31	)	$	(0.35	)	$	(0.42	)	$	(0.25	)
Basic and diluted—discontinued operations	$	(0.03	)	$	(0.05	)	$	—		$	—
Basic and diluted—net loss	$	(0.34	)	$	(0.40	)	$	(0.42	)	$	(0.25	)
Shares used in basic per share calculation		71,995			72,870			74,016			74,270
Shares used in diluted per share calculation		71,995			72,870			74,016			74,270

	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
Loss from continuing operations	$	(26,269	)	$	(10,283	)	$	(14,785	)	$	(20,013	)
Loss from discontinued operations	$	(241	)	$	(104	)	$	(96	)	$	(251	)
Net loss	$	(26,510	)	$	(10,387	)	$	(14,881	)	$	(20,264	)
Basic and diluted—continuing operations	$	(0.38	)	$	(0.15	)	$	(0.21	)	$	(0.28	)
Basic and diluted—discontinued operations	$	(0.00	)	$	(0.00	)	$	(0.00	)	$	(0.00	)
Basic and diluted—net loss	$	(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

Summary of Significant Accounting Policies (Details)	12 Months Ended
Summary of Significant Accounting Policies (Details)	Jun. 30, 2013 customer item	Jun. 30, 2012 customer
Cash, cash equivalent and investments \| Investment concentration risk
Concentration of Credit Risk and Other Risks and Uncertainties
Percentage of concentration risk	5.00%
Number of obligors or makers \| item	1
Total accounts receivable \| Customer concentration risk \| Customer one
Concentration of Credit Risk and Other Risks and Uncertainties
Percentage of concentration risk	10.00%	16.00%
Total accounts receivable \| Customer concentration risk \| Customer two
Concentration of Credit Risk and Other Risks and Uncertainties
Percentage of concentration risk		10.00%
Total accounts receivable \| Credit concentration risk \| Major customers
Concentration of Credit Risk and Other Risks and Uncertainties
Number of significant customers \| customer	1	2

Summary of Significant Accounting Policies (Details 2) $ in Millions	12 Months Ended
	Jun. 30, 2013 USD ($) item	Jun. 30, 2012 USD ($)	Jun. 30, 2011 USD ($)
Summary of Significant Accounting Policies
Number of reporting periods in which the system delivered under the sales arrangement \| item	1
Term of agreements under the shared ownership program	5 years
Revenue from shared ownership arrangements \| $	$ 1.5	$ 1.2	$ 1.4
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

Summary of Significant Accounting Policies (Details 3)	12 Months Ended
Summary of Significant Accounting Policies (Details 3)	Jun. 30, 2013
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 4) $ in Thousands	12 Months Ended
	Jun. 30, 2013 USD ($) item	Jun. 30, 2012 USD ($)	Jun. 30, 2011 USD ($)
Business Combinations
Maximum measurement period from the acquisition date up to record adjustments to the assets acquired and liabilities assumed	1 year
Goodwill and Purchased Intangible Assets
Number of reporting unit \| item	1
Impairment losses	$ 12,200
Advertising Expenses
Advertising expenses	$ 700	$ 500	$ 400
Minimum
Goodwill and Purchased Intangible Assets
Estimated useful lives of respective assets	1 year
Maximum
Goodwill and Purchased Intangible Assets
Estimated useful lives of respective assets	6 years

Summary of Significant Accounting Policies (Details 5) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011	Feb. 13, 2013	Aug. 02, 2011
Numerator:
Loss from operations used in computing loss per share from continuing operations	$ (18,715)	$ (31,203)	$ (25,513)	$ (21,930)	$ (20,013)	$ (14,785)	$ (10,283)	$ (26,269)	$ (97,361)	$ (71,350)	$ (26,657)
Loss from discontinued operations used in computing loss per share from discontinued operations									(5,858)	(692)	(25)
Net loss attributable to stockholders									$ (103,219)	$ (72,042)	$ (26,682)
Denominator:
Weighted average shares used in computing basic net loss per share	74,270	74,016	72,870	71,995	71,473	71,120	70,698	70,263	73,281	70,887	60,085
Add: Dilutive stock options and awards outstanding (in shares)									0
Weighted average shares used in computing diluted net loss per share	74,270	74,016	72,870	71,995	71,473	71,120	70,698	70,263	73,281	70,887	60,085
Anti-dilutive securities excluded from computation of earnings per share
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)									40,367	20,530	8,995
Income Taxes
Reduction in uncertain tax position due to lapse of various statutes of limitation									$ 300
Subsequent period within which no material changes in unrecognized tax benefits are expected									12 months
3.75% Convertible Notes
Anti-dilutive securities excluded from computation of earnings per share
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)									10,560	10,560
Interest rate (as a percent)													3.75%
3.50% Convertible Notes
Anti-dilutive securities excluded from computation of earnings per share
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)									21,576
Interest rate (as a percent)												3.50%
Stock options
Anti-dilutive securities excluded from computation of earnings per share
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)									4,844	7,873	8,337
RSUs, PSUs and MSUs
Anti-dilutive securities excluded from computation of earnings per share
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)									3,387	2,097	658

Summary of Significant Accounting Policies (Details 6) $ in Thousands	3 Months Ended								12 Months Ended
	Jun. 30, 2013 USD ($)	Mar. 31, 2013 USD ($)	Dec. 31, 2012 USD ($)	Sep. 30, 2012 USD ($)	Jun. 30, 2012 USD ($)	Mar. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)	Sep. 30, 2011 USD ($)	Jun. 30, 2013 USD ($) segment	Jun. 30, 2012 USD ($)	Jun. 30, 2011 USD ($)
Summary of Significant Accounting Policies
Number of operating segments \| segment									1
Revenue by geographic region
Total	$ 84,900	$ 70,547	$ 77,779	$ 82,748	$ 100,533	$ 101,816	$ 106,423	$ 100,451	$ 315,974	$ 409,223	$ 222,284
Americas (including Puerto Rico)
Revenue by geographic region
Total									143,613	189,072	122,636
Europe, Middle East, India and Africa
Revenue by geographic region
Total									101,172	110,331	67,244
Asia (excluding Japan)
Revenue by geographic region
Total									37,829	64,026	16,158
Japan
Revenue by geographic region
Total									$ 33,360	$ 45,794	$ 16,246

Balance Sheet Components (Details) - USD ($) $ in Thousands	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010
Cash and Cash Equivalents
Cash	$ 60,082	$ 96,694
Certificates of deposit	12,758	6,742
Money market funds	473	40,068
Cash and cash equivalents	73,313	143,504	$ 95,906	$ 45,434
Investments
Amortized Cost	101,541
Gross Unrealized Loss	(457)
Fair Value	101,084
Aggregate fair value of available-for-sale securities with unrealized losses	98,500
Aggregate fair value of investments in an unrealized loss position for less than 12 months	98,500
Unrealized loss of investments in an unrealized loss position for less than 12 months	500
Amortized Cost
Due in 1 year or less	40,235
Due in 1-2 years	35,428
Due in 2-3 years	25,878
Amortized cost	101,541
Fair Value
Due in 1 year or less	40,188
Due in 1-2 years	35,256
Due in 2-3 years	25,640
Fair Value	101,084
Accounts receivable, net
Accounts receivable	56,830	69,285
Unbilled fees and services	788	305
Accounts and other receivable, gross	57,618	69,590
Less: Allowance for doubtful accounts	(2,160)	(1,700)
Accounts receivable, net	55,458	67,890
Financing receivables
Accounts receivable with contractual maturities of more than one year	2,900	2,500
Allowance for doubtful financing receivable accounts related to financing receivables	0	0
Inventories
Raw materials	33,721	42,951
Work-in-process	20,564	16,932
Finished goods	27,307	21,810
Total inventories	81,592	$ 81,693
Certificates of deposits
Investments
Amortized Cost	2,607
Fair Value	2,607
Amortized Cost
Amortized cost	2,607
Fair Value
Fair Value	2,607
Commercial paper
Investments
Amortized Cost	3,993
Gross Unrealized Loss	(1)
Fair Value	3,992
Amortized Cost
Amortized cost	3,993
Fair Value
Fair Value	3,992
Corporate notes
Investments
Amortized Cost	94,941
Gross Unrealized Loss	(456)
Fair Value	94,485
Amortized Cost
Amortized cost	94,941
Fair Value
Fair Value	$ 94,485

Balance Sheet Components (Details 2) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Property and Equipment, net
Property and equipment, gross	$ 90,206	$ 82,800
Less: Accumulated depreciation and amortization	(55,473)	(45,342)
Property and equipment, net	34,733	37,458
Depreciation and amortization expense	15,200	16,400	$ 6,400
Furniture and fixtures
Property and Equipment, net
Property and equipment, gross	6,506	5,921
Computer and office equipment
Property and Equipment, net
Property and equipment, gross	9,481	9,126
Software
Property and Equipment, net
Property and equipment, gross	9,586	9,429
Leasehold improvements
Property and Equipment, net
Property and equipment, gross	19,199	16,065
Machinery and equipment
Property and Equipment, net
Property and equipment, gross	37,371	33,493
Shared ownership systems
Property and Equipment, net
Property and equipment, gross	4,979	4,979
Construction in progress
Property and Equipment, net
Property and equipment, gross	$ 3,084	$ 3,787

Financial Instruments (Details) - USD ($) $ in Thousands	Jun. 30, 2013	Feb. 13, 2013	Jun. 30, 2012	Aug. 02, 2011
3.75% Convertible Notes
Fair value measurement
Interest rate (as a percent)				3.75%
3.50% Convertible Notes
Fair value measurement
Interest rate (as a percent)		3.50%
Significant Other Observable Inputs (Level 2) \| 3.75% Convertible Notes
Fair value measurement
Interest rate (as a percent)	3.75%
Significant Other Observable Inputs (Level 2) \| 3.50% Convertible Notes
Fair value measurement
Interest rate (as a percent)	3.50%
Recurring basis \| Quoted Prices in Active Markets for Identical Instruments (Level 1)
Fair value measurement
Fair value of assets	$ 15,838		$ 46,810
Recurring basis \| Quoted Prices in Active Markets for Identical Instruments (Level 1) \| Certificates of deposits
Fair value measurement
Fair value of assets	15,365		6,742
Recurring basis \| Quoted Prices in Active Markets for Identical Instruments (Level 1) \| Certificates of deposits \| Investments
Fair value measurement
Fair value of assets	2,600
Recurring basis \| Quoted Prices in Active Markets for Identical Instruments (Level 1) \| Money market funds
Fair value measurement
Fair value of assets	473		40,068
Recurring basis \| Significant Other Observable Inputs (Level 2)
Fair value measurement
Fair value of assets	98,477
Recurring basis \| Significant Other Observable Inputs (Level 2) \| Commercial paper
Fair value measurement
Fair value of assets	3,992
Recurring basis \| Significant Other Observable Inputs (Level 2) \| Corporate notes
Fair value measurement
Fair value of assets	94,485
Recurring basis \| Total balance
Fair value measurement
Fair value of assets	114,315		46,810
Recurring basis \| Total balance \| Certificates of deposits
Fair value measurement
Fair value of assets	15,365		6,742
Recurring basis \| Total balance \| Certificates of deposits \| Investments
Fair value measurement
Fair value of assets	2,600
Recurring basis \| Total balance \| Money market funds
Fair value measurement
Fair value of assets	473		40,068
Recurring basis \| Total balance \| Commercial paper
Fair value measurement
Fair value of assets	3,992
Recurring basis \| Total balance \| Corporate notes
Fair value measurement
Fair value of assets	94,485
Non-recurring basis \| Significant Other Observable Inputs (Level 2)
Fair value measurement
Long term debt	240,862		101,400
Non-recurring basis \| Significant Other Observable Inputs (Level 2) \| 3.75% Convertible Notes
Fair value measurement
Long term debt	96,560		101,400
Non-recurring basis \| Significant Other Observable Inputs (Level 2) \| 3.50% Convertible Notes
Fair value measurement
Long term debt	144,302
Non-recurring basis \| Total balance
Fair value measurement
Long term debt	240,862		101,400
Non-recurring basis \| Total balance \| 3.75% Convertible Notes
Fair value measurement
Long term debt	96,560		$ 101,400
Non-recurring basis \| Total balance \| 3.50% Convertible Notes
Fair value measurement
Long term debt	$ 144,302

Business Combinations (Details) - USD ($) $ in Thousands			12 Months Ended
Business Combinations (Details) - USD ($) $ in Thousands	Jul. 16, 2012	Jun. 10, 2011	Jun. 30, 2013	Jun. 30, 2012
Purchase price
Fair value of pre-existing investment in Morphormics			$ 662
Morphormics
Acquisition
Acquisition of remaining outstanding shares (as a percent)	90.00%
Outstanding shares held prior to acquisition (as a percent)	10.00%
Fair value of outstanding shares prior to acquisition	$ 700			$ 0
Total acquired equity interest (as a percent)	100.00%
Purchase price
Cash paid and payable	$ 5,385
Fair value of pre-existing investment in Morphormics	662
Total purchase price	6,047
Purchase price allocation
Cash and cash equivalents	668
Accounts receivable	283
Other current assets	7
Purchased intangible assets	5,100
Goodwill	77
Accrued compensation	(88)
Total purchase price	$ 6,047
TomoTherapy
Purchase price
Total purchase price		$ 248,023
Purchase price allocation
Net tangible assets		142,220
Purchased intangible assets		66,805
Goodwill		49,979
Noncontrolling interest		(10,981)
Total purchase price		248,023
Business acquisition costs
Acquisition-related costs		18,500
TomoTherapy \| Employee severance
Business acquisition costs
Acquisition-related costs		$ 10,500

Goodwill and Purchased Intangible Assets (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Changes in the carrying amount of goodwill
Balance at the beginning of the period	$ 59,215	$ 54,474
Addition related to acquisition	77
Currency translation and other adjustment	76
Adjustments related to prior year acquisition		4,741
Balance at the end of the period	59,368	59,215	$ 54,474
Intangible Assets
Total gross carrying amount	59,290	68,615
Impairment charge recorded due to a decrease in projected future usage of the technology	12,200
Accumulated Amortization	(27,394)	(18,796)
Net Amount, Finite Lived Intangibles	31,896
Total net carrying amount	31,896	49,819
Amortization expense	10,400	16,200	$ 1,200
Estimated future amortization expense of purchased intangible assets
2014	8,380
2015	7,953
2016	7,953
2017	7,568
2018	42
Net Amount, Finite Lived Intangibles	$ 31,896
Minimum
Intangible Assets
Useful Lives	1 year
Maximum
Intangible Assets
Useful Lives	6 years
In-process research and development (CPAC)
Intangible Assets
Gross Carrying Amount, Indefinite Lived Intangibles		12,800
Impairment charge recorded due to a decrease in projected future usage of the technology	$ 12,200
Net Amount, Indefinite Lived Intangibles		12,800
Developed technology
Intangible Assets
Gross Carrying Amount, Finite Lived Intangibles	46,747	43,455
Accumulated Amortization	(15,276)	(9,161)
Net Amount, Finite Lived Intangibles	31,471	34,294
Estimated future amortization expense of purchased intangible assets
Net Amount, Finite Lived Intangibles	$ 31,471	34,294
Developed technology \| Minimum
Intangible Assets
Useful Lives	5 years
Developed technology \| Maximum
Intangible Assets
Useful Lives	6 years
Backlog
Intangible Assets
Useful Lives	1 year 3 months
Gross Carrying Amount, Finite Lived Intangibles	$ 10,500	10,500
Accumulated Amortization	(10,500)	(8,867)
Net Amount, Finite Lived Intangibles		1,633
Estimated future amortization expense of purchased intangible assets
Net Amount, Finite Lived Intangibles		1,633
Distributor license
Intangible Assets
Gross Carrying Amount, Finite Lived Intangibles	2,043	1,860
Accumulated Amortization	(1,618)	(768)
Net Amount, Finite Lived Intangibles	425	1,092
Estimated future amortization expense of purchased intangible assets
Net Amount, Finite Lived Intangibles	$ 425	$ 1,092
Distributor license \| Minimum
Intangible Assets
Useful Lives	1 year 6 months
Distributor license \| Maximum
Intangible Assets
Useful Lives	2 years 6 months

Investment in CPAC (Details) - USD ($) $ in Thousands	3 Months Ended	12 Months Ended
Investment in CPAC (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Investment in CPAC
Loss on deconsolidation of a consolidated variable interest entity		$ 3,442
Research and development expenses		66,197	$ 81,287	$ 41,301
General and administrative expenses		$ 57,726	57,672	56,589
CPAC
Investment in CPAC
Ownership interest (as a percent)		15.40%
Ownership interest on fully diluted basis (as a percent)		16.30%
Loss on deconsolidation of a consolidated variable interest entity	$ 3,400
Research and development expenses		$ 2,800	5,800	400
General and administrative expenses		600	900	100
Other expense		$ 100	$ 400
CPAC \| Maximum
Investment in CPAC
Ownership interest (as a percent)		50.00%

- Definition

The aggregate costs incurred (1) in a planned search or critical investigation aimed at discovery of new knowledge with the hope that such knowledge will be useful in developing a new product or service, a new process or technique, or in bringing about a significant improvement to an existing product or process; or (2) to translate research findings or other knowledge into a plan or design for a new product or process or for a significant improvement to an existing product or process whether intended for sale or the entity's use, during the reporting period charged to research and development projects, including the costs of developing computer software up to the point in time of achieving technological feasibility, and costs allocated in accounting for a business combination to in-process projects deemed to have no alternative future use.

+ References + Details

Commitments and Contingencies (Details) - USD ($)	12 Months Ended
Commitments and Contingencies (Details) - USD ($)	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Operating Lease Agreements and Long-term Debt
Rent expense, including common area maintenance	$ 8,700,000	$ 7,100,000	$ 4,800,000
Future minimum lease payments under non-cancelable operating lease agreements
2014	7,602,000
2015	6,067,000
2016	3,727,000
2017	3,735,000
2018	3,536,000
Thereafter	435,000
Total	25,102,000
Long-term principal and interest on Convertible Note
Liability recorded associated with indemnification agreements	0
License and royalty agreement \| RaySearch Laboratories AB
License and Royalty Agreements
Commitment amount to be paid on sale of system	25,000
Royalty costs	700,000	700,000	40,000
Royalty amount accrued	600,000	600,000
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 costs	600,000	1,000,000	$ 0
Royalty amount accrued	100,000	$ 100,000
License agreement \| WARF (Wisconsin Alumni Research Foundation) \| Minimum
License and Royalty Agreements
Annual commitment amount	300,000
3.75% Convertible Notes
Long-term principal and interest on Convertible Note
2014	7,775,000
2015	7,775,000
2016	7,775,000
2017	104,338,000
2018	117,348,000
Total	$ 245,011,000

Commitments and Contingencies (Details 2)		1 Months Ended		12 Months Ended
Commitments and Contingencies (Details 2)	May 21, 2012	Jun. 30, 2011 claim counts	Apr. 30, 2011 USD ($)	Jun. 30, 2013 USD ($)	Nov. 02, 2012 USD ($)	Mar. 31, 2011 counts patent
Contingencies
Estimated loss, low end range				$ 0
Estimated loss, high end range				3,000,000
Best Medical Trade Secret Litigation
Contingencies
Attorney fees and costs receivable				$ 512,090
Period after plaintiff's brief with the reporting entity's brief due thereafter				30 days
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 \| claim		1
Rotary Systems
Contingencies
Period to identify alleged trade secrets with specificity or face dismissal of claim with prejudice	60 days
Rotary Systems \| Minimum
Contingencies
Claim for damages			$ 50,000
Radiation stabilization solutions patent litigation
Contingencies
Amount paid to resolve outstanding claims					$ 150,000

Stockholders' Equity (Details) - shares	12 Months Ended
Stockholders' Equity (Details) - shares	Jun. 30, 2012	Jun. 30, 2013	Feb. 13, 2013	Aug. 02, 2011
Stockholders' equity
Number of shares of common stock retired	2,140,018
Number of shares of common stock reserved for issuance under stock incentive plans and employee stock purchase plan		14,200,000
3.75% Convertible Senior Notes
Stockholders' equity
Authorized common stock reserved for future issuance (in shares)		13,200,000
Interest rate (as a percent)				3.75%
3.50% Convertible Senior Notes
Stockholders' equity
Authorized common stock reserved for future issuance (in shares)		21,600,000
Interest rate (as a percent)			3.50%

Stock Incentive Plan and Employee Stock Purchase Plan (Details)	1 Months Ended	12 Months Ended
	Jun. 30, 2011 $ / shares shares	Jun. 30, 2013 item	Jun. 30, 2012	Jun. 30, 2011 shares	Jun. 30, 2010
Stock Incentive Plan
Number of stock incentive plans \| item		3
Stock options
Stock Incentive Plan
Remaining vesting term		10 years
2007 Plan \| TomoTherapy
Stock Incentive Plan
Stock options assumed (in shares)	1,539,255			1,539,255
RSAs assumed (in shares)	429,591			429,591
2007 Plan \| Incentive stock option \| Minimum
Stock Incentive Plan
Exercise price of stock options as a percentage of fair market value on the grant date		100.00%
2007 Plan \| Non-qualified stock option \| Minimum
Stock Incentive Plan
Exercise price of stock options as a percentage of fair market value on the grant date		85.00%
2007 Plan \| Stock options
Stock Incentive Plan
Exercise price of stock options as a percentage of fair market value on the grant date		25.00%
Vesting period for first 25% vesting rights		1 year
Remainder vesting period		36 months
Stock options assumed (in shares)	1,539,000			1,539,000
Remaining contractual term		6 years 2 months 1 day	5 years 6 months 25 days	5 years 1 month 17 days	5 years 11 months 8 days
Weighted average assumptions used for determining fair value of stock options
Expected life		6 years 3 months	6 years 3 months	6 years 3 months
2007 Plan \| Stock options \| TomoTherapy
Stock Incentive Plan
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
2007 Plan \| Stock options \| Minimum
Weighted average assumptions used for determining fair value of stock options
Risk-free interest rate (as a percent)		0.87%	0.85%	1.88%
Expected volatility (as a percent)		52.70%	52.00%	52.80%
2007 Plan \| Stock options \| Minimum \| TomoTherapy
Stock Incentive Plan
Remaining contractual term	1 month 6 days
2007 Plan \| Stock options \| Maximum
Weighted average assumptions used for determining fair value of stock options
Risk-free interest rate (as a percent)		1.15%	1.72%	2.44%
Expected volatility (as a percent)		63.20%	52.90%	54.90%
2007 Plan \| Stock options \| Maximum \| TomoTherapy
Stock Incentive Plan
Remaining contractual term	3 years 4 months 24 days
2007 Plan \| RSUs
Stock Incentive Plan
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%
2007 Plan \| Time-based RSUs
Stock Incentive Plan
Annual vesting percentage		25.00%
2007 Plan \| RSA \| TomoTherapy
Stock Incentive Plan
Remaining vesting term	1 year 2 months 12 days

Stock Incentive Plan and Employee Stock Purchase Plan (Details 2) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Share-based compensation charges
Share-based compensation expense	$ 8,216	$ 8,458	$ 13,365
Share-based compensation expense related to accelerated vesting of stock options, RSUs and RSAs			4,400
Capitalized share-based compensation costs	600	400	300
Cost of revenue
Share-based compensation charges
Share-based compensation expense	1,498	1,672	1,312
Selling and marketing
Share-based compensation charges
Share-based compensation expense	1,121	729	695
Research and development
Share-based compensation charges
Share-based compensation expense	1,949	2,340	2,922
General and administrative
Share-based compensation charges
Share-based compensation expense	$ 3,648	$ 3,717	$ 8,436

- 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

Stock Incentive Plan and Employee Stock Purchase Plan (Details 3) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	12 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2010	Jun. 28, 2013
Additional disclosures
Share-based compensation expense	$ 8,216	$ 8,458	$ 13,365
2007 Plan
Additional disclosures
Fair value of common stock (in dollars per share)					$ 5.74
2007 Plan \| Stock options
Options Outstanding
Balance at the beginning of the year (in shares)	7,873	8,336	7,809
Options granted (in shares)	1,250	1,399	915
Options assumed (in shares)			1,539
Options exercised (in shares)	(1,515)	(746)	(1,397)
Options forfeited/expired (in shares)	(2,764)	(1,116)	(530)
Balance at the end of the year (in shares)	4,844	7,873	8,336	7,809
Vested or Expected to vest at the end of the year (in shares)	4,843
Exercisable at the end of the year (in shares)	3,205
Weighted Average Exercise Price
Balance at the beginning of the year (in dollars per share)	$ 7.00	$ 7.39	$ 6.03
Options granted (in dollars per share)	6.54	4.53	7.30
Options assumed (in dollars per share)			10.41
Options exercised (in dollars per share)	2.77	2.50	2.58
Options forfeited/expired (in dollars per share)	8.86	9.79	8.60
Balance at the end of the year (in dollars per share)	7.15	$ 7.00	$ 7.39	$ 6.03
Vested or Expected to vest at the end of the year (in dollars per share)	7.15
Exercisable at the end of the year (in dollars per share)	$ 7.77
Weighted Average Remaining Contractual Life (In Years)
Balance at the end of the year	6 years 2 months 1 day	5 years 6 months 25 days	5 years 1 month 17 days	5 years 11 months 8 days
Vested or Expected to vest at the end of the year	6 years 2 months 1 day
Exercisable at the end of the year	4 years 9 months 22 days
Aggregate Intrinsic Value (in thousand)
Balance at the end of the year	$ 2,771	$ 12,359	$ 19,131	$ 16,651
Vested or Expected to vest at the end of the year	2,771
Exercisable at the end of the year	1,996
Additional disclosures
Total intrinsic value of options exercised	4,500	2,900	6,100
Share-based compensation expense	$ 2,900	$ 3,500	$ 4,700
Weighted average fair value (in dollars per share)	$ 3.48	$ 2.30	$ 3.91
Realized excess tax benefits related to stock options exercises	$ 0	$ 0	$ 0
Unrecognized compensation cost related to unvested stock options, net of estimated forfeitures	$ 4,900
Expected weighted average period for recognition of compensation costs	2 years 10 months 2 days

Stock Incentive Plan and Employee Stock Purchase Plan (Details 4) $ / shares in Units, shares in Thousands, $ in Thousands	1 Months Ended	12 Months Ended
	Oct. 31, 2012 USD ($) item	Jun. 30, 2013 USD ($) $ / shares shares	Jun. 30, 2012 USD ($) $ / shares shares	Jun. 30, 2011 USD ($) $ / shares shares
Additional disclosures
Share-based compensation expense \| $		$ 8,216	$ 8,458	$ 13,365
2007 Plan \| RSUs, PSUs and MSUs
Number of Shares
Balance at the beginning of the year (in shares) \| shares		2,098	658	464
Granted (in shares) \| shares		2,662	2,001	475
Vested (in shares) \| shares		(544)	(302)	(202)
Cancelled/Forfeited (in shares) \| shares		(829)	(259)	(79)
Balance at the end of the year (in shares) \| shares		3,387	2,098	658
Weighted Average Grant Date Fair Value Per Share
Balance at the beginning of the year (in dollars per share)		$ 5.16	$ 6.97	$ 12.52
Granted (in dollars per share)		5.52	4.53	6.77
Vested (in dollars per share)		5.18	4.47	7.57
Cancelled/Forfeited (in dollars per share)		5.18	5.67	9.85
Balance at the end of the year (in dollars per share)		5.66	5.16	6.97
Additional disclosures
Weighted average grant date fair value (in dollars per share)		5.52	4.53	6.77
2007 Plan \| RSUs
Weighted Average Grant Date Fair Value Per Share
Granted (in dollars per share)		$ 5.89	$ 4.80	$ 6.77
Additional disclosures
Share-based compensation expense \| $		$ 3,600	$ 2,500	$ 2,900
Weighted average grant date fair value (in dollars per share)		$ 5.89	$ 4.80	$ 6.77
Unrecognized compensation cost, net of estimated forfeitures \| $		$ 11,100
Expected weighted average period for recognition of compensation costs		2 years 29 days
Aggregate fair market value of units vested \| $		$ 3,500
2007 Plan \| RSA \| TomoTherapy
Additional disclosures
Share-based compensation expense \| $		$ 300	$ 1,400	$ 5,000
2007 Plan \| PSUs
Number of Shares
Granted (in shares) \| shares			1,000
Additional disclosures
Total fair value of awards granted to employees \| $			$ 3,900
Vesting percentage			100.00%
MSU Program \| MSU
Number of Shares
Granted (in shares) \| shares		500
Weighted Average Grant Date Fair Value Per Share
Granted (in dollars per share)		$ 5.39
Additional disclosures
Share-based compensation expense \| $		$ 300
Weighted average grant date fair value (in dollars per share)		$ 5.39
Unrecognized compensation cost, net of estimated forfeitures \| $		$ 1,000
Expected weighted average period for recognition of compensation costs	1 year 9 months 18 days	1 year 7 months 6 days
Total fair value of awards granted to employees \| $	$ 1,500	$ 500
Number of measurement periods \| item	2
MSU Program \| MSU \| Maximum
Additional disclosures
Target number of shares that participating executives may earn (as a percent)	150.00%

Stock Incentive Plan and Employee Stock Purchase Plan (Details 5) - USD ($)	12 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Employee Stock Purchase Plan
Number of shares authorized	14,200,000
Other disclosures
Share-based compensation expense	$ 8,216,000	$ 8,458,000	$ 13,365,000
ESPP
Employee Stock Purchase Plan
Purchase price expressed as percentage of fair market value of common stock	85.00%
Weighted average assumptions used for determining fair value of options
Expected life	6 months	6 months	6 months
Other disclosures
Share-based compensation expense	$ 1,300,000	$ 1,100,000	$ 800,000
Weighted average fair value (in dollars per share)	$ 2.06	$ 1.80	$ 2.03
Unrecognized compensation cost, net of estimated forfeitures	$ 600,000
Expected weighted average period for recognition of compensation costs	4 months 24 days
ESPP \| Maximum
Employee Stock Purchase Plan
Number of shares authorized	1,200,000
Payroll deductions as percentage of salaries	10.00%
Number of shares per period up to which employees may purchase	2,500
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)	0.14%	0.12%	0.23%
Expected volatility (as a percent)	53.70%	50.60%	56.70%
ESPP \| Minimum
Weighted average assumptions used for determining fair value of options
Risk-free interest rate (as a percent)	0.07%	0.05%	0.11%
Expected volatility (as a percent)	40.30%	33.60%	33.60%

Income Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Components of income (loss) before provision for income taxes
Domestic	$ (103,964)	$ (75,391)	$ (28,167)
Foreign	10,176	6,636	2,626
Loss before provision for income taxes	(93,788)	(68,755)	(25,541)
Current:
State	(21)	(7)	114
Foreign	2,647	2,107	939
Total current	2,626	2,100	1,053
Deferred:
Foreign	947	495	63
Total deferred	947	495	63
Total provision for (benefit from) income taxes	3,573	2,595	1,116
Income tax payable	1,200	1,100
Reconciliation of income taxes at the statutory federal income tax rate to net income taxes
At federal statutory rate	(32,826)	(24,064)	(8,939)
State tax, net of federal benefit	(21)	(7)	114
Stock-based compensation expense	4,061	3,645	33
Change in valuation allowance	33,454	24,796	8,883
Credits	(1,272)	(846)	(1,373)
Meals and entertainment	246	335	214
Acquisition costs		89	2,451
Other	(177)	(1,669)	(273)
Foreign taxes	108	316	6
Total U.S. federal taxes (benefits)	3,573	2,595	$ 1,116
Deferred tax assets:
Federal and state net operating losses	105,110	80,834
Accrued vacation and bonus	1,503	1,973
Deferred revenue	1,913	1,125
Deferred rent	710	1,165
Credits	16,636	13,985
Share-based compensation expense	10,691	13,103
Reserves not deductible for tax purposes	(76)	4,085
Unicap	1,540	1,347
Other	623	689
Total deferred tax assets	138,650	118,306
Deferred tax liabilities:
Fixed assets/intangibles	(11,740)	(15,198)
Foreign currency differences	(1,697)	(594)
Total deferred tax liabilities	(13,437)	(15,792)
Valuation allowance	(124,781)	(102,142)
Net deferred tax assets	432	$ 372
Income tax uncertainties
Cumulative amount of undistributed earnings upon which no U.S. income taxes provided	$ 9,800

Income Taxes (Details 2) $ in Millions	Jun. 30, 2013 USD ($)
Operating loss carryforwards
Amount expected to be credited to additional paid-in-capital	$ 3.4
Federal
Operating loss carryforwards
Net operating loss carryforwards	288.1
State
Operating loss carryforwards
Net operating loss carryforwards	$ 114.5

Income Taxes (Details 3) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details 3) - USD ($) $ in Thousands	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
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	$ 15,147	$ 14,158	$ 3,669
Tax positions related to current year: Additions	1,781	1,129	10,468
Tax positions related to prior years: Additions	564	40	58
Tax positions related to prior years: Reductions	(743)	(180)	(37)
Balance at end of year	$ 16,749	15,147	$ 14,158
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	3,600
Accrued interest and penalties related to uncertain tax positions	700	$ 600
Federal \| Research and development
Tax Credits
Tax credits	9,800
State \| Research and development
Tax Credits
Tax credits	$ 6,800

Other Income (Expense), Net (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Other Income (Expense), Net
Interest expense on convertible notes	$ (10,378)	$ (7,397)
Foreign currency transaction gain (loss)	(2,503)	(4,386)	$ 2,193
Other	(252)	(738)	95
Total other income (expense), net	$ (13,133)	$ (12,521)	$ 2,288

Debt (Details)			12 Months Ended
Debt (Details)	Feb. 13, 2013 USD ($)	Aug. 02, 2011 USD ($)	Jun. 30, 2013 USD ($) shares $ / shares	Jun. 30, 2012 USD ($)
Debt
Proceeds from debt, net of costs			$ 110,462,000	$ 96,100,000
Net carrying amount			198,768,000	79,466,000
Interest expense related to contractual interest coupon			$ 10,378,000	7,397,000
3.75% Convertible Note and 3.50% Convertible Note
Debt
Amortization period			37 months
Interest expense related to contractual interest coupon			$ 5,292,000	3,438,000
Interest expense related to amortization of debt discount			4,302,000	3,596,000
Interest expense related to amortization of debt issuance costs			784,000	363,000
Total interest expense recognized			$ 10,378,000	$ 7,397,000
3.75% Convertible 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		24,100,000	$ 23,189,000
Principal amount of the Notes		$ 75,900,000	100,000,000
Unamortized debt discount			(16,232,000)
Net carrying amount			$ 83,768,000
Amortization period			37 months
Effective interest rate (as a percent)			10.90%
3.75% Convertible 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 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%
3.50% Convertible Notes
Debt
Aggregate principal amount of debt issued	$ 115,000,000
Interest rate (as a percent)	3.50%
Proceeds from debt, net of costs	$ 110,500,000
Debt issuance costs, amortization period	5 years
Conversion rate, number of shares to be issued per $1000 of principal amount (in shares) \| shares			187.6877
Principal amount used for debt instrument conversion ratio			$ 1,000
Conversion price (in dollars per share) \| $ / shares			$ 5.33
Repurchase price, as percentage of principal amount, if company undergoes change of control			100.00%

Employee Benefit Plans (Details) - USD ($) $ in Millions	12 Months Ended
Employee Benefit Plans (Details) - USD ($) $ in Millions	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Employee Benefit Plans
Employer's contribution to the 401(k) Plan	$ 2.3	$ 2.2	$ 0.7

Restructuring Charges (Details) $ in Millions	12 Months Ended
Restructuring Charges (Details) $ in Millions	Jun. 30, 2013 USD ($)	Jun. 30, 2012 USD ($) item
Restructuring and Severance Charges
Restructuring charges	$ 9.1	$ 1.9
Reduction in workforce
Restructuring and Severance Charges
Severance-related charges	$ 7.4	$ 1.7
Reduction in headcount (as a percent)	13.00%
Restructuring related liabilities	$ 1.0
Number of full-time positions eliminated \| item		51
Office facility
Restructuring and Severance Charges
Restructuring charges	1.4
Restructuring related liabilities	1.0
Disposition of fixed assets and leasehold improvements
Restructuring and Severance Charges
Restructuring charges	$ 0.3

- Definition

Carrying amount as of the balance sheet date of known and estimated obligations associated with exit from or disposal of business activities or restructurings pursuant to a duly authorized plan, which are expected to be paid in the next twelve months or in the normal operating cycle if longer. Costs of such activities include those for one-time termination benefits, termination of an operating lease or other contract, consolidating or closing facilities, relocating employees, and costs associated with an ongoing benefit arrangement, but excludes costs associated with the retirement of a long-lived asset.

+ References + Details

- 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, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Quarterly Financial Data (unaudited)
Net revenue	$ 84,900	$ 70,547	$ 77,779	$ 82,748	$ 100,533	$ 101,816	$ 106,423	$ 100,451	$ 315,974	$ 409,223	$ 222,284
Gross profit	27,285	20,053	26,626	23,676	36,490	36,111	40,243	24,428	97,640	137,272	107,242
Loss from continuing operations	(18,715)	(31,203)	(25,513)	(21,930)	(20,013)	(14,785)	(10,283)	(26,269)	(97,361)	(71,350)	(26,657)
Loss from discontinued operations			(3,658)	(2,200)	(251)	(96)	(104)	(241)	(19,147)	(7,103)	(454)
Net loss	$ (18,715)	$ (31,203)	$ (29,171)	$ (24,130)	$ (20,264)	$ (14,881)	$ (10,387)	$ (26,510)	$ (116,508)	$ (78,453)	$ (27,111)
Basic and diluted - continuing operations (in dollars per share)	$ (0.25)	$ (0.42)	$ (0.35)	$ (0.31)	$ (0.28)	$ (0.21)	$ (0.15)	$ (0.38)	$ (1.33)	$ (1.01)	$ (0.44)
Basic and diluted - discontinued operations (in dollars per share)			(0.05)	(0.03)	0.00	0.00	0.00	0.00	(0.08)	(0.01)	0.00
Basic and diluted - net loss (in dollars per share)	$ (0.25)	$ (0.42)	$ (0.40)	$ (0.34)	$ (0.28)	$ (0.21)	$ (0.15)	$ (0.38)	$ (1.41)	$ (1.02)	$ (0.44)
Shares used in basic per share calculation	74,270	74,016	72,870	71,995	71,473	71,120	70,698	70,263	73,281	70,887	60,085
Shares used in diluted per share calculation	74,270	74,016	72,870	71,995	71,473	71,120	70,698	70,263	73,281	70,887	60,085

SCHEDULE II Valuation and Qualifying Accounts (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011
Accounts receivable
Valuation and Qualifying Accounts
Beginning Balance	$ 1,700	$ 324	$ 115
Additions (Deductions)	787	1,392	239
Write-offs/Deductions	(327)	(16)	(30)
Ending Balance	2,160	1,700	324
Accrued warranty
Valuation and Qualifying Accounts
Beginning Balance	748	6,795
Increase Due to Acquisition			7,600
Additions (Deductions)	57	48
Write-offs/Deductions	(775)	(6,095)	(805)
Ending Balance	$ 30	$ 748	$ 6,795