0001104659-13-039494 | 10-Q | XBRL Viewer

Document and Entity Information - shares	9 Months Ended
Mar. 31, 2013	Apr. 30, 2013
Document and Entity Information
Entity Registrant Name	ACCURAY INC
Entity Central Index Key	0001138723
Document Type	10-Q
Document Period End Date	Mar. 31, 2013
Amendment Flag	false
Current Fiscal Year End Date	--06-30
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		74,115,872
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	Q3

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2013	Jun. 30, 2012
Current assets:
Cash and cash equivalents	$ 181,526	$ 143,504
Restricted cash	2,613	1,560
Accounts receivable, net of allowance for doubtful accounts of $1,383 and $1,700, respectively	53,992	67,890
Inventories	92,225	81,693
Prepaid expenses and other current assets	15,869	16,715
Deferred cost of revenue - current	7,345	4,896
Total current assets	353,570	316,258
Property and equipment, net	35,325	37,458
Goodwill	59,368	59,215
Intangible assets, net	34,102	49,819
Deferred cost of revenue - noncurrent	2,295	2,433
Other assets	12,418	7,987
Total assets	497,078	473,170
Current liabilities:
Accounts payable	14,982	18,209
Accrued compensation	15,456	23,071
Other accrued liabilities	26,323	31,646
Customer advances - current	16,114	18,177
Deferred revenue - current	91,091	83,071
Total current liabilities	163,966	174,174
Long-term liabilities:
Long-term other liabilities	4,322	5,988
Deferred revenue - noncurrent	9,087	9,675
Long-term debt	197,658	79,466
Total liabilities	375,033	269,303
Commitment and contingencies (Note 5)
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 at March 31, 2013 and June 30, 2012, respectively; issued and outstanding: 74,096,245 and 71,864,268 shares at March 31, 2013 and June 30, 2012, respectively	74	72
Additional paid-in capital	420,511	409,143
Accumulated other comprehensive income	2,391	2,837
Accumulated deficit	(300,931)	(216,427)
Total stockholders' equity	122,045	195,625
Non-controlling interest		8,242
Total equity	122,045	203,867
Total liabilities and equity	$ 497,078	$ 473,170

Condensed Consolidated Balance Sheets (Parenthetical) - USD ($) $ in Thousands	Mar. 31, 2013	Jun. 30, 2012
Condensed Consolidated Balance Sheets
Accounts receivable, allowance for doubtful accounts (in dollars)	$ 1,383	$ 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	74,096,245	71,864,268
Common stock, outstanding shares	74,096,245	71,864,268

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012
Net revenue:
Products	$ 25,023	$ 59,875	$ 98,821	$ 179,851
Services	45,524	41,720	132,253	127,218
Other		221		1,621
Total net revenue	70,547	101,816	231,074	308,690
Cost of revenue:
Cost of products	18,403	32,401	60,976	103,574
Cost of services	32,091	33,100	99,743	103,626
Cost of other		204		708
Total cost of revenue	50,494	65,705	160,719	207,908
Gross profit	20,053	36,111	70,355	100,782
Operating expenses:
Selling and marketing	12,646	12,449	41,296	40,047
Research and development	15,697	22,398	51,510	59,799
General and administrative	16,745	13,964	45,479	42,047
Total operating expenses	45,088	48,811	138,285	141,893
Loss from operations	(25,035)	(12,700)	(67,930)	(41,111)
Other expense, net	(5,565)	(838)	(8,849)	(8,074)
Loss before provision for income taxes	(30,600)	(13,538)	(76,779)	(49,185)
Provision for income taxes	603	1,247	1,867	2,152
Loss from continuing operations	(31,203)	(14,785)	(78,646)	(51,337)
Loss from discontinued operations (Note 9):
Loss from operations of a discontinued variable interest entity		(1,748)	(3,505)	(5,470)
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 of $0		(1,748)	(19,147)	(5,470)
Loss from discontinued operations attributable to non-controlling interest		(1,652)	(13,289)	(5,029)
Loss from discontinued operations attributable to stockholders		(96)	(5,858)	(441)
Net loss attributable to stockholders	$ (31,203)	$ (14,881)	$ (84,504)	$ (51,778)
Loss per share attributable to stockholders
Basic and diluted - continuing operations (in dollars per share)	$ (0.42)	$ (0.21)	$ (1.08)	$ (0.73)
Basic and diluted - discontinued operations (in dollars per share)		0.00	(0.08)	0.00
Basic and diluted - net loss (in dollars per share)	$ (0.42)	$ (0.21)	$ (1.16)	$ (0.73)
Weighted average common shares used in computing loss per share
Basic and diluted (in shares)	74,016	71,120	72,953	70,692
Net loss attributable to stockholders	$ (31,203)	$ (14,881)	$ (84,504)	$ (51,778)
Foreign currency translation adjustment	(82)	(617)	(446)	1,750
Comprehensive loss	$ (31,285)	$ (15,498)	$ (84,950)	$ (50,028)

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Cash Flows From Operating Activities
Loss from continuing operations	$ (78,646)	$ (51,337)
Loss from discontinued operations	(19,147)	(5,470)
Adjustments to reconcile net loss to net cash used in operating activities
Depreciation and amortization	19,845	24,512
Impairment of indefinite lived intangible asset	12,200
Share-based compensation	6,119	6,301
Accretion of interest on long-term debt	3,192	2,590
Provision for (recovery of) bad debt	(317)	997
Provision for write-down of inventories	1,718	2,007
Loss on disposal of property and equipment	585	245
Gain on previously held equity interest in Morphormics	(662)
Loss from deconsolidation of a variable interest entity	3,442
Changes in assets and liabilities:
Restricted cash	(1,050)	(285)
Accounts receivable	13,238	(12,942)
Inventories	(12,248)	9,242
Prepaid expenses and other assets	693	4,368
Deferred cost of revenue	(2,333)	563
Accounts payable	(2,197)	(15,803)
Accrued liabilities	(12,313)	(15,577)
Customer advances	(2,185)	(6,333)
Deferred revenue	8,125	24,135
Net cash used in operating activities	(61,941)	(32,787)
Cash Flows From Investing Activities
Purchases of property and equipment, net	(11,621)	(7,714)
Purchase of intangible asset	(232)
Acquisition of business, net of cash acquired	(3,861)	(1,384)
Net cash used in investing activities	(15,714)	(9,098)
Cash Flows From Financing Activities
Proceeds from issuance of common stock	5,555	2,704
Proceeds from debt, net of costs	110,462	96,100
Net cash provided by financing activities	116,017	98,804
Effect of exchange rate changes on cash and cash equivalents	(340)	(1,497)
Net increase in cash and cash equivalents	38,022	55,422
Cash and cash equivalents at beginning of period	143,504	95,906
Cash and cash equivalents at end of period	$ 181,526	$ 151,328

Summary of Significant Accounting Policies

9 Months Ended

Mar. 31, 2013

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

1. Summary of Significant Accounting Policies

Description of Business

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.

Basis of Presentation and Principles of Consolidation

The condensed consolidated financial statements include the accounts of the Company, its wholly-owned subsidiaries and a variable interest entity, Compact Particle Acceleration Corporation (“CPAC”) until its deconsolidation on December 21, 2012 (for further information, see Note 9, “Investment in CPAC”). All significant inter-company transactions and balances have been eliminated in consolidation.

The accompanying condensed consolidated financial statements have been prepared in accordance with United States generally accepted accounting principles, (“GAAP”), pursuant to the rules and regulations of the Securities and Exchange Commission (the “SEC”). Certain information and note disclosures have been condensed or omitted pursuant to such rules and regulations. The unaudited condensed consolidated financial statements have been prepared on the same basis as the annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair presentation of the periods presented. The results for the three and nine months ended March 31, 2013 are not necessarily indicative of the results to be expected for the year ending June 30, 2013, for any other interim period or for any future year.

Use of Estimates

The preparation of condensed 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.

Concentration of Credit and Other Risks

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.

For the three and nine months ended March 31, 2013 and 2012, there were no customers that represented 10% or more of total net revenue. At March 31, 2013 and June 30, 2012, there was one customer and two customers, respectively, whose accounts receivable balances were 10% or more of the Company’s total accounts receivable.

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

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

Revenue Recognition

The Company earns revenue from the sale of products, the operation of its shared ownership program, and the provision of related services, which include post-contract customer support (“PCS”), installation services, training and other professional services. The Company records its revenues net of any value added or sales tax. For arrangements with multiple elements, the Company allocates arrangement fees to product and services based upon Vendor Specific Objective Evidence of fair value of the respective elements, or Third-Party Evidence, or Best Estimate of Selling Price using the relative selling price method.

Product Revenue

The majority of product revenue is normally 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.

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 also 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 condensed consolidated statements of operations and comprehensive loss.

Other revenue

Other revenue primarily consists of research and development and construction 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 condensed 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.

Loss Per 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 Restricted Stock Units (RSUs), Market Stock Units (MSUs) and Performance-based Stock Units (PSUs), and the purchase of shares under the Employee Stock Purchase Plan (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.

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

	Three Months Ended						Nine Months Ended
	March 31,						March 31,
	2013			2012			2013			2012
Numerator:
Loss from operations used in computing loss per share from continuing operations	$	(31,203	)	$	(14,785	)	$	(78,646	)	$	(51,337	)
Loss from discontinued operations used in computing loss per share from discontinued operations	$	—		$	(96	)	$	(5,858	)	$	(441	)
Net loss used in computing net loss per share	$	(31,203	)	$	(14,881	)	$	(84,504	)	$	(51,778	)
Denominator:
Weighted average shares used in computing basic loss per share	74,016			71,120			72,953			70,692
Add: Dilutive stock options and awards outstanding	—			—			—			—
Weighted average shares used in computing diluted loss per share	74,016			71,120			72,953			70,692

The 3.75% Convertible Senior Notes due August 1, 2016 (the “3.75% Convertible Notes”) and the 3.50% Convertible Senior Notes due February 1, 2018 (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. 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
	March 31,
	2013	2012
Stock options	5,257	7,925
RSUs, MSUs and PSUs	3,321	2,097
3.75% Convertible Notes	10,560	10,560
3.50% Convertible Notes	21,576	—
	40,714	20,582

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):

	Three Months Ended				Nine Months Ended
	March 31,				March 31,
	2013		2012		2013		2012
Americas	$	28,372	$	46,655	$	99,262	$	149,766
Europe, Middle East, India and Africa	25,290		25,825		78,246		79,770
Asia (excluding Japan)	8,496		17,059		29,154		52,931
Japan	8,389		12,277		24,412		26,223
Total	$	70,547	$	101,816	$	231,074	$	308,690

Recent Accounting Pronouncements

In February 2013, the Financial Accounting Standards Board issued Accounting Standards Update No. 2013-02, Comprehensive Income (Topic 220)—Reporting of Amounts Reclassified Out of Accumulated Other Comprehensive Income (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 with earlier adoption permitted, which should 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

9 Months Ended

Mar. 31, 2013

Balance Sheet Components

Balance Sheet Components

2. Balance Sheet Components

Accounts receivable, net

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

	March 31,			June 30,
	2013			2012
Accounts receivable	$	54,970		$	69,285
Unbilled fees and services	405			305
	55,375			69,590
Less: Allowance for doubtful accounts	(1,383		)	(1,700		)
Accounts receivable, net	$	53,992		$	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 $3.0 million and $2.5 million at March 31, 2013 and June 30, 2012, respectively and are included in Other Assets in the condensed consolidated balance sheets. There was no balance in the allowance for doubtful accounts related to such financing receivables as of March 31, 2013 and June 30, 2012, respectively.

Inventories

Inventories consisted of the following (in thousands):

	March 31,		June 30,
	2013		2012
Raw materials	$	37,780	$	34,579
Work-in-process	24,729		16,547
Finished goods	29,716		30,567
Inventories	$	92,225	$	81,693

Property and equipment, net

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

	March 31,			June 30,
	2013			2012
Furniture and fixtures	$	6,495		$	5,921
Computer and office equipment	9,166			9,126
Software	9,420			9,429
Leasehold improvements	19,301			16,065
Machinery and equipment	37,173			33,493
Shared ownership systems	4,979			4,979
Construction in progress	1,241			3,787
	87,775			82,800
Less: Accumulated depreciation	(52,450		)	(45,342		)
Property and equipment, net	$	35,325		$	37,458

Depreciation expense related to property and equipment for the three and nine months ended March 31, 2013 was $3.7 million and $11.6 million, respectively. Depreciation expense related to property and equipment for the three and nine months ended March 31, 2012 was $4.0 million and $12.3 million, respectively.

Goodwill and Intangible Assets

9 Months Ended

Mar. 31, 2013

Goodwill and Intangible Assets

Goodwill and Intangible Assets

3. Goodwill and Intangible Assets

Goodwill

Activity related to goodwill consisted of the following (in thousands):

	Nine Months
	Ended		Year Ended
	March 31,		June 30,
	2013		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.

Intangible Assets

The Company’s intangible assets associated with completed acquisitions at March 31, 2013 and June 30, 2012 are as follows (in thousands):

		March 31, 2013							June 30, 2012
		Gross							Gross
		Carrying		Accumulated			Net		Carrying		Accumulated			Net
	Useful Lives	Amount		Amortization			Amount		Amount		Amortization			Amount
	(in years)
Developed technology	5 - 6	$	48,556	$	(15,096	)	$	33,460	$	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	2,052		(1,410		)	642		1,860		(768		)	1,092
In-process research and development (CPAC)	Indefinite	—		—			—		12,800		—			12,800
		$	61,108	$	(27,006	)	$	34,102	$	68,615	$	(18,796	)	$	49,819

Prior to the deconsolidation of CPAC on December 21, 2012 (see Note 9, “Investment in CPAC”), the Company had noted certain impairment triggers based on results of research and development work carried out by CPAC. As a result, based on projected future usage of the in-process research and development (“IPR&D”) technology by CPAC, an impairment charge of $12.2 million was recorded during the three months ended September 30, 2012. The Company did not identify any impairment triggers on goodwill or any of its other definite-lived intangible and long-lived assets.

Amortization expense related to intangible assets for the three and nine months ended March 31, 2013 was $2.2 million and $8.2 million, respectively. Amortization expense related to intangible assets for the three and nine months ended March 31, 2012 was $4.0 million and $12.2 million, respectively.

The estimated future amortization expense of purchased intangible assets as of March 31, 2013 is as follows (in thousands):

Year Ending June 30,	Amount
2013 (remaining 3 months)	$	2,203
2014	8,382
2015	7,953
2016	7,953
2017	7,568
Thereafter	43
	$	34,102

- 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

Financial Instruments

9 Months Ended

Mar. 31, 2013

Financial Instruments

Financial Instruments

4. Financial Instruments

The following tables summarize the fair value of financial instruments measured on a recurring basis as of March 31, 2013 and June 30, 2012 (in thousands):

	Fair value measurement using
Type of instrument and line item in condensed consolidated balance sheets	Quoted Prices in Active Markets for Identical Instruments (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Total balance

Assets at March 31, 2013
Money market funds - included in cash and cash equivalents	$	—	$	—	$	—	$	—
Certificate of deposits - included in cash and cash equivalents	$	5,038	$	—	$	—	$	5,038

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

The following tables summarize the fair value of financial instruments that are not measured on a recurring basis as of March 31, 2013 and June 30, 2012 (in thousands):

	Fair value measurement using
Type of instrument and line item in condensed consolidated balance sheets	Quoted Prices in Active Markets for Identical Instruments (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Total balance

At March 31, 2013
3.75% Convertible Notes - included in long term debt	$	—	$	89,200	$	—	$	89,200
3.50% Convertible Notes - included in long term debt	$	—	$	123,200	$	—	$	123,200

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

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

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Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
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Reference 8: http://www.xbrl.org/2003/role/presentationRef
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+ Details

Commitments and Contingencies

9 Months Ended

Mar. 31, 2013

Commitments and Contingencies

Commitments and Contingencies

5. Commitments and Contingencies

Commitments

The Company’s contractual obligations were presented in the Annual Report on Form 10-K for the previous annual reporting period ended June 30, 2012. There have been no material changes outside of the ordinary course of business in those obligations during the three and nine months ended March 31, 2013, except for the issuance of the 3.50% Convertible Notes during February 2013. See Note 8, “Debt” for additional information about the 3.50% Convertible Notes. Future payments expected for the 3.75% Convertible Notes and the 3.50% Convertible Notes as of March 31, 2013 are as follows (in thousands):

Year Ending June 30,	Amount
2013 (remaining 3 months)	$	1,944
2014	7,775
2015	7,775
2016	7,775
2017	104,338
2018	117,348
Thereafter	—
	$	246,955

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 condensed consolidated balance sheet. Any conversion, redemption or purchase of Convertible Notes would impact cash payments.

Litigation

From time to time, the Company is involved in legal proceedings arising in the ordinary course of its business. Currently, management believes the Company does not have any probable and estimable loss related to any current legal proceedings and claims that would individually or in the aggregate materially adversely affect its financial condition or operating results. In excess of amounts accrued, management believes that there is a reasonable possibility that losses may be incurred for current legal proceedings. 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. 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.

Best Medical Trade Secret Litigation

On September 3, 2009, Best Medical International, Inc. (“Best Medical”) filed a lawsuit against the Company in the U.S. District Court for the Western District of Pennsylvania, claiming that the Company induced certain individuals to leave the employment of Best Medical and join the Company in order to gain access to Best Medical’s confidential information and trade secrets. Best Medical is seeking monetary damages and other relief. The Company filed a motion for summary judgment on May 20, 2011, Best Medical filed its response on June 21, 2011, and the Company filed a response to their response on July 8, 2011. On October 25, 2011, the court granted summary judgment in favor of the Company on all counts. On November 21, 2011 Best Medical filed a notice of appeal, and the parties await a ruling by the appellate court.

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. A mandatory mediation hearing was held in March 2013 during which the parties failed to reach settlement and another mediation hearing is scheduled for May 2013. If the parties fail to reach settlement then, we will continue to litigate this case. Best Medical is seeking declaratory and injunctive relief, as well as unspecified compensatory and treble damages and other relief.

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 (“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 are inadequate and constitute 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.

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 March 31, 2013.

- Definition

The entire disclosure for commitments and contingencies.

+ References

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-Publisher FASB
-Name Accounting Standards Codification
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-SubTopic 20
-Section 50
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Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
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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.

+ Details

Debt

9 Months Ended

Mar. 31, 2013

Debt

Debt

8. 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. 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 (“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 will be 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 March 31, 2013 (in thousands):

Carrying amount of the equity conversion component	$	23,189
Principal amount of the 3.75% Convertible Notes	$	100,000
Unamortized debt discount (1)	(17,342		)
Net carrying amount	$	82,658

(1)As of March 31, 2013, the remaining period over which the unamortized debt discount will be amortized is 40 months using an effective interest rate of 10.0%.

3.50% Convertible Senior Notes due February 2018

In February 2013, the Company issued $115 million aggregate principal amount of its 3.50% Convertible Notes to certain qualified institutional buyers or QIBs. The 3.50% Convertible Notes were offered and sold to the QIBs pursuant to Rule 144A under the Securities Act of 1933, as amended. The net proceeds from the offering, after deducting the initial purchaser’s discount and commission and the related offering costs, were approximately $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 million principal amount of the 3.50% Convertible Note has been recorded in Long-term Debt on the condensed consolidated balance sheet as of March 31, 2013.

A summary of interest expenses on the 3.75% Convertible Note and the 3.50% Convertible Note for the three and nine months ended March 31, 2013 and 2012 were as follows (in thousands):

	Three months ended March 31,				Nine months ended March 31,
	2013		2012		2013		2012
Interest expense related to contractual interest coupon	$	1,441	$	937	$	3,316	$	2,500
Interest expense related to amortization of debt discount	1,093		992		3,192		2,590
	$	2,534	$	1,929	$	6,508	$	5,090

- 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

Summary of Significant Accounting Policies (Policies)

9 Months Ended

Mar. 31, 2013

Summary of Significant Accounting Policies

Basis of Presentation and Principles of Consolidation

Basis of Presentation and Principles of Consolidation

Use of Estimates

Use of Estimates

Concentration of Credit and Other Risks

Concentration of Credit and Other Risks

Revenue Recognition

Revenue Recognition

Product Revenue

Service Revenue

Shared ownership program

Other revenue

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

Long-term construction and manufacturing contracts

Loss Per Share

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):

	Three Months Ended						Nine Months Ended
	March 31,						March 31,
	2013			2012			2013			2012
Numerator:
Loss from operations used in computing loss per share from continuing operations	$	(31,203	)	$	(14,785	)	$	(78,646	)	$	(51,337	)
Loss from discontinued operations used in computing loss per share from discontinued operations	$	—		$	(96	)	$	(5,858	)	$	(441	)
Net loss used in computing net loss per share	$	(31,203	)	$	(14,881	)	$	(84,504	)	$	(51,778	)
Denominator:
Weighted average shares used in computing basic loss per share	74,016			71,120			72,953			70,692
Add: Dilutive stock options and awards outstanding	—			—			—			—
Weighted average shares used in computing diluted loss per share	74,016			71,120			72,953			70,692

	As of
	March 31,
	2013	2012
Stock options	5,257	7,925
RSUs, MSUs and PSUs	3,321	2,097
3.75% Convertible Notes	10,560	10,560
3.50% Convertible Notes	21,576	—
	40,714	20,582

Segment Information

Segment Information

	Three Months Ended				Nine Months Ended
	March 31,				March 31,
	2013		2012		2013		2012
Americas	$	28,372	$	46,655	$	99,262	$	149,766
Europe, Middle East, India and Africa	25,290		25,825		78,246		79,770
Asia (excluding Japan)	8,496		17,059		29,154		52,931
Japan	8,389		12,277		24,412		26,223
Total	$	70,547	$	101,816	$	231,074	$	308,690

Recent Accounting Pronouncements

Recent Accounting Pronouncements

- Definition

Disclosure of accounting policy for credit risk.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
-SubTopic 10
-Section 55
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6875567&loc=d3e14489-108613

Reference 2: http://www.xbrl.org/2003/role/presentationRef
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-URI http://asc.fasb.org/extlink&oid=6487554&loc=d3e32600-158583

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-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 15A
-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 113
-Paragraph 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 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Statement of Position (SOP)
-Number 01-6
-Paragraph 14
-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.

+ Details

- Definition

Disclosure of accounting policy regarding (1) the principles it follows in consolidating or combining the separate financial statements, including the principles followed in determining the inclusion or exclusion of subsidiaries or other entities in the consolidated or combined financial statements and (2) its treatment of interests (for example, common stock, a partnership interest or other means of exerting influence) in other entities, for example consolidation or use of the equity or cost methods of accounting. The accounting policy may also address the accounting treatment for intercompany accounts and transactions, noncontrolling interest, and the income statement treatment in consolidation for issuances of stock by a subsidiary.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 810
-SubTopic 10
-URI http://asc.fasb.org/subtopic&trid=2197480

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 860
-SubTopic 40
-Section 45
-URI http://asc.fasb.org/section&trid=2197723

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 323
-SubTopic 10
-URI http://asc.fasb.org/subtopic&trid=2196966

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 325
-SubTopic 20
-URI http://asc.fasb.org/subtopic&trid=2197087

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6367646&loc=d3e18780-107790

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 810
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SX 210.3A-02)
-URI http://asc.fasb.org/extlink&oid=6959686&loc=d3e355033-122828

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 323
-SubTopic 10
-Section 45
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=16385135&loc=d3e33801-111570

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 810
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=18733093&loc=d3e5614-111684

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Interpretation (FIN)
-Number 46R
-Paragraph 4
-Subparagraph c
-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 AICPA
-Name Accounting Principles Board Opinion (APB)
-Number 18
-Paragraph 5, 6, 16-19
-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 Emerging Issues Task Force (EITF)
-Number 96-16
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Interpretation (FIN)
-Number 46R
-Paragraph 4
-Subparagraph 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 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Principles Board Opinion (APB)
-Number 18
-Paragraph 20
-Subparagraph a(2)
-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 Research Bulletin (ARB)
-Number 51
-Paragraph 2-6
-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
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 97-2
-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
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 02
-Paragraph k
-Article 1

Reference 17: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 140
-Paragraph 46
-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 18: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 02, 03
-Article 3A

Reference 19: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Interpretation (FIN)
-Number 46R
-Paragraph 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

- Definition

Disclosure of accounting policy for computing basic and diluted earnings or loss per share for each class of common stock and participating security. Addresses all significant policy factors, including any antidilutive items that have been excluded from the computation and takes into account stock dividends, splits and reverse splits that occur after the balance sheet date of the latest reporting period but before the issuance of the financial statements.

+ References + Details

- Definition

Disclosure of accounting policy for revenue recognition. If the entity has different policies for different types of revenue transactions, the policy for each material type of transaction is generally disclosed. If a sales transaction has multiple element arrangements (for example, delivery of multiple products, services or the rights to use assets) the disclosure may indicate the accounting policy for each unit of accounting as well as how units of accounting are determined and valued. The disclosure may encompass important judgment as to appropriateness of principles related to recognition of revenue. The disclosure also may indicate the entity's treatment of any unearned or deferred revenue that arises from the transaction.

+ References + Details

Summary of Significant Accounting Policies (Tables)

9 Months Ended

Mar. 31, 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):

	Three Months Ended						Nine Months Ended
	March 31,						March 31,
	2013			2012			2013			2012
Numerator:
Loss from operations used in computing loss per share from continuing operations	$	(31,203	)	$	(14,785	)	$	(78,646	)	$	(51,337	)
Loss from discontinued operations used in computing loss per share from discontinued operations	$	—		$	(96	)	$	(5,858	)	$	(441	)
Net loss used in computing net loss per share	$	(31,203	)	$	(14,881	)	$	(84,504	)	$	(51,778	)
Denominator:
Weighted average shares used in computing basic loss per share	74,016			71,120			72,953			70,692
Add: Dilutive stock options and awards outstanding	—			—			—			—
Weighted average shares used in computing diluted loss per share	74,016			71,120			72,953			70,692

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
	March 31,
	2013	2012
Stock options	5,257	7,925
RSUs, MSUs and PSUs	3,321	2,097
3.75% Convertible Notes	10,560	10,560
3.50% Convertible Notes	21,576	—
	40,714	20,582

Schedule of revenue by geographic region

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

	Three Months Ended				Nine Months Ended
	March 31,				March 31,
	2013		2012		2013		2012
Americas	$	28,372	$	46,655	$	99,262	$	149,766
Europe, Middle East, India and Africa	25,290		25,825		78,246		79,770
Asia (excluding Japan)	8,496		17,059		29,154		52,931
Japan	8,389		12,277		24,412		26,223
Total	$	70,547	$	101,816	$	231,074	$	308,690

Balance Sheet Components (Tables)

9 Months Ended

Mar. 31, 2013

Balance Sheet Components

Schedule of accounts receivable, net

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

	March 31,			June 30,
	2013			2012
Accounts receivable	$	54,970		$	69,285
Unbilled fees and services	405			305
	55,375			69,590
Less: Allowance for doubtful accounts	(1,383		)	(1,700		)
Accounts receivable, net	$	53,992		$	67,890

Schedule of inventories

Inventories consisted of the following (in thousands):

	March 31,		June 30,
	2013		2012
Raw materials	$	37,780	$	34,579
Work-in-process	24,729		16,547
Finished goods	29,716		30,567
Inventories	$	92,225	$	81,693

Schedule of property and equipment, net

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

	March 31,			June 30,
	2013			2012
Furniture and fixtures	$	6,495		$	5,921
Computer and office equipment	9,166			9,126
Software	9,420			9,429
Leasehold improvements	19,301			16,065
Machinery and equipment	37,173			33,493
Shared ownership systems	4,979			4,979
Construction in progress	1,241			3,787
	87,775			82,800
Less: Accumulated depreciation	(52,450		)	(45,342		)
Property and equipment, net	$	35,325		$	37,458

Goodwill and Intangible Assets (Tables)

9 Months Ended

Mar. 31, 2013

Goodwill and Intangible Assets

Schedule of activity related to goodwill

Activity related to goodwill consisted of the following (in thousands):

	Nine Months
	Ended		Year Ended
	March 31,		June 30,
	2013		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 at March 31, 2013 and June 30, 2012 are as follows (in thousands):

		March 31, 2013							June 30, 2012
		Gross							Gross
		Carrying		Accumulated			Net		Carrying		Accumulated			Net
	Useful Lives	Amount		Amortization			Amount		Amount		Amortization			Amount
	(in years)
Developed technology	5 - 6	$	48,556	$	(15,096	)	$	33,460	$	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	2,052		(1,410		)	642		1,860		(768		)	1,092
In-process research and development (CPAC)	Indefinite	—		—			—		12,800		—			12,800
		$	61,108	$	(27,006	)	$	34,102	$	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 March 31, 2013 is as follows (in thousands):

Year Ending June 30,	Amount
2013 (remaining 3 months)	$	2,203
2014	8,382
2015	7,953
2016	7,953
2017	7,568
Thereafter	43
	$	34,102

- Definition

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

+ References + Details

Financial Instruments (Tables)

9 Months Ended

Mar. 31, 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 March 31, 2013 and June 30, 2012 (in thousands):

	Fair value measurement using
Type of instrument and line item in condensed consolidated balance sheets	Quoted Prices in Active Markets for Identical Instruments (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Total balance

Assets at March 31, 2013
Money market funds - included in cash and cash equivalents	$	—	$	—	$	—	$	—
Certificate of deposits - included in cash and cash equivalents	$	5,038	$	—	$	—	$	5,038

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

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 March 31, 2013 and June 30, 2012 (in thousands):

	Fair value measurement using
Type of instrument and line item in condensed consolidated balance sheets	Quoted Prices in Active Markets for Identical Instruments (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Total balance

At March 31, 2013
3.75% Convertible Notes - included in long term debt	$	—	$	89,200	$	—	$	89,200
3.50% Convertible Notes - included in long term debt	$	—	$	123,200	$	—	$	123,200

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

Summary of Significant Accounting Policies (Details 3) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012	Feb. 13, 2013	Aug. 02, 2011
Numerator:
Loss from operations used in computing loss per share from continuing operations	$ (31,203)	$ (14,785)	$ (78,646)	$ (51,337)
Loss from discontinued operations used in computing loss per share from discontinued operations		(96)	(5,858)	(441)
Net loss attributable to stockholders	$ (31,203)	$ (14,881)	$ (84,504)	$ (51,778)
Denominator:
Weighted average shares used in computing basic loss per share	74,016	71,120	72,953	70,692
Weighted average shares used in computing diluted loss per share	74,016	71,120	72,953	70,692
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)			40,714	20,582
3.75% Convertible Senior Notes due August 2016
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%		3.75%			3.75%
3.50% Convertible Senior Notes due February 2018
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%		3.50%		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)			3,321	2,097
RSUs, MSUs and PSUs
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)			5,257	7,925

Balance Sheet Components (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Balance Sheet Components (Details) - USD ($) $ in Thousands	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012	Jun. 30, 2012
Accounts receivable, net
Accounts receivable	$ 54,970		$ 54,970		$ 69,285
Unbilled fees and services	405		405		305
Accounts and other receivable, gross	55,375		55,375		69,590
Less: Allowance for doubtful accounts	(1,383)		(1,383)		(1,700)
Accounts receivable, net	53,992		53,992		67,890
Financing receivables
Accounts receivable with contractual maturities of more than one year	3,000		3,000		2,500
Allowance for doubtful financing receivable accounts related to financing receivables	0		0		0
Inventories
Raw materials	37,780		37,780		34,579
Work-in-process	24,729		24,729		16,547
Finished goods	29,716		29,716		30,567
Total inventories	92,225		92,225		81,693
Property and Equipment, net
Property and equipment, gross	87,775		87,775		82,800
Less: Accumulated depreciation and amortization	(52,450)		(52,450)		(45,342)
Property and equipment, net	35,325		35,325		37,458
Depreciation and amortization expense	3,700	$ 4,000	11,600	$ 12,300
Furniture and fixtures
Property and Equipment, net
Property and equipment, gross	6,495		6,495		5,921
Computer and office equipment
Property and Equipment, net
Property and equipment, gross	9,166		9,166		9,126
Software
Property and Equipment, net
Property and equipment, gross	9,420		9,420		9,429
Leasehold improvements
Property and Equipment, net
Property and equipment, gross	19,301		19,301		16,065
Machinery and equipment
Property and Equipment, net
Property and equipment, gross	37,173		37,173		33,493
CyberKnife shared ownership systems
Property and Equipment, net
Property and equipment, gross	4,979		4,979		4,979
Construction in progress
Property and Equipment, net
Property and equipment, gross	$ 1,241		$ 1,241		$ 3,787

Goodwill and Intangible Assets (Details) - USD ($) $ in Thousands	3 Months Ended			9 Months Ended		12 Months Ended
	Mar. 31, 2013	Sep. 30, 2012	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012	Jun. 30, 2012
Changes in the carrying amount of goodwill
Balance at the beginning of the period		$ 59,215		$ 59,215	$ 54,474	$ 54,474
Goodwill resulting from acquisition of TomoTherapy				77
Currency translation and other adjustment				76
Adjustments related to acquisition of TomoTherapy						4,741
Balance at the end of the period	$ 59,368			59,368		59,215
Intangible Assets
Total gross carrying amount	61,108			61,108		68,615
Impairment Charges				12,200
Accumulated Amortization	(27,006)			(27,006)		(18,796)
Net Amount, Finite Lived Intangibles	34,102			34,102
Total net carrying amount	34,102			34,102		49,819
Amortization expense	2,200		$ 4,000	8,200	$ 12,200
Estimated future amortization expense of purchased intangible assets
2013 (remaining three months)	2,203			2,203
2014	8,382			8,382
2015	7,953			7,953
2016	7,953			7,953
2017	7,568			7,568
Thereafter	43			43
Net Amount, Finite Lived Intangibles	34,102			34,102
In-process research and development (CPAC)
Intangible Assets
Gross Carrying Amount, Indefinite Lived Intangibles						12,800
Impairment Charges		$ 12,200
Net Amount, Indefinite Lived Intangibles						12,800
Developed technology
Intangible Assets
Gross Carrying Amount, Finite Lived Intangibles	48,556			48,556		43,455
Accumulated Amortization	(15,096)			(15,096)		(9,161)
Net Amount, Finite Lived Intangibles	33,460			33,460		34,294
Estimated future amortization expense of purchased intangible assets
Net Amount, Finite Lived Intangibles	33,460			$ 33,460		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		10,500
Accumulated Amortization	(10,500)			(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	2,052			2,052		1,860
Accumulated Amortization	(1,410)			(1,410)		(768)
Net Amount, Finite Lived Intangibles	642			642		1,092
Estimated future amortization expense of purchased intangible assets
Net Amount, Finite Lived Intangibles	$ 642			$ 642		$ 1,092
Distributor license \| Minimum
Intangible Assets
Useful Lives				1 year 6 months
Distributor license \| Maximum
Intangible Assets
Useful Lives				2 years 6 months

Commitments and Contingencies (Details 2)		1 Months Ended
Commitments and Contingencies (Details 2)	May 21, 2012	Jun. 30, 2011 claim counts	Apr. 30, 2011 USD ($)	Mar. 31, 2013 USD ($)	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 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

Acquisition (Details) - USD ($) $ in Thousands		9 Months Ended
Acquisition (Details) - USD ($) $ in Thousands	Jul. 16, 2012	Mar. 31, 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
Purchase consideration payable on April 16, 2013		$ 900
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
Amortizable intangible assets - developed technology	5,100
Goodwill	77
Accrued compensation	$ (88)

Debt (Details)		1 Months Ended	3 Months Ended		9 Months Ended
Debt (Details)	Feb. 13, 2013 USD ($)	Aug. 31, 2011 USD ($)	Mar. 31, 2013 USD ($) $ / shares	Mar. 31, 2012 USD ($)	Mar. 31, 2013 USD ($) shares $ / shares	Mar. 31, 2012 USD ($)	Jun. 30, 2012 USD ($)	Aug. 02, 2011 USD ($)
Debt
Proceeds from debt, net of costs					$ 110,462,000	$ 96,100,000
Net carrying amount			$ 197,658,000		$ 197,658,000		$ 79,466,000
3.75% Convertible Senior Notes due August 2016
Debt
Aggregate principal amount of debt issued		$ 100,000,000
Interest rate (as a percent)			3.75%		3.75%			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		$ 1,000
Conversion price (in dollars per share) \| $ / shares			$ 9.47		$ 9.47
Number of consecutive trading days during which the closing price of the entity's common stock must exceed the conversion price for at least 20 days in order for the notes to be convertible into common stock					30 days
Number of consecutive business days immediately after any five consecutive trading day period during the note measurement period					5 days
Number of consecutive trading days before five consecutive business days during the note measurement period					5 days
Number of working days preceding maturity date for delivery of shares or payment of cash					33 days
Repurchase price, as percentage of principal amount, if company undergoes change of control					100.00%
Number of consecutive trading days during which the closing price of the entity's common stock must exceed the conversion price for at least 20 days in order for the notes to be redeemable					30 days
Discount rate on liability component (as a percent)		10.00%
Debt issuance costs and discount allocated to equity conversion component								$ 900,000
Carrying amount of the equity conversion component			$ 23,189,000		$ 23,189,000			24,100,000
Principal amount of the Notes			100,000,000		100,000,000			$ 75,900,000
Unamortized debt discount			(17,342,000)		(17,342,000)
Net carrying amount			82,658,000		$ 82,658,000
Amortization period					40 months
Effective interest rate (as a percent)					10.00%
Interest expense related to contractual interest coupon			1,441,000	$ 937,000	$ 3,316,000	2,500,000
Interest expense related to amortization of debt discount			1,093,000	992,000	3,192,000	2,590,000
Total interest expense recognized			$ 2,534,000	$ 1,929,000	$ 6,508,000	$ 5,090,000
3.75% Convertible Senior Notes due August 2016 \| Minimum
Debt
Number of days within 30 consecutive trading days in which the closing price of the entity's common stock must exceed the conversion price for the notes to be convertible into common stock					20 days
Percentage of the closing sales price of the entity's common stock that the conversion price must exceed in order for the notes to be convertible					130.00%
Percentage of the closing sales price of the entity's common stock that the conversion price must exceed in order for the notes to be redeemable					130.00%
Number of days within 30 consecutive trading days in which the closing price of the entity's common stock must exceed the conversion price for the notes to be redeemable					20 days
3.75% Convertible Senior Notes due August 2016 \| 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 Senior Notes due February 2018
Debt
Aggregate principal amount of debt issued	$ 115,000,000
Interest rate (as a percent)	3.50%		3.50%		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		$ 1,000
Conversion price (in dollars per share) \| $ / shares			$ 5.33		$ 5.33
Repurchase price, as percentage of principal amount, if company undergoes change of control					100.00%

Restructuring Charges (Details) $ in Millions	3 Months Ended		9 Months Ended
Restructuring Charges (Details) $ in Millions	Mar. 31, 2013 USD ($) item	Dec. 31, 2012 USD ($)	Mar. 31, 2013 USD ($)
Restructuring and Severance Charges
Charges for severance and related benefits		$ 2.2
Compensation related expenses \| Minimum
Restructuring and Severance Charges
Expected annualized savings			$ 17.0
Compensation related expenses \| Maximum
Restructuring and Severance Charges
Expected annualized savings			19.0
Reduction in workforce
Restructuring and Severance Charges
Expected reduction of staffing (as a percent)	13.00%
Number of full-time employees eliminated \| item	108
Charges for severance and related benefits	$ 4.9
Restructuring related liabilities	$ 0.2		$ 0.2
Office facility
Restructuring and Severance Charges
Restructuring charges		1.4
Disposition of fixed assets and leasehold improvements
Restructuring and Severance Charges
Restructuring charges		$ 0.3

Investment in CPAC	9 Months Ended
Investment in CPAC	Mar. 31, 2013
Investment in CPAC
Investment in CPAC	9. Investment in CPAC On December 21, 2012, the Company and CPAC entered into a Purchase Agreement and Release (the “Purchase Agreement”), whereby all the equity and debt investments held by the Company in CPAC were purchased by CPAC for a nominal consideration. Additionally, the Company assigned all its rights to the Dielectric Wall Accelerator (“DWA”) technology licensed from Lawrence Livermore National Security, LLC to CPAC. As a result of the Purchase Agreement, the Company has concluded that it is no longer the primary beneficiary of CPAC since it does not have any variable interests in that entity. Accordingly, the Company has deconsolidated CPAC and recorded a loss of $3.4 million during the three months ended December 31, 2012 due to the write-down of the carrying value of CPAC’s net liabilities, the write-off of the 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 during the three and nine months ended March 31, 2013 and 2012 have been disclosed as discontinued operations in the condensed consolidated statements of operations and comprehensive loss.

Restructuring Charges	9 Months Ended
Restructuring Charges	Mar. 31, 2013
Restructuring Charges
Restructuring Charges	10. Restructuring Charges During December 2012, the company vacated an office facility and recorded a charge of $1.4 million in general and administrative expenses during the three months ended December 31, 2012 for the remaining lease obligations on the facility, net of estimated sub-lease income. The company also recorded a change of $0.3 million in general and administrative expenses during the three months ended December 31, 2012 related to the disposition of certain fixed assets and leasehold improvements at this facility. During the three months ended December 31, 2012, the company also recorded severance related charges of $2.2 million in general and administrative expenses due to the departure of Dr. Euan S.Thomson (former Chief Executive Officer), Mr. Chris Raanes (former Chief Operating Officer) and certain other employees. On January 3, 2013, the Company announced a restructuring of operations to focus on improving commercial execution and position the Company to support sustainable revenue growth and profitability. The restructuring is expected to reduce staffing by approximately 13 percent and was heavily concentrated in the United States. During the three months ended March 31, 2013, the Company substantially completed the restructuring exercise, reduced its global workforce under this program by 108 full-time employees and recorded $4.9 million in charges for severance and related benefits for all affected employees. At March 31, 2013, approximately $2.0 million of the restructuring related liabilities were included in accrued compensation in the condensed consolidated balance sheet. The Company does not expect any significant severance-related charges to be incurred during the fourth quarter of fiscal 2013 and expects the remaining activities under this program to be substantially completed by the end of fiscal 2013. The Company expects annualized savings of approximately $17 million to $19 million of compensation related expenses as a result of this restructuring of operations. Restructuring charges are reflected within general and administrative expenses in the condensed consolidated statements of operations and comprehensive loss.

Summary of Significant Accounting Policies (Details 2)	9 Months Ended
Summary of Significant Accounting Policies (Details 2)	Mar. 31, 2013
Revenue recognition
Term of agreements under the shared ownership program	5 years

Financial Instruments (Details) - USD ($) $ in Thousands	Mar. 31, 2013	Feb. 13, 2013	Jun. 30, 2012	Aug. 02, 2011
3.75% Convertible Senior Notes due August 2016
Fair value measurement
Interest rate (as a percent)	3.75%			3.75%
3.50% Convertible Senior Notes due February 2018
Fair value measurement
Interest rate (as a percent)	3.50%	3.50%
Recurring basis \| Quoted Prices in Active Markets for Identical Instruments (Level 1) \| Money market funds
Fair value measurement
Fair value of assets			$ 40,068
Recurring basis \| Quoted Prices in Active Markets for Identical Instruments (Level 1) \| Certificates of deposits
Fair value measurement
Fair value of assets	$ 5,038		6,742
Recurring basis \| Total balance \| Money market funds
Fair value measurement
Fair value of assets			40,068
Recurring basis \| Total balance \| Certificates of deposits
Fair value measurement
Fair value of assets	5,038		6,742
Non-recurring basis \| Significant Other Observable Inputs (Level 2) \| 3.75% Convertible Senior Notes due August 2016
Fair value measurement
Long term debt	89,200		101,400
Non-recurring basis \| Significant Other Observable Inputs (Level 2) \| 3.50% Convertible Senior Notes due February 2018
Fair value measurement
Long term debt	123,200
Non-recurring basis \| Total balance \| 3.75% Convertible Senior Notes due August 2016
Fair value measurement
Long term debt	89,200		$ 101,400
Non-recurring basis \| Total balance \| 3.50% Convertible Senior Notes due February 2018
Fair value measurement
Long term debt	$ 123,200

Share-Based Compensation (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended		12 Months Ended
Share-Based Compensation (Details) - USD ($) $ in Thousands	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012	Jun. 30, 2012
Share-based compensation charges
Share-based compensation expense	$ 2,068	$ 1,745	$ 6,119	$ 6,301
Capitalized share-based compensation costs			600		$ 400
Cost of revenue
Share-based compensation charges
Share-based compensation expense	477	276	1,043	1,271
Selling and marketing
Share-based compensation charges
Share-based compensation expense	256	165	803	545
Research and development
Share-based compensation charges
Share-based compensation expense	462	504	1,455	1,673
General and administrative
Share-based compensation charges
Share-based compensation expense	$ 873	$ 800	$ 2,818	$ 2,812

Summary of Significant Accounting Policies (Details 4) $ in Thousands	3 Months Ended		9 Months Ended
	Mar. 31, 2013 USD ($)	Mar. 31, 2012 USD ($)	Mar. 31, 2013 USD ($) segment	Mar. 31, 2012 USD ($)
Summary of Significant Accounting Policies
Number of operating segments \| segment			1
Revenue by geographic region
Total	$ 70,547	$ 101,816	$ 231,074	$ 308,690
Americas
Revenue by geographic region
Total	28,372	46,655	99,262	149,766
Europe, Middle East, India and Africa
Revenue by geographic region
Total	25,290	25,825	78,246	79,770
Asia (excluding Japan)
Revenue by geographic region
Total	8,496	17,059	29,154	52,931
Japan
Revenue by geographic region
Total	$ 8,389	$ 12,277	$ 24,412	$ 26,223

Commitments and Contingencies (Details) - USD ($) $ in Thousands	Mar. 31, 2013	Feb. 13, 2013	Aug. 02, 2011
Future payments expected for the convertible notes
2013 (remaining 3 months)	$ 1,944
2014	7,775
2015	7,775
2016	7,775
2017	104,338
2018	117,348
Total	$ 246,955
3.75% Convertible Senior Notes due August 2016
Commitments and Contingencies
Interest rate (as a percent)	3.75%		3.75%
3.50% Convertible Senior Notes due February 2018
Commitments and Contingencies
Interest rate (as a percent)	3.50%	3.50%

Share-Based Compensation (Details 2) shares in Millions, $ in Millions	1 Months Ended	9 Months Ended	12 Months Ended
	Oct. 31, 2012	Mar. 31, 2013 USD ($) item shares	Jun. 30, 2012 USD ($) shares
MSU
Performance-Based Awards
Number of awards granted to employees (in shares) \| shares		0.4
Total fair value of awards granted to employees \| $		$ 1.5
Number of measurement periods \| item		2
Weighted average period for recognition of compensation costs		1 year 9 months 18 days
MSU \| Maximum
Performance-Based Awards
Target number of shares that participating executives may earn (as a percent)	150.00%
PSUs
Performance-Based Awards
Number of awards granted to employees (in shares) \| shares			1.0
Total fair value of awards granted to employees \| $			$ 3.9
Number of awards at the end of the period (in shares) \| shares		0.6
Unrecognized compensation cost \| $		$ 0.0

Investment in CPAC (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
Investment in CPAC (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Mar. 31, 2013
Investment in CPAC
Loss on deconsolidation of a consolidated variable interest entity		$ 3,442
CPAC
Investment in CPAC
Loss on deconsolidation of a consolidated variable interest entity	$ 3,400