Accuray (ARAY) 10-Q 8 Nov 13 2014 Q1 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	3 Months Ended
	Sep. 30, 2013	Oct. 25, 2013
Document and Entity Information	'	'
Entity Registrant Name	'ACCURAY INC	'
Entity Central Index Key	'0001138723	'
Document Type	'10-Q	'
Document Period End Date	30-Sep-13	'
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	'	74,872,923
Document Fiscal Year Focus	'2014	'
Document Fiscal Period Focus	'Q1	'

Condensed_Consolidated_Balance

Condensed Consolidated Balance Sheets (USD $)	Sep. 30, 2013	Jun. 30, 2013
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$62,436	$73,313
Short-term investments	99,159	101,084
Restricted cash	2,783	2,728
Accounts receivable, net of allowance for doubtful accounts of $1,958 and $2,160, respectively	60,136	55,458
Inventories	87,989	81,592
Prepaid expenses and other current assets	13,083	12,595
Deferred cost of revenue	8,658	9,165
Total current assets	334,244	335,935
Property and equipment, net	34,728	34,733
Goodwill	58,124	59,368
Intangible assets, net	29,695	31,896
Deferred cost of revenue	3,069	2,149
Other assets	13,301	11,848
Total assets	473,161	475,929
Current liabilities:	'	'
Accounts payable	18,146	15,920
Accrued compensation	15,045	12,461
Other accrued liabilities	21,300	22,893
Customer advances	19,883	17,692
Deferred revenue	88,433	86,893
Total current liabilities	162,807	155,859
Long-term liabilities:	'	'
Long-term other liabilities	5,467	5,382
Deferred revenue	10,305	9,085
Long-term debt	199,916	198,768
Total liabilities	378,495	369,094
Commitment and contingencies (Note 5)	'	'
Stockholders' 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 shares as of September 30, 2013 and June 30, 2013, respectively; issued and outstanding: 74,820,153 and 74,587,231 shares at September 30, 2013 and June 30, 2013, respectively	75	75
Additional paid-in capital	427,433	424,524
Accumulated other comprehensive income	2,337	1,882
Accumulated deficit	-335,179	-319,646
Total stockholders' equity	94,666	106,835
Total liabilities and stockholders' equity	$473,161	$475,929

Condensed_Consolidated_Balance1

Condensed Consolidated Balance Sheets (Parenthetical) (USD $)	Sep. 30, 2013	Jun. 30, 2013
In Thousands, except Share data, unless otherwise specified
Condensed Consolidated Balance Sheets	'	'
Accounts receivable, allowance for doubtful accounts (in dollars)	$1,958	$2,160
Preferred stock, par value (in dollars per share)	$0.00	$0.00
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)	$0.00	$0.00
Common stock, authorized shares	200,000,000	200,000,000
Common stock, issued shares	74,820,153	74,587,231
Common stock, outstanding shares	74,820,153	74,587,231

Condensed_Consolidated_Stateme

Condensed Consolidated Statements of Operations and Comprehensive Loss (USD $)	3 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012
Net revenue:	'	'
Products	$29,568	$40,628
Services	47,073	42,120
Total net revenue	76,641	82,748
Cost of revenue:	'	'
Cost of products	18,601	24,009
Cost of services	31,562	35,063
Total cost of revenue	50,163	59,072
Gross profit	26,478	23,676
Operating expenses:	'	'
Selling and marketing	14,454	12,889
Research and development	12,950	18,574
General and administrative	11,360	12,842
Total operating expenses	38,764	44,305
Loss from operations	-12,286	-20,629
Other expense, net	-2,460	-704
Loss before provision for income taxes	-14,746	-21,333
Provision for income taxes	787	597
Loss from continuing operations	-15,533	-21,930
Loss from discontinued operations (Note 9):	'	'
Loss from operations of a discontinued variable interest entity	'	-2,105
Impairment of indefinite lived intangible asset of discontinued variable interest entity	'	-12,200
Loss from discontinued operations, net of tax of $0	'	-14,305
Loss from discontinued operations attributable to non-controlling interest	'	-12,105
Loss from discontinued operations attributable to stockholders	'	-2,200
Net loss attributable to stockholders	-15,533	-24,130
Loss per share attributable to stockholders	'	'
Basic and diluted - continuing operations (in dollars per share)	($0.21)	($0.31)
Basic and diluted - discontinued operations (in dollars per share)	'	($0.03)
Basic and diluted - net loss (in dollars per share)	($0.21)	($0.34)
Weighted average common shares used in computing loss per share	'	'
Basic and diluted (in shares)	74,700	71,995
Net loss attributable to stockholders	-15,533	-24,130
Foreign currency translation adjustment	165	-535
Unrealized gain on investments, net of tax	290	'
Comprehensive loss	($15,078)	($24,665)

Condensed_Consolidated_Stateme1

Condensed Consolidated Statements of Operations and Comprehensive Loss (Parenthetical) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013
Condensed Consolidated Statements of Operations and Comprehensive Loss	'
Loss from discontinued operations, tax	$0

Condensed_Consolidated_Stateme2

Condensed Consolidated Statements of Cash Flows (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012
Cash Flows From Operating Activities	'	'
Loss from continuing operations	($15,533)	($21,930)
Loss from discontinued operations	'	-14,305
Adjustments to reconcile net loss to net cash used in operating activities	'	'
Depreciation and amortization	5,448	7,827
Impairment of indefinite lived intangible asset	'	12,200
Share-based compensation	2,180	1,755
Amortization and accretion of discount and premium on investments	490	'
Accretion of interest on long-term debt	1,148	1,041
Provision for (recovery of) bad debt	-10	73
Provision for write-down of inventories	790	375
Gain on previously held equity interest in Morphormics	'	-662
Changes in assets and liabilities:	'	'
Restricted cash	'	-1,050
Accounts receivable	-4,000	10,769
Inventories	-6,821	-320
Prepaid expenses and other assets	-1,741	-3,673
Deferred cost of revenue	-405	-322
Accounts payable	2,219	9,805
Accrued liabilities	1,623	-14,872
Customer advances	1,932	2,834
Deferred revenue	1,426	-2,707
Net cash used in operating activities	-11,254	-13,162
Cash Flows From Investing Activities	'	'
Purchases of property and equipment, net	-3,206	-5,319
Purchase of intangible asset	'	-232
Purchases of investments	-5,125	'
Sales and maturities of investments	6,851	'
Acquisition of business, net of cash acquired (Note 6)	'	-3,861
Net cash used in investing activities	-1,480	-9,412
Cash Flows From Financing Activities	'	'
Proceeds from issuance of common stock	629	251
Net cash provided by financing activities	629	251
Effect of exchange rate changes on cash and cash equivalents	1,228	680
Net decrease in cash and cash equivalents	-10,877	-21,643
Cash and cash equivalents at beginning of period	73,313	143,504
Cash and cash equivalents at end of period	$62,436	$121,861

Summary_of_Significant_Account

Summary of Significant Accounting Policies	3 Months Ended
	Sep. 30, 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. The Company conducts its business worldwide. The Company has its headquarters in Sunnyvale, California, with additional locations in other regions in the United States, Europe and Asia.
	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 months ended September 30, 2013 are not necessarily indicative of the results to be expected for the year ending June 30, 2014, for any other interim period or for any future year.
	These condensed consolidated financial statements should be read in conjunction with the Company’s audited consolidated financial statements and accompanying notes for the year ended June 30, 2013 included in the Company’s Annual Report on Form 10-K filed with the SEC. The Company’s significant accounting policies are described in Note 2 to those audited consolidated financial statements.
	Reclassification
	As a result of the deconsolidation of CPAC, the results of operations of CPAC and the losses attributable to the non-controlling interest recorded for the three month period ended September 30, 2012 have been presented as discontinued operations. Accordingly, the Company made reclassifications to its previously reported consolidated statements of operations and comprehensive loss and consolidated statement of cash flows for the three month period ended September 30, 2012.
	Recently Issued Accounting Standards
	In July 2013, the Financial Accounting Standards Board (“FASB”) issued authoritative guidance that requires an entity to present an unrecognized tax benefit, or a portion of an unrecognized tax benefit, in the financial statements as a reduction to a deferred tax asset for a net operating loss carryforward, a similar tax loss, or a tax credit carryforward, except as follows. To the extent a net operating loss carryforward, a similar tax loss, or a tax credit carryforward is not available at the reporting date under the tax law of the applicable jurisdiction to settle any additional income taxes that would result from the disallowance of a tax position or the tax law of the applicable jurisdiction does not require the entity to use, and the entity does not intend to use, the deferred tax asset for such purpose, the unrecognized tax benefit should be presented in the financial statements as a liability and should not be combined with deferred tax assets. The guidance is effective prospectively for fiscal years and interim reporting periods within those years, beginning after December 15, 2013. The Company is currently evaluating the impact of this guidance on our consolidated financial statements.
	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 months ended September 30, 2013 and 2012, there were no customers that represented 10% or more of total net revenue. At September 30, 2013, one customer accounted for 15% of the Company’s total accounts receivable. At June 30, 2013, one customer accounted for 10% of accounts receivable.
	Accounts receivable are typically not collateralized. The Company performs ongoing credit evaluations of its customers and maintains reserves for potential credit losses. Accounts receivable are deemed past due in accordance with the contractual terms of the agreement. Accounts are charged against the allowance for doubtful accounts once collection efforts are unsuccessful. Historically, such losses have been within management’s expectations.
	Single source suppliers presently provide the Company with several components. In most cases, if a supplier was unable to deliver these components, the Company believes that it would be able to find other sources for these components subject to any regulatory qualifications, if required.
	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 (“VSOE”) of fair value of the respective elements, Third-Party Evidence (“TPE”), or Best Estimate of Selling Price (“BESP”), using the relative selling price method.
	Product Revenue
	The majority of product revenue is generated from sales of CyberKnife and TomoTherapy systems. The Company sells its systems with PCS contracts, installation services, training, and at times, professional services. PCS contracts provide planned and corrective maintenance services, software updates, bug fixes, as well as call-center support. If the Company is responsible for installation, the Company recognizes revenue after installation and acceptance of the system. Otherwise, revenue is recognized upon delivery, assuming all other revenue recognition criteria are met.
	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 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.
	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 cost-to-cost 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.
	Net Loss Per Common Share
	Basic and diluted net loss per share is computed by dividing net loss attributable to stockholders by the weighted average number of common shares outstanding during the period.
	A reconciliation of the numerator and denominator used in the calculation of basic and diluted net loss per share attributable to stockholders follows (in thousands):
		Three Months Ended
		September 30,
		2013			2012
	Numerator:
	Loss from operations used in computing loss per share from continuing operations	$	(15,533	)	$	(21,930	)
	Loss from discontinued operations used in computing loss per share from discontinued operations	$	—		$	(2,200	)
	Net loss used in computing net loss per share	$	(15,533	)	$	(24,130	)
	Denominator:
	Weighted average shares used in computing basic and diluted loss per share	74,700			71,995
	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 net loss per share because their effect would have been anti-dilutive. 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 net income per share if their inclusion is dilutive under the if-converted method. For the three months ended September 30, 2013 and 2012, the potential dilutive shares under the Convertible Notes were excluded from the calculation of diluted net loss per share as their inclusion would be anti-dilutive. 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 at
		September 30,
		2013		2012
	Stock options	4,436		7,703
	Restricted Stock Units	3,011		2,007
	3.75% Convertible Notes	10,560		10,560
	3.50% Convertible Notes	21,576		—
		39,583		20,270
	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. 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
		September 30,
		2013			2012
	Americas	$	39,253		$	35,811
	Europe, Middle East, India and Africa	18,766			25,118
	Asia (excluding Japan)	7,299			15,121
	Japan	11,323			6,698
	Total	$	76,641		$	82,748
	Information regarding geographic areas in which the Company has long lived assets (includes all tangible assets) is as follows (in thousands):
		September 30,			June 30,
		2013			2013
Americas	$	31,987		$	31,797
Europe, Middle East, India and Africa	1,373			1,431
Asia (excluding Japan)	463			498
Japan	905			1,007
Total	$	34,728		$	34,733

Balance_Sheet_Components

Balance Sheet Components	3 Months Ended
	Sep. 30, 2013
Balance Sheet Components	'
Balance Sheet Components	'
	2. Balance Sheet Components
	Accounts receivable, net
	Accounts receivable, net consisted of the following (in thousands):
		September 30,			June 30,
		2013			2013
	Accounts receivable	$	61,633		$	56,830
	Unbilled fees and services	461			788
		62,094			57,618
	Less: Allowance for doubtful accounts	(1,958		)	(2,160		)
	Accounts receivable, net	$	60,136		$	55,458
	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, were $4.3 million and $2.9 million at September 30, 2013 and June 30, 2013, 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 September 30, 2013 and June 30, 2013, respectively.
	Inventories
	Inventories consisted of the following (in thousands):
		September 30,			June 30,
		2013			2013
	Raw materials	$	34,215		$	33,721
	Work-in-process	21,421			20,564
	Finished goods	32,353			27,307
	Inventories	$	87,989		$	81,592
	Property and equipment, net
	Property and equipment, net consisted of the following (in thousands):
		September 30,			June 30,
		2013			2013
	Furniture and fixtures	$	6,530		$	6,506
	Computer and office equipment	9,934			9,481
	Software	9,712			9,586
	Leasehold improvements	17,767			19,199
	Machinery and equipment	37,588			37,371
	Shared ownership systems	6,266			4,979
	Construction in progress	4,067			3,084
		91,864			90,206
	Less: Accumulated depreciation	(57,136		)	(55,473		)
	Property and equipment, net	$	34,728		$	34,733
	Depreciation expense related to property and equipment for the three months ended September 30, 2013 and 2012 was $3.2 million and $4.0 million, respectively.

Goodwill_and_Intangible_Assets

Goodwill and Intangible Assets	3 Months Ended
	Sep. 30, 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):
		Three Months
		Ended			Year Ended
		September 30,			June 30,
		2013			2013
	Balance at the beginning of the period	$	59,368		$	59,215
	Addition related to acquisition	—			77
	Currency translation and other adjustments	(1,244		)	76
	Balance at the end of the period	$	58,124		$	59,368
	In connection with the acquisition of TomoTherapy in fiscal year 2011, the Company recognized liabilities related to unrecognized tax benefits as part of purchase accounting. During its first quarter of fiscal year 2014, the Company determined that certain of these liabilities related to unrecognized tax benefits were recorded in error. The Company evaluated the effects of this error on the financial statements and concluded that the error was not material to any prior annual or interim periods or the current period. In September of 2013, the Company reduced goodwill and accrued liabilities by $1.3 million to remove the liability recorded in error.
	Intangible Assets
	The Company’s intangible assets associated with completed acquisitions at September 30, 2013 and June 30, 2013 are as follows (in thousands):
				September 30, 2013								June 30, 2013
				Gross								Gross
				Carrying			Accumulated			Net		Carrying		Accumulated			Net
		Useful Lives		Amount			Amortization			Amount		Amount		Amortization			Amount
		(in years)
	Developed technology	6-May		$	46,747		$	(17,265	)	$	29,482	$	46,747	$	(15,276	)	$	31,471
	Distributor license	1.5 - 2.5			2,043		(1,830		)		213	2,043		(1,618		)	425
				$	48,790		$	(19,095	)	$	29,695	$	48,790	$	(16,894	)	$	31,896
	In the quarter ended September 30, 2012, the Company recorded an impairment charge of $12.2 million relating to the CPAC in-process research and development (“IPR&D”) asset, which was presented as part of loss from discontinued operations (Note 9).
	The Company did not identify any impairment triggers on goodwill or any of its definite intangible and long-lived assets as of September 30, 2013 and June 30, 2013.
	Amortization expense related to intangible assets was $2.2 million and $3.8 million for the three months ended September 30, 2013 and 2012, respectively.
	The estimated future amortization expense of purchased intangible assets as of September 30, 2013 is as follows (in thousands):
	Year Ending June 30,	Amount
	2014 (remaining 9 months)	$	6,178
	2015	7,953
	2016	7,953
	2017	7,568
	2018	43
	Thereafter	—
		$	29,695

Financial_Instruments

Financial Instruments	3 Months Ended
	Sep. 30, 2013
Financial Instruments	'
Financial Instruments	'
	4. Financial Instruments
	The Company considers all highly liquid investments held at major banks, certificates of deposit and other securities with original maturities of three months or less to be cash equivalents.
	The Company classifies all of its investments as available-for-sale at the time of purchase because it is management’s intent that these investments are available for current operations and includes these investments on its balance sheets as short-term investments. Investments with original maturities longer than three months include commercial paper and investment-grade corporate debt securities. Investments classified as available-for-sale are recorded at fair market value with the related unrealized gains and losses included in accumulated other comprehensive income (loss), a component of stockholders’ equity. Realized gains and losses are recorded based on specific identification of each security’s cost basis.
	The Company defines fair value as the price that would be received to sell an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. The fair value hierarchy contains three levels of inputs that may be used to measure fair value, as follows:
	Level 1— Unadjusted quoted prices that are available in active markets for the identical assets or liabilities at the measurement date.
	Level 2— Other observable inputs available at the measurement date, other than quoted prices included in Level 1, either directly or indirectly, including:
	·                  Quoted prices for similar assets or liabilities in active markets;
	·                  Quoted prices for identical or similar assets in non-active markets;
	·                  Inputs other than quoted prices that are observable for the asset or liability; and
	·                  Inputs that are derived principally from or corroborated by other observable market data.
	Level 3— Unobservable inputs that cannot be corroborated by observable market data and reflect the use of significant management judgment. These values are generally determined using pricing models for which the assumptions utilize management’s estimates of market participant assumptions.
	The following tables summarize the amortized cost, gross unrealized gains, gross unrealized losses and fair value by significant investment category for cash, cash equivalents and short-term investments (in thousands):
		September 30, 2013
				Gross		Gross			Estimated Market Value
		Amortized		Unrealized		Unrealized			Cash and Cash		Short-term
		Cost		Gains		Losses			Equivalents		Investments
	Cash	$	50,528	$	—	$	—		$	50,528	$	—
	Level 1
	Certificates of deposit	11,634		—		—			11,634		—
	Money market funds	274		—		—			274		—
		11,908		—		—			11,908		—
	Level 2
	Commercial paper	3,995		1		—			—		3,996
	Corporate notes	95,330		7		(174		)	—		95,163
		99,325		8		(174		)	—		99,159
	Total	$	161,761	$	8	$	(174	)	$	62,436	$	99,159
		June 30, 2013
				Gross		Gross			Estimated Market Value
		Amortized		Unrealized		Unrealized			Cash and Cash		Short-term
		Cost		Gains		Losses			Equivalents		Investments
	Cash	$	60,082	$	—	$	—		$	60,082	$	—
	Level 1
	Certificates of deposit	15,365		—		—			12,758		2,607
	Money market funds	473		—		—			473		—
		15,838		—		—			13,231		2,607
	Level 2
	Commercial paper	3,993		—		(1		)	—		3,992
	Corporate notes	94,941		—		(456		)	—		94,485
		98,934		—		(457		)	—		98,477
	Total	$	174,854	$	—	$	(457	)	$	73,313	$	101,084
	The Company’s Level 2 investments in the table above are classified as Level 2 items because quoted prices in an active market are not readily accessible for those specific financial assets, or the Company may have relied on alternative pricing methods that do not rely exclusively on quoted prices to determine the fair value of the investments.
	The Company had investments that were in an unrealized loss position as of September 30, 2013. The Company determined that (i) it does not have the intent to sell any of these investments and (ii) it is not likely that it will be required to sell any of these investments before recovery of the entire amortized cost basis. The Company reviews its investments to identify and evaluate investments that have an indication of possible impairment. As of September 30, 2013, the Company anticipates that it will recover the entire carrying value of such investments and has determined that no other-than-temporary impairments associated with credit losses were required to be recognized during the three months ended September 30, 2013.
	Contractual maturities of available-for-sale securities at September 30, 2013 were as follows (in thousands):
		September 30, 2013
		Amortized		Fair Value
		Cost
	Due in 1 year or less	$	38,409	$	38,394
	Due in 1-2 years	34,607		34,555
	Due in 2-3 years	26,309		26,210
		$	99,325	$	99,159
	The following table summarizes the carrying values and estimated fair values of our long-term debt (in thousands):
		September 30, 2013				June 30, 2013
		Carrying Value		Fair Value		Carrying Value			Fair Value
	3.75% Convertible Notes	$	84,916	$	104,270	$	83,768		$	96,560
	3.50% Convertible Notes	115,000		174,145		115,000			144,302
	Total	$	199,916	$	278,415	$	198,768		$	240,862
	The 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 an observable quoted price of the Convertible Notes is not readily available.

Commitments_and_Contingencies

Commitments and Contingencies	3 Months Ended
	Sep. 30, 2013
Commitments and Contingencies	'
Commitments and Contingencies	'
	5. Commitments and Contingencies
	The Company’s contractual obligations were presented in the Annual Report on Form 10-K for the previous annual reporting period ended June 30, 2013. There have been no material changes outside of the ordinary course of business in those obligations during the three months ended September 30, 2013.
	Litigation
	From time to time, the Company is involved in legal proceedings arising in the ordinary course of its business. Currently, management believes the Company does not have any probable and estimable losses related to any current legal proceedings and claims that would individually or in the aggregate materially adversely affect its financial condition or operating results. For certain legal proceedings, management believes that there is a reasonable possibility that losses may be incurred. Management currently estimates a range of loss (in excess of amounts accrued) 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 that could have a material impact on its results of operations, financial position and cash flows.
	Best Medical Trade Secret Litigation
	On September 3, 2009, Best Medical International, Inc., or Best Medical, filed a lawsuit against the Company in the U.S. District Court for the Western District of Pennsylvania, claiming that the Company induced certain individuals to leave the employment of Best Medical and join the Company in order to gain access to Best Medical’s confidential information and trade secrets. Best Medical is seeking monetary damages and other relief. On October 25, 2011, the court presiding over the case granted summary judgment in favor of the Company on all counts. On November 21, 2011, Best Medical filed a notice of appeal. On December 22, 2011, the Court awarded attorney fees and costs to the Company and ordered the Company to file an accounting of its fees and costs. Following the filing of the accounting of the Company’s fees and costs, the magistrate judge presiding over the case issued a report on the Company’s accounting and recommended an award to the Company in the amount of $512,090 in attorney fees and costs, which was adopted in its entirety by the district court on September 27, 2013. On July 3, 2013, the Court of Appeals for the Third Circuit issued a briefing schedule for the appeal of this case. Best Medical’s brief was filed on September 16, 2013 and the Company’s brief is due on November 19, 2013.
	Best Medical Patent Litigation
	On August 6, 2010, Best Medical filed an additional lawsuit against the Company in the U.S. District Court for the Western District of Pennsylvania, claiming that the Company has infringed U.S. Patent No. 5,596,619, a patent that Best Medical alleges protects a method and apparatus for conformal radiation therapy. In December 2010, Best Medical amended its complaint by claiming that the Company also infringed U.S. Patent Nos. 6,038,283 and 7,266,175, both of which Best Medical alleges cover methods and apparatus for conformal radiation therapy. In March 2011, the Court dismissed with prejudice all counts against the Company, except for two counts of alleged willful infringement of two of the patents. Following several procedural rulings by the court, Best Medical moved to voluntarily dismiss one of the two remaining patent claims on June 28, 2011, which the court granted on June 30, 2011, leaving only one patent (U.S. Patent No. 6,038,283) at issue in the case. The parties failed to a reach settlement during mandatory settlement conferences held in March and May 2013. Best Medical is seeking declaratory and injunctive relief, as well as unspecified compensatory and treble damages and other relief. The Company will continue to litigate this case, and discovery is expected to be completed by February 2014.
	Rotary Systems
	On April 28, 2011, a former supplier to TomoTherapy, Rotary Systems Incorporated, filed suit in Minnesota state court, Tenth Judicial District, Anoka County, against TomoTherapy alleging misappropriation of trade secrets, as well as several other counts alleging various theories of injury. Rotary Systems alleges TomoTherapy misappropriated Rotary Systems’ trade secrets pertaining to a component previously purchased from Rotary Systems, which component TomoTherapy now purchases from a different supplier. The suit alleges TomoTherapy improperly supplied the alleged trade secrets to its present supplier, Dynamic Sealing Technologies Inc. (also a named defendant in the suit). Rotary Systems has made an unspecified claim for damages of greater than $50,000. TomoTherapy moved to dismiss the case on May 19, 2011, and on August 29, 2011, the court granted the motion to dismiss with respect to all counts other than the count alleging misappropriation of trade secrets. On May 21, 2012, the court granted the Company’s motion for sanctions, in part, and gave Rotary Systems sixty days to identify the alleged trade secrets with specificity or face dismissal of its claim with prejudice. The court held a hearing on September 20, 2012 to review Rotary System’s amended complaint and set a calendar for discovery. The court ruled on the amended complaint, and the parties have started discovery, which was originally expected to be completed by October 2013.  The parties have jointly asked the Court to extend discovery until February 2014.  The Company has filed a motion for summary judgment, but the Court has not yet ruled on the motion.
	Sarif Biomedical Patent Litigation
	On January 28, 2013, Sarif Biomedical filed a patent infringement complaint against the Company in the United States District Court for Delaware. The complaint alleges the Company’s CyberKnife System directly infringes U.S. Patent No. 5,755,725 and seeks unspecified monetary damages for the alleged infringement. Accuray filed an answer to the complaint in March 2013.
	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 September 30, 2013.

Acquisition

Acquisition	3 Months Ended
	Sep. 30, 2013
Acquisition	'
Acquisition	'
	6. Acquisition
	On July 16, 2012, the Company acquired the remaining 90% of the outstanding shares of Morphormics, Inc., or Morphormics, a privately-held developer of medical imaging software based in North Carolina. This acquisition enables the Company to extend auto-contouring capabilities for both the CyberKnife and TomoTherapy systems to improve disease specific workflows. The Company previously held 10% of the outstanding shares of Morphormics, which had a carrying value of zero prior to the acquisition date and was valued at $0.7 million as of the acquisition date based on the fair value of the consideration paid. The acquisition was accounted for as a business combination, and accordingly, Morphormics’ results of operations were included in the consolidated financial statements from July 16, 2012. This transaction was not considered a material business combination, and Company did not incur significant severance or acquisition-related costs in connection with the transaction.
	The fair value of total purchase consideration paid and payable for 100% of Morphormics’ equity interest as of the acquisition date was as follows (in thousands):
	Cash paid and payable	$	5,385
	Fair value of pre-existing investment in Morphormics	662
	Total	$	6,047
	The total purchase price was allocated to the net tangible and intangible assets acquired and liabilities assumed based on their fair values as of the acquisition date as follows (in thousands):
	Cash and cash equivalents	$	668
	Accounts receivable	283
	Other current assets	7
	Amortizable intangible assets - developed technology	5,100
	Goodwill	77
	Accrued compensation	(88		)
	Total purchase price	$	6,047

ShareBased_Compensation

Share-Based Compensation	3 Months Ended
	Sep. 30, 2013
Share-Based Compensation	'
Share-Based Compensation	'
	7. Share-Based Compensation
	The following table summarizes the share-based compensation charges included in the Company’s condensed consolidated statements of operations and comprehensive loss (in thousands):
		Three Months Ended
		September 30,
		2013		2012
	Cost of revenue	$	454	$	247
	Selling and marketing	371		220
	Research and development	478		516
	General and administrative	877		772
		$	2,180	$	1,755

Debt

Debt	3 Months Ended
	Sep. 30, 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, or Rule 144A. The net proceeds from the $100 million offering, after deducting the initial purchaser’s discount and commission and the related offering costs, were approximately $96.1 million. The offering costs and the initial purchaser’s discount and commission (which are recorded in Other Assets) are both being amortized to interest expense using the effective interest method over five years. The 3.75% Convertible Notes bear interest at a rate of 3.75% per year, payable semi-annually in arrears in cash on February 1 and August 1 of each year, beginning on February 1, 2012. The 3.75% Convertible Notes will mature on August 1, 2016, unless earlier repurchased, redeemed or converted.
	The 3.75% Convertible Notes were issued under an Indenture between the Company and The Bank of New York Mellon Trust Company, N.A., as trustee. Holders of the 3.75% Convertible Notes may convert their 3.75% Convertible Notes at any time on or after May 1, 2016 until the close of business on the business day immediately preceding the maturity date. Prior to May 1, 2016, holders of the 3.75% Convertible Notes may convert their 3.75% Convertible Notes only under the following circumstances: (1) during any calendar quarter after the calendar quarter ending September 30, 2011, and only during such calendar quarter, if the closing sale price of the Company’s common stock for each of 20 or more trading days in the 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter exceeds 130% of the conversion price in effect on the last trading day of the immediately preceding calendar quarter; (2) during the five consecutive business days immediately after any five consecutive trading-day period (such five consecutive trading-day period, the “Note Measurement Period”) in which the trading price per $1,000 principal amount of 3.75% Convertible Notes for each trading day of that Note Measurement Period was equal to or less than 98% of the product of the closing sale price of shares of the Company’s common stock and the applicable conversion rate for such trading day; (3) if the Company calls any or all of the 3.75% Convertible Notes for redemption, at any time prior to the close of business on the business day immediately preceding the redemption date; or (4) upon the occurrence of specified corporate transactions as described in the Indenture. Upon conversion by holders of the 3.75% Convertible Notes, the Company will have the right to pay or deliver, as the case may be, cash, shares of common stock of the Company or a combination thereof, at the Company’s election. At any time on or prior to the 33rd business day immediately preceding the maturity date, the Company may irrevocably elect to (a) deliver solely shares of common stock of the Company in respect of the Company’s conversion obligation or (b) pay cash up to the aggregate principal amount of the 3.75% Convertible Notes to be converted and pay or deliver, as the case may be, cash, shares of common stock of the Company or a combination thereof in respect of the remainder, if any, of the Company’s conversion obligation in excess of the aggregate principal amount of the 3.75% Convertible Notes being converted. The initial conversion rate is 105.5548 shares of the Company’s common stock per $1,000 principal amount of 3.75% Convertible Notes (which represents an initial conversion price of approximately $9.47 per share of the Company’s common stock). The conversion rate, and thus the conversion price, are subject to adjustment as further described below.
	Holders of the 3.75% Convertible Notes who convert their 3.75% Convertible Notes in connection with a “make-whole fundamental change,” as defined in the Indenture, may be entitled to a make-whole premium in the form of an increase in the conversion rate. Additionally, in the event of a “fundamental change,” as defined in the Indenture, holders of the 3.75% Convertible Notes may require the Company to purchase all or a portion of their 3.75% Convertible Notes at a fundamental change repurchase price equal to 100% of the principal amount of 3.75% Convertible Notes, plus accrued and unpaid interest, if any, to, but not including, the fundamental change repurchase date.
	On or after August 1, 2014 and prior to the maturity date, the Company may redeem for cash all or a portion of the 3.75% Convertible Notes if the closing sale price of its common stock exceeds 130% of the applicable conversion price (the initial conversion price is approximately $9.47 per share of common stock) of such 3.75% Convertible Notes for at least 20 trading days during any consecutive 30 trading-day period (including the last trading day of such period).
	In accordance with Accounting Standards Codification, or ASC 470-20, Debt with Conversion and Other Options, the Company separately accounts for the liability and equity conversion components of the 3.75% Convertible Notes. The principal amount of the liability component of the 3.75% Convertible Notes was $75.9 million as of the date of issuance based on the present value of its cash flows using a discount rate of 10%, our approximate borrowing rate at the date of the issuance for a similar debt instrument without the conversion feature. The carrying value of the equity conversion component was $24.1 million. A portion of the initial purchaser’s discount and commission and the offering costs totaling $0.9 million was allocated to the equity conversion component. The liability component is being accreted to the principal amount of the 3.75% Convertible Notes using the effective interest method over five years.
	The following table presents the carrying value of the Convertible Notes as of September 30, 2013 (in thousands):
		As at
		September
		30, 2013
	3.75% Convertible Note
	Carrying amount of the equity conversion component	$	23,189
	Principal amount of the 3.75% Convertible Notes	$	100,000
	Unamortized debt discount (1)	(15,084		)
	Net carrying amount	$	84,916
	(1)As of September 30, 2013, the remaining period over which the unamortized debt discount will be amortized is 34 months.
	3.50% Convertible Senior Notes due February 2018
	In February 2013, the Company issued $115.0 million aggregate principal amount of its 3.50% Convertible Notes to certain QIBs. The 3.50% Convertible Notes were offered and sold to the QIBs pursuant to Rule 144A. The net proceeds from the offering, after deducting the initial purchaser’s discount and commission and the related offering costs, were approximately $110.5 million. The offering costs and the initial purchaser’s discount and commission (which are recorded in Other Assets) are both being amortized to interest expense using the effective interest method over five years. The 3.50% Convertible Notes bear interest at a rate of 3.50% per year, payable semi-annually in arrears in cash on February 1 and August 1 of each year, beginning on August 1, 2013. The 3.50% Convertible Notes will mature on February 1, 2018, unless earlier repurchased, redeemed or converted.
	The 3.50% Convertible Notes were issued under an Indenture between the Company and The Bank of New York Mellon Trust Company, N.A., as trustee. Holders of the 3.50% Convertible Notes may convert their 3.50% Convertible Notes at any time until the close of business on the business day immediately preceding the maturity date. The 3.50% Convertible Notes are convertible, as described below, into common stock of Accuray at an initial conversion rate equal to 187.6877 shares of common stock per $1,000 principal amount of the 3.50% Convertible Notes, which is equivalent to a conversion price of approximately $5.33 per share of common stock, subject to adjustment.
	Holders of the 3.50% Convertible Notes who convert their 3.50% Convertible Notes in connection with a “make-whole fundamental change”, as defined in the Indenture, may be entitled to a make-whole premium in the form of an increase in the conversion rate. Additionally, in the event of a “fundamental change,” as defined in the Indenture, holders of the 3.50% Convertible Notes may require the Company to purchase all or a portion of their 3.50% Convertible Notes at a fundamental change repurchase price equal to 100% of the principal amount of 3.50% Convertible Notes, plus accrued and unpaid interest, if any, to, but not including, the fundamental change repurchase date.
	In accordance with guidance in ASC 470-20, Debt with Conversion and Other Options and ASC 815-15, Embedded Derivatives, the Company determined that the embedded conversion components of the 3.50% Convertible Note do not require bifurcation and separate accounting. The $115.0 million principal amount of the 3.50% Convertible Note has been recorded in Long-term Debt on the condensed consolidated balance sheet as of September 30, 2013.
	A summary of interest expense related to the Convertible Notes for the three months ended September 30, 2013 and 2012 was as follows (in thousands):
		Three months ended
		September 30,
		2013			2012
	Interest expense related to contractual interest coupon	$	1,944		$	938
	Interest expense related to amortization of debt discount	1,148			1,041
	Interest expense related to amortization of debt issuance costs	343			111
		$	3,435		$	2,090

Investment_in_CPAC

Investment in CPAC	3 Months Ended
	Sep. 30, 2013
Investment in CPAC	'
Investment in CPAC	'
	9. Investment in CPAC
	In April 2008, TomoTherapy established a new affiliate, CPAC, to develop a compact proton therapy system for the treatment of cancer. Between the date of formation of CPAC through December 2012, the Company and TomoTherapy contributed both cash and intellectual property to CPAC, resulting in a combined equity interest of approximately 15.4% of the outstanding stock of CPAC and approximately 16.3% on a fully diluted basis. As of the Company’s acquisition of TomoTherapy on June 10, 2011, the Company determined that CPAC was a variable interest entity or VIE, as CPAC depended on the Company, TomoTherapy and other investors to fund its operations. Under the accounting standards for consolidating variable interest entities, the consolidating investor is the entity with the power to direct the activities of the venture that most significantly impact the venture’s economic performance and with the obligation to absorb losses or the right to receive benefits from the venture that could potentially be significant to the venture. Although the Company and its subsidiary held less than a 50% ownership interest in CPAC, it was determined that the Company met these two characteristics, and therefore, was the primary beneficiary of CPAC. The Company consolidated the results of operations of CPAC from June 10, 2011 to December 21, 2012.
	On December 21, 2012, the Company and CPAC entered into a Purchase Agreement and Release, or Purchase Agreement, which provided for all the equity and debt investments held by the Company in CPAC to be purchased by CPAC for a nominal consideration. In addition, the Company assigned all its rights to the Dielectric Wall Accelerator, or DWA technology licensed from Lawrence Livermore National Security, LLC to CPAC. As a result of the Purchase Agreement, the Company concluded that it was no longer the primary beneficiary of CPAC since it did not have any variable interest in CPAC. In the second quarter of fiscal 2013, the Company deconsolidated CPAC and recorded a loss of $3.4 million, resulting from the write-down of the carrying value of CPAC’s net liabilities, the write-off of receivables from CPAC and the non-controlling interest in CPAC, net of cash consideration received. The results of operations of CPAC, including the loss on deconsolidation of CPAC and the losses attributable to the non-controlling interest recorded during the three months ended September 30, 2012 have been disclosed as discontinued operations in the condensed consolidated statements of operations and comprehensive loss.

Accumulated_Other_Comprehensiv

Accumulated Other Comprehensive Income	3 Months Ended
	Sep. 30, 2013
Accumulated Other Comprehensive Income	'
Accumulated Other Comprehensive Income	'
	10. Accumulated Other Comprehensive Income
	The components of comprehensive loss consist of net loss, unrealized gains and losses on available-for-sale investments and foreign currency translation. The unrealized gains and losses on available-for-sale investments and foreign currency translation are excluded from earnings and reported as a component of stockholders’ equity. The foreign currency translation adjustment results from those subsidiaries not using the United States dollar as their functional currency since the majority of their economic activities are primarily denominated in their applicable local currency. Accordingly, all assets and liabilities related to these operations are translated at the current exchange rates at the end of each period. The resulting cumulative translation adjustments are recorded directly to the accumulated other comprehensive loss account in stockholders’ equity. Revenues and expenses are translated at average exchange rates in effect during the period.
	The components of accumulated other comprehensive income in the equity section of the balance sheets are as follows (in thousands):
		September 30,			June 30,
		2013			2013
	Net unrealized loss on short-term investments, net of taxes	$	(166	)	$	(457	)
	Cumulative foreign currency translation gain	2,503			2,339
	Accumulated other comprehensive income	$	2,337		$	1,882

Summary_of_Significant_Account1

Summary of Significant Accounting Policies (Policies)	3 Months Ended
	Sep. 30, 2013
Summary of Significant Accounting Policies	'
Basis of Presentation and Principles of Consolidation	'
	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 months ended September 30, 2013 are not necessarily indicative of the results to be expected for the year ending June 30, 2014, for any other interim period or for any future year.
	These condensed consolidated financial statements should be read in conjunction with the Company’s audited consolidated financial statements and accompanying notes for the year ended June 30, 2013 included in the Company’s Annual Report on Form 10-K filed with the SEC. The Company’s significant accounting policies are described in Note 2 to those audited consolidated financial statements.
Reclassification	'
	Reclassification
	As a result of the deconsolidation of CPAC, the results of operations of CPAC and the losses attributable to the non-controlling interest recorded for the three month period ended September 30, 2012 have been presented as discontinued operations. Accordingly, the Company made reclassifications to its previously reported consolidated statements of operations and comprehensive loss and consolidated statement of cash flows for the three month period ended September 30, 2012.
Recently Issued Accounting Standards	'
	Recently Issued Accounting Standards
	In July 2013, the Financial Accounting Standards Board (“FASB”) issued authoritative guidance that requires an entity to present an unrecognized tax benefit, or a portion of an unrecognized tax benefit, in the financial statements as a reduction to a deferred tax asset for a net operating loss carryforward, a similar tax loss, or a tax credit carryforward, except as follows. To the extent a net operating loss carryforward, a similar tax loss, or a tax credit carryforward is not available at the reporting date under the tax law of the applicable jurisdiction to settle any additional income taxes that would result from the disallowance of a tax position or the tax law of the applicable jurisdiction does not require the entity to use, and the entity does not intend to use, the deferred tax asset for such purpose, the unrecognized tax benefit should be presented in the financial statements as a liability and should not be combined with deferred tax assets. The guidance is effective prospectively for fiscal years and interim reporting periods within those years, beginning after December 15, 2013. The Company is currently evaluating the impact of this guidance on our consolidated financial statements.
Use of Estimates	'
	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	'
	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 months ended September 30, 2013 and 2012, there were no customers that represented 10% or more of total net revenue. At September 30, 2013, one customer accounted for 15% of the Company’s total accounts receivable. At June 30, 2013, one customer accounted for 10% of accounts receivable.
	Accounts receivable are typically not collateralized. The Company performs ongoing credit evaluations of its customers and maintains reserves for potential credit losses. Accounts receivable are deemed past due in accordance with the contractual terms of the agreement. Accounts are charged against the allowance for doubtful accounts once collection efforts are unsuccessful. Historically, such losses have been within management’s expectations.
	Single source suppliers presently provide the Company with several components. In most cases, if a supplier was unable to deliver these components, the Company believes that it would be able to find other sources for these components subject to any regulatory qualifications, if required.
Revenue Recognition	'
	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 (“VSOE”) of fair value of the respective elements, Third-Party Evidence (“TPE”), or Best Estimate of Selling Price (“BESP”), using the relative selling price method.
	Product Revenue
	The majority of product revenue is generated from sales of CyberKnife and TomoTherapy systems. The Company sells its systems with PCS contracts, installation services, training, and at times, professional services. PCS contracts provide planned and corrective maintenance services, software updates, bug fixes, as well as call-center support. If the Company is responsible for installation, the Company recognizes revenue after installation and acceptance of the system. Otherwise, revenue is recognized upon delivery, assuming all other revenue recognition criteria are met.
	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 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.
	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 cost-to-cost 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.
Net Loss Per Common Share	'
	Net Loss Per Common Share
	Basic and diluted net loss per share is computed by dividing net loss attributable to stockholders by the weighted average number of common shares outstanding during the period.
	A reconciliation of the numerator and denominator used in the calculation of basic and diluted net loss per share attributable to stockholders follows (in thousands):
		Three Months Ended
		September 30,
		2013			2012
	Numerator:
	Loss from operations used in computing loss per share from continuing operations	$	(15,533	)	$	(21,930	)
	Loss from discontinued operations used in computing loss per share from discontinued operations	$	—		$	(2,200	)
	Net loss used in computing net loss per share	$	(15,533	)	$	(24,130	)
	Denominator:
	Weighted average shares used in computing basic and diluted loss per share	74,700			71,995
	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 net loss per share because their effect would have been anti-dilutive. 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 net income per share if their inclusion is dilutive under the if-converted method. For the three months ended September 30, 2013 and 2012, the potential dilutive shares under the Convertible Notes were excluded from the calculation of diluted net loss per share as their inclusion would be anti-dilutive. 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 at
		September 30,
		2013		2012
	Stock options	4,436		7,703
	Restricted Stock Units	3,011		2,007
	3.75% Convertible Notes	10,560		10,560
	3.50% Convertible Notes	21,576		—
		39,583		20,270
Segment Information	'
	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. 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
		September 30,
		2013			2012
	Americas	$	39,253		$	35,811
	Europe, Middle East, India and Africa	18,766			25,118
	Asia (excluding Japan)	7,299			15,121
	Japan	11,323			6,698
	Total	$	76,641		$	82,748
	Information regarding geographic areas in which the Company has long lived assets (includes all tangible assets) is as follows (in thousands):
		September 30,			June 30,
		2013			2013
	Americas	$	31,987		$	31,797
	Europe, Middle East, India and Africa	1,373			1,431
	Asia (excluding Japan)	463			498
	Japan	905			1,007
	Total	$	34,728		$	34,733

Summary_of_Significant_Account2

Summary of Significant Accounting Policies (Tables)	3 Months Ended
	Sep. 30, 2013
Summary of Significant Accounting Policies	'
Schedule of reconciliation of the numerator and denominator used in the calculation of basic and diluted net loss per share	'
	A reconciliation of the numerator and denominator used in the calculation of basic and diluted net loss per share attributable to stockholders follows (in thousands):
		Three Months Ended
		September 30,
		2013			2012
	Numerator:
	Loss from operations used in computing loss per share from continuing operations	$	(15,533	)	$	(21,930	)
	Loss from discontinued operations used in computing loss per share from discontinued operations	$	—		$	(2,200	)
	Net loss used in computing net loss per share	$	(15,533	)	$	(24,130	)
	Denominator:
	Weighted average shares used in computing basic and diluted loss per share	74,700			71,995
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 at
		September 30,
		2013		2012
	Stock options	4,436		7,703
	Restricted Stock Units	3,011		2,007
	3.75% Convertible Notes	10,560		10,560
	3.50% Convertible Notes	21,576		—
		39,583		20,270
Summary of revenue by geographic region	'
	The following summarizes revenue by geographic region (in thousands):
		Three Months Ended
		September 30,
		2013			2012
	Americas	$	39,253		$	35,811
	Europe, Middle East, India and Africa	18,766			25,118
	Asia (excluding Japan)	7,299			15,121
	Japan	11,323			6,698
	Total	$	76,641		$	82,748
Schedule of geographic areas in which the Company has long lived assets (includes all tangible assets)	'
	Information regarding geographic areas in which the Company has long lived assets (includes all tangible assets) is as follows (in thousands):
		September 30,			June 30,
		2013			2013
	Americas	$	31,987		$	31,797
	Europe, Middle East, India and Africa	1,373			1,431
	Asia (excluding Japan)	463			498
	Japan	905			1,007
	Total	$	34,728		$	34,733

Balance_Sheet_Components_Table

Balance Sheet Components (Tables)	3 Months Ended
	Sep. 30, 2013
Balance Sheet Components	'
Schedule of accounts receivable, net	'
	Accounts receivable, net consisted of the following (in thousands):
		September 30,			June 30,
		2013			2013
	Accounts receivable	$	61,633		$	56,830
	Unbilled fees and services	461			788
		62,094			57,618
	Less: Allowance for doubtful accounts	(1,958		)	(2,160		)
	Accounts receivable, net	$	60,136		$	55,458
Schedule of inventories	'
	Inventories consisted of the following (in thousands):
		September 30,			June 30,
		2013			2013
	Raw materials	$	34,215		$	33,721
	Work-in-process	21,421			20,564
	Finished goods	32,353			27,307
	Inventories	$	87,989		$	81,592
Schedule of property and equipment, net	'
	Property and equipment, net consisted of the following (in thousands):
		September 30,			June 30,
		2013			2013
	Furniture and fixtures	$	6,530		$	6,506
	Computer and office equipment	9,934			9,481
	Software	9,712			9,586
	Leasehold improvements	17,767			19,199
	Machinery and equipment	37,588			37,371
	Shared ownership systems	6,266			4,979
	Construction in progress	4,067			3,084
		91,864			90,206
	Less: Accumulated depreciation	(57,136		)	(55,473		)
	Property and equipment, net	$	34,728		$	34,733

Goodwill_and_Intangible_Assets1

Goodwill and Intangible Assets (Tables)	3 Months Ended
	Sep. 30, 2013
Goodwill and Intangible Assets	'
Schedule of goodwill	'
	Activity related to goodwill consisted of the following (in thousands):
		Three Months
		Ended			Year Ended
		September 30,			June 30,
		2013			2013
	Balance at the beginning of the period	$	59,368		$	59,215
	Addition related to acquisition	—			77
	Currency translation and other adjustments	(1,244		)	76
	Balance at the end of the period	$	58,124		$	59,368
Schedule of intangible assets associated with completed acquisitions	'
	The Company’s intangible assets associated with completed acquisitions at September 30, 2013 and June 30, 2013 are as follows (in thousands):
				September 30, 2013								June 30, 2013
				Gross								Gross
				Carrying			Accumulated			Net		Carrying		Accumulated			Net
		Useful Lives		Amount			Amortization			Amount		Amount		Amortization			Amount
		(in years)
	Developed technology	6-May		$	46,747		$	(17,265	)	$	29,482	$	46,747	$	(15,276	)	$	31,471
	Distributor license	1.5 - 2.5			2,043		(1,830		)		213	2,043		(1,618		)	425
				$	48,790		$	(19,095	)	$	29,695	$	48,790	$	(16,894	)	$	31,896
Schedule of estimated future amortization expense of purchased intangible assets	'
	The estimated future amortization expense of purchased intangible assets as of September 30, 2013 is as follows (in thousands):
	Year Ending June 30,	Amount
	2014 (remaining 9 months)	$	6,178
	2015	7,953
	2016	7,953
	2017	7,568
	2018	43
	Thereafter	—
		$	29,695

Financial_Instruments_Tables

Financial Instruments (Tables)	3 Months Ended
	Sep. 30, 2013
Financial Instruments	'
Summary of amortized cost, gross unrealized gains, gross unrealized losses and fair value by significant investment category for cash, cash equivalents and short-term investments	'
	The following tables summarize the amortized cost, gross unrealized gains, gross unrealized losses and fair value by significant investment category for cash, cash equivalents and short-term investments (in thousands):
		September 30, 2013
				Gross		Gross			Estimated Market Value
		Amortized		Unrealized		Unrealized			Cash and Cash		Short-term
		Cost		Gains		Losses			Equivalents		Investments
	Cash	$	50,528	$	—	$	—		$	50,528	$	—
	Level 1
	Certificates of deposit	11,634		—		—			11,634		—
	Money market funds	274		—		—			274		—
		11,908		—		—			11,908		—
	Level 2
	Commercial paper	3,995		1		—			—		3,996
	Corporate notes	95,330		7		(174		)	—		95,163
		99,325		8		(174		)	—		99,159
	Total	$	161,761	$	8	$	(174	)	$	62,436	$	99,159
		June 30, 2013
				Gross		Gross			Estimated Market Value
		Amortized		Unrealized		Unrealized			Cash and Cash		Short-term
		Cost		Gains		Losses			Equivalents		Investments
	Cash	$	60,082	$	—	$	—		$	60,082	$	—
	Level 1
	Certificates of deposit	15,365		—		—			12,758		2,607
	Money market funds	473		—		—			473		—
		15,838		—		—			13,231		2,607
	Level 2
	Commercial paper	3,993		—		(1		)	—		3,992
	Corporate notes	94,941		—		(456		)	—		94,485
		98,934		—		(457		)	—		98,477
	Total	$	174,854	$	—	$	(457	)	$	73,313	$	101,084
Schedule of contractual maturities of available-for-sale securities	'
	Contractual maturities of available-for-sale securities at September 30, 2013 were as follows (in thousands):
		September 30, 2013
		Amortized		Fair Value
		Cost
	Due in 1 year or less	$	38,409	$	38,394
	Due in 1-2 years	34,607		34,555
	Due in 2-3 years	26,309		26,210
		$	99,325	$	99,159
Schedule of carrying values and estimated fair values of long-term debt that are measured on a non-recurring basis	'
	The following table summarizes the carrying values and estimated fair values of our long-term debt (in thousands):
		September 30, 2013				June 30, 2013
		Carrying Value		Fair Value		Carrying Value			Fair Value
	3.75% Convertible Notes	$	84,916	$	104,270	$	83,768		$	96,560
	3.50% Convertible Notes	115,000		174,145		115,000			144,302
	Total	$	199,916	$	278,415	$	198,768		$	240,862

Acquisition_Tables

Acquisition (Tables)	3 Months Ended
	Sep. 30, 2013
Acquisition	'
Schedule of components of purchase price	'
	The fair value of total purchase consideration paid and payable for 100% of Morphormics’ equity interest as of the acquisition date was as follows (in thousands):
	Cash paid and payable	$	5,385
	Fair value of pre-existing investment in Morphormics	662
	Total	$	6,047
Schedule of identifiable net tangible and intangible assets acquired and liabilities assumed in the acquisition	'
	The total purchase price was allocated to the net tangible and intangible assets acquired and liabilities assumed based on their fair values as of the acquisition date as follows (in thousands):
	Cash and cash equivalents	$	668
	Accounts receivable	283
	Other current assets	7
	Amortizable intangible assets - developed technology	5,100
	Goodwill	77
	Accrued compensation	(88		)
	Total purchase price	$	6,047

ShareBased_Compensation_Tables

Share-Based Compensation (Tables)	3 Months Ended
	Sep. 30, 2013
Share-Based Compensation	'
Summary of share-based compensation charges	'
	The following table summarizes the share-based compensation charges included in the Company’s condensed consolidated statements of operations and comprehensive loss (in thousands):
		Three Months Ended
		September 30,
		2013		2012
	Cost of revenue	$	454	$	247
	Selling and marketing	371		220
	Research and development	478		516
	General and administrative	877		772
		$	2,180	$	1,755

Debt_Tables

Debt (Tables)	3 Months Ended
	Sep. 30, 2013
Debt	'
Schedule of carrying value of the Convertible Notes	'
	The following table presents the carrying value of the Convertible Notes as of September 30, 2013 (in thousands):
		As at
		September
		30, 2013
	3.75% Convertible Note
	Carrying amount of the equity conversion component	$	23,189
	Principal amount of the 3.75% Convertible Notes	$	100,000
	Unamortized debt discount (1)	(15,084		)
	Net carrying amount	$	84,916
	(1)As of September 30, 2013, the remaining period over which the unamortized debt discount will be amortized is 34 months.
Summary of interest expense related to the Convertible Notes	'
	A summary of interest expense related to the Convertible Notes for the three months ended September 30, 2013 and 2012 was as follows (in thousands):
		Three months ended
		September 30,
		2013			2012
	Interest expense related to contractual interest coupon	$	1,944		$	938
	Interest expense related to amortization of debt discount	1,148			1,041
	Interest expense related to amortization of debt issuance costs	343			111
		$	3,435		$	2,090

Accumulated_Other_Comprehensiv1

Accumulated Other Comprehensive Income (Tables)	3 Months Ended
	Sep. 30, 2013
Accumulated Other Comprehensive Income	'
Schedule of accumulated other comprehensive income in the equity section of the balance sheets	'
	The components of accumulated other comprehensive income in the equity section of the balance sheets are as follows (in thousands):
		September 30,			June 30,
		2013			2013
	Net unrealized loss on short-term investments, net of taxes	$	(166	)	$	(457	)
	Cumulative foreign currency translation gain	2,503			2,339
	Accumulated other comprehensive income	$	2,337		$	1,882

Summary_of_Significant_Account3

Summary of Significant Accounting Policies (Details) (Total accounts receivable, Major customers)	3 Months Ended	12 Months Ended
	Sep. 30, 2013	Jun. 30, 2013	Sep. 30, 2013
	Customer concentration risk	Credit concentration risk	Credit concentration risk
		customer	customer
Concentration of Credit Risk and Other Risks and Uncertainties	'	'	'
Number of significant customers	'	1	1
Percentage of concentration risk	15.00%	10.00%	'

Summary_of_Significant_Account4

Summary of Significant Accounting Policies (Details 2)	3 Months Ended
	Sep. 30, 2013
Summary of Significant Accounting Policies	'
Term of agreements under the shared ownership program	'5 years

Summary_of_Significant_Account5

Summary of Significant Accounting Policies (Details 3) (USD $)	3 Months Ended					3 Months Ended		3 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Aug. 02, 2011	Sep. 30, 2013	Feb. 13, 2013	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
			3.75% Convertible Notes	3.75% Convertible Notes	3.75% Convertible Notes	3.50% Convertible Notes	3.50% Convertible Notes	Stock options	Stock options	Restricted Stock Units	Restricted Stock Units
Numerator:	'	'	'	'	'	'	'	'	'	'	'
Loss from operations used in computing loss per share from continuing operations	($15,533)	($21,930)	'	'	'	'	'	'	'	'	'
Loss from discontinued operations used in computing loss per share from discontinued operations	'	-2,200	'	'	'	'	'	'	'	'	'
Net loss attributable to stockholders	($15,533)	($24,130)	'	'	'	'	'	'	'	'	'
Denominator:	'	'	'	'	'	'	'	'	'	'	'
Weighted average shares used in computing basic and diluted loss per share	74,700	71,995	'	'	'	'	'	'	'	'	'
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)	39,583	20,270	10,560	10,560	'	21,576	'	4,436	7,703	3,011	2,007
Interest rate (as a percent)	'	'	'	'	3.75%	'	3.50%	'	'	'	'

Summary_of_Significant_Account6

Summary of Significant Accounting Policies (Details 4) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Jun. 30, 2013
	segment
Summary of Significant Accounting Policies	'	'	'
Number of operating segments	1	'	'
Segment Information	'	'	'
Revenue	$76,641	$82,748	'
Long lived assets	34,728	'	34,733
Americas	'	'	'
Segment Information	'	'	'
Revenue	39,253	35,811	'
Long lived assets	31,987	'	31,797
Europe, Middle East, India and Africa	'	'	'
Segment Information	'	'	'
Revenue	18,766	25,118	'
Long lived assets	1,373	'	1,431
Asia (excluding Japan)	'	'	'
Segment Information	'	'	'
Revenue	7,299	15,121	'
Long lived assets	463	'	498
Japan	'	'	'
Segment Information	'	'	'
Revenue	11,323	6,698	'
Long lived assets	$905	'	$1,007

Balance_Sheet_Components_Detai

Balance Sheet Components (Details) (USD $)	3 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Jun. 30, 2013
Accounts receivable, net	'	'	'
Accounts receivable	$61,633,000	'	$56,830,000
Unbilled fees and services	461,000	'	788,000
Accounts and other receivable, gross	62,094,000	'	57,618,000
Less: Allowance for doubtful accounts	-1,958,000	'	-2,160,000
Accounts receivable, net	60,136,000	'	55,458,000
Financing receivables	'	'	'
Accounts receivable with contractual maturities of more than one year	4,300,000	'	2,900,000
Allowance for doubtful financing receivable accounts related to financing receivables	0	'	0
Inventories	'	'	'
Raw materials	34,215,000	'	33,721,000
Work-in-process	21,421,000	'	20,564,000
Finished goods	32,353,000	'	27,307,000
Total inventories	87,989,000	'	81,592,000
Property and Equipment, net	'	'	'
Property and equipment, gross	91,864,000	'	90,206,000
Less: Accumulated depreciation and amortization	-57,136,000	'	-55,473,000
Property and equipment, net	34,728,000	'	34,733,000
Depreciation and amortization expense	3,200,000	4,000,000	'
Furniture and fixtures	'	'	'
Property and Equipment, net	'	'	'
Property and equipment, gross	6,530,000	'	6,506,000
Computer and office equipment	'	'	'
Property and Equipment, net	'	'	'
Property and equipment, gross	9,934,000	'	9,481,000
Software	'	'	'
Property and Equipment, net	'	'	'
Property and equipment, gross	9,712,000	'	9,586,000
Leasehold improvements	'	'	'
Property and Equipment, net	'	'	'
Property and equipment, gross	17,767,000	'	19,199,000
Machinery and equipment	'	'	'
Property and Equipment, net	'	'	'
Property and equipment, gross	37,588,000	'	37,371,000
Shared ownership systems	'	'	'
Property and Equipment, net	'	'	'
Property and equipment, gross	6,266,000	'	4,979,000
Construction in progress	'	'	'
Property and Equipment, net	'	'	'
Property and equipment, gross	$4,067,000	'	$3,084,000

Goodwill_and_Intangible_Assets2

Goodwill and Intangible Assets (Details) (USD $)	3 Months Ended		12 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Jun. 30, 2013
Changes in the carrying amount of goodwill	'	'	'
Balance at the beginning of the period	$59,368,000	$59,215,000	$59,215,000
Addition related to acquisition	'	'	77,000
Currency translation and other adjustment	-1,244,000	'	76,000
Balance at the end of the period	58,124,000	'	59,368,000
Intangible Assets	'	'	'
Goodwill	58,124,000	'	59,368,000
Total gross carrying amount	48,790,000	'	48,790,000
Impairment charge recorded due to a decrease in projected future usage of the technology	'	12,200,000	'
Accumulated Amortization	-19,095,000	'	-16,894,000
Net Amount, Finite Lived Intangibles	29,695,000	'	31,896,000
Amortization expense	2,200,000	3,800,000	'
Estimated future amortization expense of purchased intangible assets	'	'	'
2014 (remaining 9 months)	6,178,000	'	'
2015	7,953,000	'	'
2016	7,953,000	'	'
2017	7,568,000	'	'
2018	43,000	'	'
Net Amount, Finite Lived Intangibles	29,695,000	'	31,896,000
TomoTherapy | Liabilities related to unrecognized tax	'	'	'
Changes in the carrying amount of goodwill	'	'	'
Balance at the end of the period	1,300,000	'	'
Intangible Assets	'	'	'
Goodwill	1,300,000	'	'
Accrued liabilities	1,300,000	'	'
IPR&D technology carried out by CPAC	'	'	'
Intangible Assets	'	'	'
Impairment charge recorded due to a decrease in projected future usage of the technology	'	12,200,000	'
Developed technology	'	'	'
Intangible Assets	'	'	'
Gross Carrying Amount, Finite Lived Intangibles	46,747,000	'	46,747,000
Accumulated Amortization	-17,265,000	'	-15,276,000
Net Amount, Finite Lived Intangibles	29,482,000	'	31,471,000
Estimated future amortization expense of purchased intangible assets	'	'	'
Net Amount, Finite Lived Intangibles	29,482,000	'	31,471,000
Developed technology | Minimum	'	'	'
Intangible Assets	'	'	'
Useful Lives	'5 years	'	'
Developed technology | Maximum	'	'	'
Intangible Assets	'	'	'
Useful Lives	'6 years	'	'
Distributor license	'	'	'
Intangible Assets	'	'	'
Gross Carrying Amount, Finite Lived Intangibles	2,043,000	'	2,043,000
Accumulated Amortization	-1,830,000	'	-1,618,000
Net Amount, Finite Lived Intangibles	213,000	'	425,000
Estimated future amortization expense of purchased intangible assets	'	'	'
Net Amount, Finite Lived Intangibles	$213,000	'	$425,000
Distributor license | Minimum	'	'	'
Intangible Assets	'	'	'
Useful Lives	'1 year 6 months	'	'
Distributor license | Maximum	'	'	'
Intangible Assets	'	'	'
Useful Lives	'2 years 6 months	'	'

Financial_Instruments_Details

Financial Instruments (Details) (USD $)	3 Months Ended
	Sep. 30, 2013	Jun. 30, 2013	Sep. 30, 2012	Jun. 30, 2012
Cash, cash equivalents and short-term investments	'	'	'	'
Cash	$50,528,000	$60,082,000	'	'
Amortized Cost	99,325,000	'	'	'
Gross Unrealized Gains	8,000	'	'	'
Gross Unrealized Losses	-174,000	-457,000	'	'
Total Amortized Cost	161,761,000	174,854,000	'	'
Cash and Cash Equivalents	62,436,000	73,313,000	121,861,000	143,504,000
Short-term Investments	99,159,000	101,084,000	'	'
Other-than-temporary impairments associated with credit losses	0	'	'	'
Amortized Cost	'	'	'	'
Due in 1 year or less	38,409,000	'	'	'
Due in 1-2 years	34,607,000	'	'	'
Due in 2-3 years	26,309,000	'	'	'
Amortized cost	99,325,000	'	'	'
Fair Value	'	'	'	'
Due in 1 year or less	38,394,000	'	'	'
Due in 1-2 years	34,555,000	'	'	'
Due in 2-3 years	26,210,000	'	'	'
Fair value	99,159,000	'	'	'
Level 1	'	'	'	'
Cash, cash equivalents and short-term investments	'	'	'	'
Cash Equivalents	11,908,000	13,231,000	'	'
Cash Equivalents and Short-term Investments including Available-for-sale Securities	'	15,838,000	'	'
Available-for-sale Securities	'	2,607,000	'	'
Level 1 | Certificates of deposits	'	'	'	'
Cash, cash equivalents and short-term investments	'	'	'	'
Cash Equivalents	11,634,000	12,758,000	'	'
Cash Equivalents and Short-term Investments including Available-for-sale Securities	'	15,365,000	'	'
Available-for-sale Securities	'	2,607,000	'	'
Level 1 | Money market funds	'	'	'	'
Cash, cash equivalents and short-term investments	'	'	'	'
Cash Equivalents	274,000	473,000	'	'
Level 2	'	'	'	'
Cash, cash equivalents and short-term investments	'	'	'	'
Amortized Cost	99,325,000	98,934,000	'	'
Gross Unrealized Gains	8,000	'	'	'
Gross Unrealized Losses	-174,000	-457,000	'	'
Available-for-sale Securities	99,159,000	98,477,000	'	'
Amortized Cost	'	'	'	'
Amortized cost	99,325,000	98,934,000	'	'
Level 2 | Commercial paper	'	'	'	'
Cash, cash equivalents and short-term investments	'	'	'	'
Amortized Cost	3,995,000	3,993,000	'	'
Gross Unrealized Gains	1,000	'	'	'
Gross Unrealized Losses	'	-1,000	'	'
Available-for-sale Securities	3,996,000	3,992,000	'	'
Amortized Cost	'	'	'	'
Amortized cost	3,995,000	3,993,000	'	'
Level 2 | Corporate notes	'	'	'	'
Cash, cash equivalents and short-term investments	'	'	'	'
Amortized Cost	95,330,000	94,941,000	'	'
Gross Unrealized Gains	7,000	'	'	'
Gross Unrealized Losses	-174,000	-456,000	'	'
Available-for-sale Securities	95,163,000	94,485,000	'	'
Amortized Cost	'	'	'	'
Amortized cost	$95,330,000	$94,941,000	'	'

Financial_Instruments_Details_

Financial Instruments (Details 2) (USD $)

Aug. 02, 2011

Feb. 13, 2013

Sep. 30, 2013

Jun. 30, 2013

Sep. 30, 2013

Jun. 30, 2013

Sep. 30, 2013

Jun. 30, 2013

Sep. 30, 2013

Jun. 30, 2013

Sep. 30, 2013

Jun. 30, 2013

Sep. 30, 2013

Jun. 30, 2013

In Thousands, unless otherwise specified

3.75% Convertible Notes

3.50% Convertible Notes

Non-recurring basis

Non-recurring basis

Non-recurring basis

Non-recurring basis

Non-recurring basis

Non-recurring basis

Non-recurring basis

Non-recurring basis

Non-recurring basis

Non-recurring basis

Non-recurring basis

Non-recurring basis

Carrying Value

Carrying Value

Carrying Value

Carrying Value

Carrying Value

Carrying Value

Fair Value

Fair Value

Fair Value

Fair Value

Fair Value

Fair Value

3.75% Convertible Notes

3.75% Convertible Notes

3.50% Convertible Notes

3.50% Convertible Notes

3.75% Convertible Notes

3.75% Convertible Notes

3.50% Convertible Notes

3.50% Convertible Notes

Fair value measurement

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Long term debt

'

'

$199,916

$198,768

$84,916

$83,768

$115,000

$115,000

$278,415

$240,862

$104,270

$96,560

$174,145

$144,302

Interest rate (as a percent)

3.75%

3.50%

'

'

3.75%

3.75%

3.50%

3.50%

'

'

3.75%

3.75%

3.50%

3.50%

Commitments_and_Contingencies_

Commitments and Contingencies (Details) (USD $)	Sep. 30, 2013	Sep. 27, 2013	Jun. 30, 2011	Mar. 31, 2011	21-May-12	Apr. 30, 2011
		Best Medical Trade Secret Litigation	Best Medical Patent Litigation	Best Medical Patent Litigation	Rotary Systems	Rotary Systems
			claim	counts		Minimum
			counts	patent
Contingencies	'	'	'	'	'	'
Estimated loss, low end range	$0	'	'	'	'	'
Estimated loss, high end range	3,000,000	'	'	'	'	'
Attorney fees and costs receivable	'	512,090	'	'	'	'
Number of counts of alleged willful infringement of patents	'	'	'	2	'	'
Number of patents against which lawsuit is not dismissed	'	'	1	2	'	'
Number of patent claims dismissed	'	'	1	'	'	'
Claim for damages	'	'	'	'	'	$50,000
Period to identify alleged trade secrets with specificity or face dismissal of claim with prejudice	'	'	'	'	'60 days	'

Acquisition_Details

Acquisition (Details) (USD $)	3 Months Ended	0 Months Ended
	Sep. 30, 2012	Jul. 16, 2012	Jun. 30, 2012
		Morphormics	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	'	$700,000	$0
Total acquired equity interest (as a percent)	'	100.00%	'
Purchase price	'	'	'
Cash paid and payable	'	5,385,000	'
Fair value of pre-existing investment in Morphormics	662,000	662,000	'
Total purchase price	'	6,047,000	'
Purchase price allocation	'	'	'
Cash and cash equivalents	'	668,000	'
Accounts receivable	'	283,000	'
Other current assets	'	7,000	'
Amortizable intangible assets - developed technology	'	5,100,000	'
Goodwill	'	77,000	'
Accrued compensation	'	-88,000	'
Total purchase price	'	$6,047,000	'

ShareBased_Compensation_Detail

Share-Based Compensation (Details) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012
Share-based compensation charges	'	'
Share-based compensation expense	$2,180	$1,755
Cost of revenue	'	'
Share-based compensation charges	'	'
Share-based compensation expense	454	247
Selling and marketing	'	'
Share-based compensation charges	'	'
Share-based compensation expense	371	220
Research and development	'	'
Share-based compensation charges	'	'
Share-based compensation expense	478	516
General and administrative	'	'
Share-based compensation charges	'	'
Share-based compensation expense	$877	$772

Debt_Details

Debt (Details) (USD $)	Sep. 30, 2013	Jun. 30, 2013	Sep. 30, 2013	Sep. 30, 2012	Aug. 02, 2011	Sep. 30, 2013	Sep. 30, 2013	Sep. 30, 2013	Feb. 13, 2013	Sep. 30, 2013
			3.75% Convertible Note and 3.50% Convertible Note	3.75% Convertible Note and 3.50% Convertible Note	3.75% Convertible Notes	3.75% Convertible Notes	3.75% Convertible Notes	3.75% Convertible Notes	3.50% Convertible Notes	3.50% Convertible Notes
							Minimum	Maximum
Debt	'	'	'	'	'	'	'	'	'	'
Aggregate principal amount of debt issued	'	'	'	'	$100,000,000	'	'	'	$115,000,000	'
Interest rate (as a percent)	'	'	'	'	3.75%	'	'	'	3.50%	'
Proceeds from debt, net of costs	'	'	'	'	96,100,000	'	'	'	110,500,000	'
Debt issuance costs, amortization period	'	'	'	'	'5 years	'	'	'	'5 years	'
Conversion rate, number of shares to be issued per $1000 of principal amount (in shares)	'	'	'	'	'	105.5548	'	'	'	187.6877
Principal amount used for debt instrument conversion ratio	'	'	'	'	'	1,000	'	'	'	1,000
Conversion price (in dollars per share)	'	'	'	'	'	$9.47	'	'	'	$5.33
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	'	'	'
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	'	'	'	'
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%	'	'	'
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	'	'	'	'
Percentage of the trading price to the product of the sale price of the entity's common stock and the conversion rate	'	'	'	'	'	'	'	98.00%	'	'
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%	'	'	'	100.00%
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	'	'	'
Number of consecutive trading days during which the closing price of the entity's common stock must exceed the conversion price for at least 20 days in order for the notes to be redeemable	'	'	'	'	'	'30 days	'	'	'	'
Discount rate on liability component (as a percent)	'	'	'	'	10.00%	'	'	'	'	'
Debt issuance costs and discount allocated to equity conversion component	'	'	'	'	900,000	'	'	'	'	'
Carrying amount of the equity conversion component	'	'	'	'	24,100,000	23,189,000	'	'	'	'
Principal amount of the Notes	'	'	'	'	75,900,000	100,000,000	'	'	'	'
Unamortized debt discount	'	'	'	'	'	-15,084,000	'	'	'	'
Net carrying amount	199,916,000	198,768,000	'	'	'	84,916,000	'	'	'	'
Amortization period	'	'	'	'	'	'34 months	'	'	'	'
Interest expense related to contractual interest coupon	'	'	1,944,000	938,000	'	'	'	'	'	'
Interest expense related to amortization of debt discount	'	'	1,148,000	1,041,000	'	'	'	'	'	'
Interest expense related to amortization of debt issuance costs	'	'	343,000	111,000	'	'	'	'	'	'
Total interest expense recognized	'	'	$3,435,000	$2,090,000	'	'	'	'	'	'

Investment_in_CPAC_Details

Investment in CPAC (Details) (CPAC, USD $)	3 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2012	Sep. 30, 2012
CPAC	'	'
Investment in CPAC	'	'
Ownership interest (as a percent)	'	15.40%
Ownership interest on fully diluted basis (as a percent)	'	16.30%
Loss on deconsolidation of a consolidated variable interest entity	$3.40	'

Accumulated_Other_Comprehensiv2

Accumulated Other Comprehensive Income (Details) (USD $)	Sep. 30, 2013	Jun. 30, 2013
In Thousands, unless otherwise specified
Accumulated Other Comprehensive Income	'	'
Net unrealized loss on short-term investments, net of taxes	($166)	($457)
Cumulative foreign currency translation gain	2,503	2,339
Accumulated other comprehensive income	$2,337	$1,882