Azenta (AZTA) 10-Q 4 Aug 17 2017 Q3 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	9 Months Ended
	Jun. 30, 2017	Jul. 27, 2017
Document and Entity Information [Abstract]
Trading Symbol	BRKS
Entity Registrant Name	BROOKS AUTOMATION INC
Entity Central Index Key	933,974
Current Fiscal Year End Date	--09-30
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Document Type	10-Q
Document Period End Date	Jun. 30, 2017
Document Fiscal Year Focus	2,017
Document Fiscal Period Focus	Q3
Amendment Flag	false
Entity Common Stock, Shares Outstanding		69,759,300

CONSOLIDATED BALANCE SHEETS (un

CONSOLIDATED BALANCE SHEETS (unaudited) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Current assets
Cash and cash equivalents	$ 117,081	$ 85,086
Marketable securities	12	39
Accounts receivable, net	120,752	106,372
Inventories	105,304	92,572
Prepaid expenses and other current assets	22,215	15,265
Total current assets	365,364	299,334
Property, plant and equipment, net	52,949	54,885
Long-term marketable securities	2,565	6,096
Long-term deferred tax assets	1,460	1,982
Goodwill	210,609	202,138
Intangible assets, net	75,458	81,843
Equity method investments	32,628	27,273
Other assets	5,738	12,354
Total assets	746,771	685,905
Current liabilities
Accounts payable	49,991	41,128
Deferred revenue	33,062	14,966
Accrued warranty and retrofit costs	7,646	6,324
Accrued compensation and benefits	21,718	21,254
Accrued restructuring costs	1,690	5,939
Accrued income taxes payable	10,466	7,554
Accrued expenses and other current liabilities	20,686	22,628
Total current liabilities	145,259	119,793
Long-term tax reserves	1,782	2,681
Long-term deferred tax liabilities	2,950	2,913
Long-term pension liabilities	2,469	2,557
Other long-term liabilities	4,539	4,271
Total liabilities	156,999	132,215
Commitments and contingencies (Note 18)
Stockholders' Equity
Preferred stock, $0.01 par value- 1,000,000 shares authorized, no shares issued or outstanding	0	0
Common stock, $0.01 par value- 125,000,000 shares authorized, 83,216,169 shares issued and 69,754,300 shares outstanding at June 30, 2017, 82,220,270 shares issued and 68,758,401 shares outstanding at September 30, 2016	832	821
Additional paid-in capital	1,867,645	1,855,703
Accumulated other comprehensive income	15,000	15,166
Treasury stock, at cost- 13,461,869 shares	(200,956)	(200,956)
Accumulated deficit	(1,092,749)	(1,117,044)
Total stockholders' equity	589,772	553,690
Total liabilities and stockholders' equity	$ 746,771	$ 685,905

CONSOLIDATED BALANCE SHEETS (u3

CONSOLIDATED BALANCE SHEETS (unaudited) (Parenthetical) - $ / shares	Jun. 30, 2017	Sep. 30, 2016
Statement of Financial Position [Abstract]
Preferred stock, par value (USD per share)	$ 0.01	$ 0.01
Preferred stock, shares authorized	1,000,000	1,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (USD per share)	$ 0.01	$ 0.01
Common stock, shares authorized	125,000,000	125,000,000
Common stock, shares issued	83,216,169	82,220,270
Common stock, shares outstanding	69,754,300	68,758,401
Treasury stock, shares	13,461,869	13,461,869

CONSOLIDATED STATEMENTS OF OPER

CONSOLIDATED STATEMENTS OF OPERATIONS (unaudited) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Revenue
Product	$ 141,957	$ 111,596	$ 396,684	$ 302,238
Services	39,760	35,938	114,321	100,532
Total revenue	181,717	147,534	511,005	402,770
Cost of revenue
Products	85,658	69,557	243,360	192,816
Services	24,487	23,814	74,606	68,437
Total cost of revenue	110,145	93,371	317,966	261,253
Gross profit	71,572	54,163	193,039	141,517
Operating expenses
Research and development	11,958	12,819	34,148	39,208
Selling, general and administrative	40,016	31,854	109,496	98,667
Restructuring charges	828	996	2,663	9,807
Total operating expenses	52,802	45,669	146,307	147,682
Operating income (loss)	18,770	8,494	46,732	(6,165)
Interest income	137	55	432	310
Interest expense	(93)	(37)	(286)	(56)
Gain on settlement of equity method investment			1,847
Other loss, net	(314)	(107)	(848)	(289)
Income (loss) before income taxes and earnings of equity method investments	18,500	8,405	47,877	(6,200)
Income tax provision	3,680	220	9,900	75,070
Income (loss) before equity in earnings of equity method investments	14,820	8,185	37,977	(81,270)
Equity in earnings of equity method investments	2,530	379	7,249	1,248
Net income (loss)	$ 17,350	$ 8,564	$ 45,226	$ (80,022)
Basic net income (loss) per share (in dollars per share)	$ 0.25	$ 0.12	$ 0.65	$ (1.17)
Diluted net income (loss) per share (in dollars per share)	0.25	0.12	0.64	(1.17)
Dividend declared per share (in dollars per share)	$ 0.10	$ 0.10	$ 0.30	$ 0.30
Weighted-average shares used in computing net income (loss) per share:
Basic (shares)	69,711	68,628	69,496	68,437
Diluted (shares)	70,405	69,166	70,198	68,437

CONSOLIDATED STATEMENTS OF COMP

CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) (unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Statement of Comprehensive Income [Abstract]
Net income (loss)	$ 17,350	$ 8,564	$ 45,226	$ (80,022)
Other comprehensive income (loss), net of tax:
Cumulative foreign currency translation adjustments	4,592	1,766	(164)	6,793
Unrealized gains (losses) on marketable securities, net of tax effects of $0 during each of the three and nine months ended June 30, 2017, and $0 and ($58) during the three and nine months ended June 30, 2016	4	11	2	(92)
Actuarial gains (losses), net of tax effects of $0 and $5 during the three and nine months ended June 30, 2017, $1 and $0 during the three and nine months ended June 30, 2016	2	(1)	(4)	2
Total other comprehensive income (loss), net of tax	4,598	1,776	(166)	6,703
Comprehensive income (loss)	$ 21,948	$ 10,340	$ 45,060	$ (73,319)

CONSOLIDATED STATEMENTS OF COM6

CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) (unaudited) (Parenthetical) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Statement of Comprehensive Income [Abstract]
Unrealized gains (losses) on marketable securities, tax	$ 0	$ 0	$ 0	$ (58)
Actuarial (loss) gain, tax	$ 0	$ 1	$ 5	$ 0

CONSOLIDATED STATEMENTS OF CASH

CONSOLIDATED STATEMENTS OF CASH FLOWS (unaudited) - USD ($) $ in Thousands	9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Cash flows from operating activities
Net income (loss)	$ 45,226	$ (80,022)
Adjustments to reconcile net income (loss) to net cash provided by operating activities:
Depreciation and amortization	20,649	21,320
Gain on settlement of equity method investment	(1,847)
Stock-based compensation	11,081	8,206
Amortization of premium on marketable securities and deferred financing costs	24	368
Undistributed earnings of equity method investments	(7,249)	(1,248)
Deferred income tax provision	498	71,875
Gain on disposal of long-lived assets	(106)
Changes in operating assets and liabilities, net of acquisitions:
Accounts receivable	(14,644)	2,862
Inventories	(12,851)	2,110
Prepaid expenses and other current assets	(6,076)	(3,909)
Accounts payable	9,470	(4,689)
Deferred revenue	17,875	7,171
Accrued warranty and retrofit costs	1,299	(87)
Accrued compensation and tax withholdings	279	(6,558)
Accrued restructuring costs	(4,201)	3,720
Accrued expenses and other current liabilities	1,954	(5,010)
Net cash provided by operating activities	61,381	16,109
Cash flows from investing activities
Purchases of property, plant and equipment	(6,827)	(9,414)
Purchases of technology intangibles	(240)
Purchases of marketable securities		(12,901)
Sales and maturities of marketable securities	3,590	139,388
Disbursement for a loan receivable		(1,491)
Acquisitions, net of cash acquired	(5,346)	(125,498)
Purchases of other investments	(170)	(500)
Net cash used in investing activities	(8,993)	(10,416)
Cash flows from financing activities
Proceeds from issuance of common stock	960	948
Payment of deferred financing costs	(27)	(508)
Common stock dividends paid	(20,932)	(20,613)
Net cash used in financing activities	(19,999)	(20,173)
Effects of exchange rate changes on cash and cash equivalents	(394)	(126)
Net increase (decrease) in cash and cash equivalents	31,995	(14,606)
Cash and cash equivalents, beginning of period	85,086	80,722
Cash and cash equivalents, end of period	117,081	66,116
Supplemental disclosure of non-cash investing and financing activities:
Purchases of property, plant and equipment included in accounts payable	1,009	$ 1,245
Fair value of non-cash consideration for the acquisition of Cool Lab, LLC	$ 10,348

Basis of Presentation

Basis of Presentation	9 Months Ended
	Jun. 30, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Basis of Presentation	1. Basis of Presentation The unaudited consolidated financial statements of Brooks Automation, Inc. and its subsidiaries (“Brooks”, or the “Company”) included herein have been prepared in accordance with accounting principles generally accepted in the United States ("GAAP"). All intercompany accounts and transactions have been eliminated in consolidation. In the opinion of management, all material adjustments, which are of a normal and recurring nature and necessary for a fair statement of the financial position and results of operations and cash flows for the periods presented, have been reflected in the accompanying unaudited consolidated financial statements. The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the full fiscal year. Certain information and footnote disclosures normally included in the Company’s annual consolidated financial statements have been condensed or omitted and, accordingly, the accompanying financial information should be read in conjunction with the audited consolidated financial statements and notes thereto contained on the Company’s Annual Report on Form 10‑K filed with the United States Securities and Exchange Commission (the “SEC”) for the fiscal year ended September 30, 2016 (the "2016 Annual Report on Form 10‑K"). The accompanying Consolidated Balance Sheet as of September 30, 2016 was derived from the audited annual consolidated financial statements as of the period then ended.

Summary of Significant Accounti

Summary of Significant Accounting Policies	9 Months Ended
	Jun. 30, 2017
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies Foreign Currency Translation Certain transactions of the Company and its subsidiaries are denominated in currencies other than their functional currency. Foreign currency exchange losses generated from the settlement and remeasurement of these transactions are recognized in earnings and presented within “Other loss, net” in the Company’s unaudited Consolidated Statements of Operations. Net foreign currency transaction and remeasurement losses totaled $0.7 million and $0.5 million, respectively, during the three months ended June 30, 2017 and 2016 and $1.6 million and $1.5 million, respectively, during the nine months ended June 30, 2017 and 2016. Use of Estimates The preparation of unaudited consolidated financial statements in conformity with GAAP requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the unaudited consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Significant estimates are associated with accounts receivable, inventories, goodwill, intangible assets other than goodwill, long-lived assets, derivative financial instruments, deferred income taxes, warranty obligations, revenue recognized using the percentage of completion method, pension obligations and stock-based compensation expense. The Company bases its estimates on historical experience and various other assumptions, including in certain circumstances, future projections that management believes to be reasonable under the circumstances. Although the Company regularly assesses these estimates, actual results could differ from those estimates. Changes in estimates are recorded in the period in which they occur and become known. Recently Issued Accounting Pronouncements In January 2017, the Financial Accounting Standards Board (the "FASB") issued an amendment to the accounting guidance related to goodwill impairment testing which eliminates the requirement to calculate the fair value of individual assets and liabilities of a reporting unit to measure goodwill impairment. In accordance with the provisions of the newly issued guidance, an entity should perform its goodwill impairment test by comparing the fair value of the reporting unit with its carrying value and recognize an impairment charge for the amount by which the carrying amount exceeds the reporting unit’s fair value, up to the amount of goodwill allocated to that reporting unit. The guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2019 and should be adopted prospectively. Early adoption of the newly issued guidance is permitted for interim or annual goodwill impairment tests performed after January 1, 2017. The Company performs its annual goodwill impairment assessment on April 1 st of each fiscal year. The Company adopted the guidance during the third quarter of fiscal year 2017. The adoption of the guidance did not have an impact on the Company’s financial position or results of operations. No triggering events indicating goodwill impairment occurred during the three and nine months ended June 30, 2017. Please refer to Note 5, “Goodwill and Intangible Assets” for further discussion. In January 2017, the FASB issued an amendment to the accounting guidance on business combinations to clarify the definition of a business when assessing whether a set of transferred assets and activities represents a business. Such set of transferred assets and activities does not represent a business if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or a group of similar identifiable assets. If the threshold is not met, entities need to evaluate whether the set of assets and activities meets the requirement that a business includes, at a minimum, an input and a substantive process that together significantly contribute to the ability to create outputs. The guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2017 and should be adopted prospectively. Early adoption of the newly issued guidance is permitted. The Company is currently evaluating the impact of this guidance on its financial position and results of operations. In February 2016, the FASB issued new accounting guidance for reporting lease transactions. In accordance with the provisions of the newly issued guidance, a lessee should recognize at the inception of the arrangement a right-of-use asset and a corresponding lease liability initially measured at the present value of lease payments over the lease term. For finance leases, interest on a lease liability should be recognized separately from the amortization of the right-of-use asset, while for operating leases, total lease costs are recorded on a straight-line basis over the lease term. For leases with a term of twelve months or less, a lessee is permitted to make an accounting policy election by class of underlying assets to forgo a recognition of right-of-use assets and corresponding lease liabilities and record a lease expense on a straight-line basis. Entities should determine at the inception of the arrangement whether a contract represents a lease or contains a lease which is defined as a right to control the use of identified property for a period of time in exchange for consideration. Additionally, entities should separate the lease components from the non-lease components and allocate the contract consideration on a relative standalone price basis in accordance with provisions of ASC Topic 606, Revenue from Contracts with Customers . The guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2018 and should be adopted via a modified retrospective approach with certain optional practical expedients that entities may elect to apply. The Company expects to adopt the guidance during the first quarter of fiscal year 2020 and is currently evaluating the impact of this guidance on its financial position and results of operations. In June 2016, the FASB issued new accounting guidance for reporting credit losses. The new guidance introduces a new "expected loss" impairment model that applies to most financial assets measured at amortized cost and certain other instruments, including trade and other receivables, loans, held-to-maturity debt securities and other financial assets. Entities are required to estimate expected credit losses over the life of financial assets and record an allowance against the assets’ amortized cost basis to present them at the amount expected to be collected. Additionally, the guidance amends the impairment model for available for sale debt securities and requires entities to determine whether all or a portion of the unrealized loss on such debt security is a credit loss. The guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2019. Early adoption of the newly issued guidance is permitted for fiscal years, and interim periods within those years, beginning after December 15, 2018. The standard should be applied as a cumulative-effect adjustment to retained earnings as of the beginning of the first reporting period in which the guidance is effective. The Company expects to adopt the guidance during the first quarter of fiscal year 2021 and is currently evaluating the impact of this guidance on its financial position and results of operations. In February 2015, the FASB issued an amendment to the accounting guidance for consolidations of financial statements by changing the analysis that a reporting entity must perform to determine whether it should consolidate certain types of variable interest entities. The guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2015. The guidance can be adopted either via a full retrospective approach or a modified retrospective approach by recording a cumulative-effect adjustment to beginning equity in the period of adoption. The Company adopted the guidance during the first quarter of fiscal year 2017. The adoption of the guidance did not have an impact on the Company’s financial position or results of operations. Please refer to Note 9, "Other Balance Sheet Information" for further discussion. In August 2014, the FASB issued new accounting guidance related to evaluation of relevant conditions or events that raise substantial doubt about the entity’s ability to continue as a going concern within one year after the financial statements issuance date. The guidance is effective for fiscal years ending after December 15, 2016, and for annual periods and interim periods thereafter. The Company expects to adopt the guidance during the fourth quarter of fiscal year 2017. Early adoption of the newly issued guidance is permitted. The adoption of the guidance is not expected to have an impact on the Company’s financial position or results of operations. In May 2014, the FASB issued new accounting guidance for reporting revenue recognition. The guidance provides for the recognition of revenue when promised goods or services are transferred to customers in an amount that reflects the consideration that is expected to be received for those goods or services. A five-step process set forth in the guidance may require more judgment and estimation within the revenue recognition process than the current GAAP, including identifying performance obligations in the contract, estimating the amount of variable consideration to include in the transaction price and allocating the transaction price to each separate performance obligation. The guidance was initially effective for fiscal years, and interim periods within those years, beginning after December 15, 2016. In August 2015, the FASB issued an amendment deferring the effective date of the guidance by one year. The guidance should be adopted retrospectively either for each reporting period presented or via recognizing the cumulative effect at the date of the initial application. Early adoption is permitted only as of annual reporting periods, including the interim periods, beginning after December 15, 2016. The Company expects to adopt the guidance during the first quarter of fiscal year 2019. The Company has initiated the evaluation of the potential impact of adopting the new guidance on its financial position and results of operations, but has not yet completed such assessment or determined the transition method that will be used to adopt the new guidance. Other For further information with regard to the Company’s Significant Accounting Policies, please refer to Note 2 "Summary of Significant Accounting Policies" to the Company’s consolidated financial statements included in the 2016 Annual Report on Form 10‑K.

Marketable Securities

Marketable Securities	9 Months Ended
	Jun. 30, 2017
Investments, Debt and Equity Securities [Abstract]
Marketable Securities	3. Marketable Securities The Company invests in marketable securities that are classified as available-for-sale and records them at fair value in the Company’s unaudited Consolidated Balance Sheets. Marketable securities reported as current assets represent investments that mature within one year from the balance sheet date. Long-term marketable securities represent investments with maturity dates greater than one year from the balance sheet date. Unrealized gains and losses are excluded from earnings and reported as a separate component of accumulated other comprehensive income until the security is sold or matures. Gains or losses realized from sales of marketable securities are computed based on the specific identification method and recognized as a component of "Other loss, net" in the accompanying unaudited Consolidated Statements of Operations. During the three and nine months ended June 30, 2017, the Company sold marketable securities with a fair value and amortized cost of $3.6 million each and recognized net losses of less than $0.1 million. The Company collected cash proceeds of $3.5 million from the sale of marketable securities and reclassified net unrealized holding losses of less than $0.1 million from accumulated other comprehensive income into "Other loss, net" in the accompanying unaudited Consolidated Statements of Operations as a result of these transactions. There were no sales of marketable securities during the three months ended June 30, 2016. During the nine months ended June 30, 2016, the Company sold marketable securities with a fair value of $127.6 million and amortized cost of $127.7 million and recognized net losses of $0.2 million. Gross gains reported as a component of net losses recognized on the sale of marketable securities were insignificant during the nine months ended June 30, 2016. The Company collected cash proceeds of $127.0 million from the sale of marketable securities and reclassified net unrealized holding losses of $0.2 million from accumulated other comprehensive income into "Other loss, net" in the accompanying unaudited Consolidated Statements of Operations as a result of these transactions. There were no unrealized losses on available for sale securities presented as a component of accumulated other comprehensive income at June 30, 2017. Unrealized losses on available for sale securities presented as a component of accumulated other comprehensive income were insignificant at September 30, 2016. The following is a summary of the amortized cost and the fair value, including accrued interest receivable, as well as unrealized holding gains (losses) on the short-term and long-term marketable securities as of June 30, 2017 and September 30, 2016 (in thousands): Gross Gross Amortized Unrealized Unrealized Cost Gains Losses Fair Value June 30, 2017 : Corporate securities $ 2,565 $ — $ — $ 2,565 Other debt securities 12 — — 12 $ 2,577 $ — $ — $ 2,577 September 30, 2016 : Corporate securities $ 2,394 $ — $ — $ 2,394 Other debt securities 39 — — 39 Municipal securities 3,704 1 (3) 3,702 $ 6,137 $ 1 $ (3) $ 6,135 The fair values of the marketable securities by contractual maturities at June 30, 2017 are presented below (in thousands): Fair Value Due in one year or less $ 12 Due after ten years 2,565 Total marketable securities $ 2,577 Expected maturities could differ from contractual maturities because the security issuers may have the right to prepay obligations without prepayment penalties. The Company reviews the marketable securities for impairment at each reporting period to determine if any of the securities have experienced an other-than-temporary decline in fair value. The Company considers factors, such as the length of time and extent to which the market value has been less than the cost, the financial condition and near-term prospects of the issuer, the Company’s intent to sell, or whether it is more likely than not it will be required to sell the investment before recovery of its amortized cost basis. If the Company believes that an other-than-temporary decline in fair value has occurred, it writes down the investment to fair value and recognizes the credit loss in earnings and the non-credit loss in accumulated other comprehensive income. There were no marketable securities in unrealized loss position as of June 30, 2017. As of September 30, 2016, aggregate fair value of the marketable securities in an unrealized loss position was $2.5 million and was comprised entirely of municipal securities. Aggregate unrealized losses for these securities were insignificant as of September 30, 2016 and are presented in the table above. These securities were not considered other-than-temporarily impaired and, as such, the Company did not recognize impairment losses during the period then ended. The unrealized losses were attributable to changes in interest rates that impacted the value of the investments.

Acquisitions

Acquisitions	9 Months Ended
	Jun. 30, 2017
Business Combinations [Abstract]
Acquisitions	4. Acquisitions Acquisitions Completed in Fiscal Year 2017 Acquisition of Cool Lab, LLC On November 28, 2016, the Company acquired 100% of the equity of Cool Lab, LLC ("Cool Lab") from BioCision, LLC ("BioCision"). The Company held a 20% equity ownership interest in BioCision prior to the acquisition. Cool Lab was established as a subsidiary of BioCision on November 28, 2016 upon a transfer of certain assets related to cell cryopreservation solutions with net carrying values of $0.9 million. Cool Lab provides a range of patented and/or patent-pending offerings for sample cooling and freezing, controlled rate freezing, portable cryogenic transport and archival storage solutions for customers with temperature-sensitive workflow process. Cool Lab’s offerings assist in managing the temperature stability of therapeutics, biological samples, and related biomaterials in ultra-cold and cryogenic environments. The acquisition of Cool Lab is expected to allow the Company to extend its comprehensive sample management solutions across the cold chain of custody, which is consistent with the other offerings it brings to its life sciences customers. Please refer to Note 6, "Equity Method Investments" for further information on the equity interest in BioCision held by the Company immediately before the acquisition date. The aggregate purchase price of $15.2 million consisted of a cash payment of $4.8 million, a liability to the seller of $0.1 million and the settlement of certain preexisting relationships with Cool Lab and BioCision, disclosed as non-cash consideration of $10.3 million, which has been measured at fair value on the acquisition date. The non-cash consideration of $10.3 million consisted of financial instruments of BioCision held by the Company prior to the acquisition of Cool Lab that were subsequently measured at fair value on the acquisition date and delineated as non-cash consideration paid for Cool Lab. Such non-cash consideration was comprised of: (i) the redeemable fair value of the Company’s existing 20% equity ownership interest in BioCision of $3.1 million, (ii) convertible debt securities of BioCision and warrants of $5.6 million to purchase BioCision’s preferred units, and (iii) term notes of BioCision of $1.6 million including accrued interest. Such pre-acquisition financial instruments had an aggregate carrying value of $8.6 million and were measured at an aggregated fair value of $10.3 million on the acquisition date. As a result of such measurement, the Company recognized a net gain of $1.6 million in its unaudited Consolidated Statements of Operations during the nine months ended June 30, 2017. Please refer to Note 6, "Equity Method Investments" and Note 17, "Fair Value Measurements" for further information on the financial instruments included in the non-cash consideration and the valuation techniques and inputs used in fair value measurements. The Company used a market participant approach to record the assets acquired and liabilities assumed in the Cool Lab acquisition. The purchase price allocation is based on a preliminary valuation and subject to further adjustments within the measurement period as additional information becomes available related to the fair value of such assets acquired and liabilities assumed. The fair values of intangible assets acquired and residual goodwill were preliminary as of June 30, 2017. The Company will refine such fair value estimates as new information becomes available during the measurement period. Any adjustments to the purchase price allocation will be made as soon as practicable but no later than one year from the acquisition date. The preliminary amounts recorded were as follows (in thousands): Fair Value of Assets Liabilities Inventory $ 1,283 Intangible assets 6,100 Goodwill 8,527 Accrued liabilities (30) Other liabilities (686) Total purchase price $ 15,194 Fair values of intangible assets acquired consisted of: (i) a customer relationship intangible asset of $3.6 million attributable to a certain customer, (ii) completed technology of $1.2 million and (iii) other customer relationship intangible assets of $1.3 million. The Company used the income approach in accordance with the excess-earnings method to estimate the fair value of customer relationship intangible assets which is equal to the present value of the after-tax cash flows attributable to the intangible asset only. The Company used the income approach in accordance with the relief-from-royalty method to estimate the fair value of the completed technology which is equal to the present value of the after-tax royalty savings attributable to owning that intangible asset. The weighted average amortization periods for intangible assets acquired are 3 years for the customer relationship intangible asset attributable to a certain customer, 8 years for completed technology and 10 years for other customer relationship intangible assets. The intangible assets acquired are amortized over the total weighted average period of 5.5 years using methods that approximate the pattern in which the economic benefits are expected to be realized, including percentage of revenue expected to be generated from sales to a certain customer over the contract term. Goodwill represents the excess of the consideration transferred over the fair value of the net assets acquired and has been assigned to the Brooks Life Science Systems segment. Goodwill is primarily the result of expected synergies from combining the operations of Cool Lab with the Company’s operations and is deductible for tax purposes. The Company recorded a liability of $0.7 million in the purchase price allocation that represented a preacquisition contingency incurred on the acquisition date. The obligation is related to a rebate that is due to a particular customer if the annual product sales volume metrics exceed threshold amounts under the provisions of the contract assumed by the Company. Fair value of such liability was determined based on a probability weighted discounted cash flow model. The carrying amount of the liability was $0.7 million at June 30, 2017. Additionally, the Company recognized a customer relationship intangible asset of $3.6 million related to this arrangement, as discussed above. The operating results of Cool Lab have been reflected in the results of operations for the Brooks Life Science Systems segment from the date of the acquisition, which included approximately one month of activity during the first quarter of fiscal year 2017. During the three months ended June 30, 2017, revenue and net loss from Cool Lab recognized in the Company’s results of operations were $1.1 million and less than $0.1 million, respectively. During the nine months ended June 30, 2017, revenue and net loss from Cool Lab recognized in the Company’s results of operations were $2.5 million and $0.3 million, respectively. During the three and nine months ended June 30, 2017, the net loss included charges of $0.1 million and $0.4 million, respectively, related to the step-up in value of the acquired inventories and amortization expense $0.4 million and $0.8 million, respectively, related to acquired intangible assets. During the three and nine months ended June 30, 2017, the Company incurred $0.1 million and $0.4 million, respectively, in non-recurring transaction costs with respect to the Cool Lab acquisition which were recorded in "Selling, general and administrative" expenses within the accompanying unaudited Consolidated Statements of Operations. The Company did not present a pro forma information summary for its consolidated results of operations for the three and nine months ended June 30, 2017 and 2016 as if the acquisition of Cool Lab occurred on October 1, 2015 because such results were immaterial. Acquisitions Completed in Fiscal Year 2016 Acquisition of BioStorage Technologies, Inc. On November 30, 2015, the Company completed its acquisition of BioStorage Technologies, Inc., or BioStorage, an Indiana-based global provider of comprehensive sample management and integrated cold chain solutions for the biosciences industry. These solutions include collection, transportation, processing, storage, protection, retrieval and disposal of biological samples. These solutions combined with the Company’s existing offerings, particularly automation for sample storage and formatting, provide customers with fully integrated sample management cold chain solutions which will help them increase productivity, efficiencies and speed to market. This acquisition will allow the Company to access a broader customer base that is storing samples at ultra cold temperatures and simultaneously provide opportunities for BioStorage to use the Company’s capabilities to expand into new markets. Please refer to Note 4, "Acquisitions" to the Company’s consolidated financial statements included in the 2016 Annual Report on Form 10‑K for further information on this transaction. At the closing of the acquisition of BioStorage, a cash payment of $5.4 million was placed into escrow which consisted of $2.9 million ascribed to the purchase price and $2.5 million related to retention arrangements with certain employees. The escrow balance was reduced by its full amount subsequent to the acquisition date, and there was no escrow balance outstanding as of June 30, 2017. The operating results of BioStorage have been reflected in the results of operations for the Brooks Life Science Systems segment from the date of the acquisition, which included one month of activity during the first quarter of fiscal year 2016. During the three months ended June 30, 2017, revenue and net income from BioStorage recognized in the Company’s results of operations were $15.3 million and $2.4 million, respectively. During the three months ended June 30, 2016, revenue and net income from BioStorage recognized in the Company’s results of operations were $12.4 million and $1.1 million, respectively. During the nine months ended June 30, 2017, revenue and net income from BioStorage recognized in the Company’s results of operations were $46.0 million and $6.0 million, respectively. During the nine months ended June 30, 2016, revenue and net income from BioStorage recognized in the Company’s results of operations were $30.3 million and $0.3 million, respectively. During the three and nine months ended June 30, 2017, the net income included amortization expense of $1.1 million and $3.4 million, respectively, related to acquired intangible assets. During the three and nine months ended June 30, 2016, the net income included amortization expense of $0.9 million and $2.0 million, respectively, related to acquired intangible assets. During each of the three months ended June 30, 2017 and 2016, the Company incurred $0.1 million in non-recurring transaction costs with respect to the BioStorage acquisition which were recorded in "Selling, general and administrative" expenses within the unaudited Consolidated Statements of Operations. The Company incurred $0.2 million and $3.2 million, respectively, of such costs during the nine months ended June 30, 2017 and 2016. The retention payment of $2.5 million was recorded within prepaid expenses and other current assets at the acquisition date and is recognized as compensation expense over the service period or upon a triggering event in the underlying change in control agreements. The Company recorded $0.1 million of compensation expense related to this arrangement during the nine months ended June 30, 2017 and $0.3 million and $0.7 million, respectively, during the three and nine months ended June 30, 2016. There were no such charges recorded during the three months ended June 30, 2017. The retention payment balance was $0.1 million at September 30, 2016. There was no balance related to the retention payment at June 30, 2017. The following unaudited pro forma financial information represents a summary of the consolidated results of operations for the Company and BioStorage for the three and nine months ended June 30, 2016 as if the acquisition of BioStorage occurred on October 1, 2014 (in thousands): Three Months Ended Nine Months Ended June 30, 2016 June 30, 2016 Revenue $ 147,534 $ 413,816 Net income (loss) 9,163 (74,024) Basic income (loss) per share $ 0.13 $ (1.08) Diluted income (loss) per share $ 0.13 $ (1.08) Weighted average shares outstanding used in computing net income (loss) per share: Basic 68,628 68,437 Diluted 69,166 68,437 The unaudited pro forma information presented above reflects historical operating results of the Company and BioStorage and includes the impact of certain adjustments directly attributable to the business combination. The unaudited pro forma financial information is presented for informational purposes only and is not necessarily indicative of the results of operations that would have been achieved if the acquisition of BioStorage had taken place on October 1, 2014. During the nine months ended June 30, 2016, the adjustments reflected in the unaudited proforma information included aggregate amortization and depreciation expense of $0.6 million and tax effects of $0.5 million. The impact of the restructuring charges and transaction costs was excluded from the pro forma net income (loss) during the three and nine months ended June 30, 2016. The Company did not present unaudited pro forma financial information for the three and nine months ended June 30, 2017 since the results of BioStorage were included in the Company’s consolidated results of operations during the periods then ended.

Goodwill and Intangible Assets

Goodwill and Intangible Assets	9 Months Ended
	Jun. 30, 2017
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill and Intangible Assets	5. Goodwill and Intangible Assets Goodwill represents the excess of net book value over the estimated fair value of net tangible and identifiable intangible assets of a reporting unit. Goodwill is tested for impairment annually or more often if impairment indicators are present at the reporting unit level. If the existence of events or circumstances indicates that it is more likely than not that fair values of the reporting units are below their carrying values, the Company performs additional impairment tests during interim periods to evaluate goodwill for impairment. No triggering events indicating goodwill impairment occurred during the three and nine months ended June 30, 2017. The Company performs its annual goodwill impairment assessment on April 1 st of each fiscal year. During the three months ended June 30, 2017, the Company adopted on a prospective basis the Accounting Standard Update 2017-04, Intangibles- Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment issued by the FASB as a part of simplification initiative. The adoption of the guidance is expected to reduce the cost and complexity of evaluating goodwill for impairment and did not have an impact on the Company’s financial position or results of operations during the three and nine months ended June 30, 2017. In accordance with provisions of the guidance, the Company initially assesses q ualitative factors to determine whether the existence of events or circumstances indicates that it is more likely than not that the fair value of a reporting unit is less than its carrying value. If the Company determines, based on this assessment, that it is more likely than not that the fair value of the reporting unit is less than its carrying value, it performs a quantitative goodwill impairment test by comparing the reporting unit’s fair value with its carrying value. An impairment loss is recognized for the amount by which the reporting unit’s carrying value exceeds its fair value, up to the total amount of goodwill allocated to the reporting unit. No impairment loss is recognized if the fair value of the reporting exceeds its carrying value As of June 30, 2017, the Company completed the annual goodwill impairment test for its five reporting units and determined that no adjustment to goodwill was necessary. The Company conducted a qualitative assessment for three reporting units within the Brooks Semiconductor Solutions Group segment and determined that it was not likely that their fair values were less than their carrying values. As a result of the analysis, the Company did not perform the quantitative assessment for these reporting units and did not recognize impairment losses. The Company also performed the quantitative goodwill impairment test for the fourth reporting unit within the Brooks Semiconductor Solutions Group segment and for the Brooks Life Science Systems reporting unit. The Company determined that no adjustment to goodwill was necessary for these two reporting units since their fair values substantially exceeded their respective carrying values. If events occur or circumstances change that would more likely than not reduce the fair value of any reporting unit below its carrying value, the Company will evaluate such reporting unit’s goodwill for impairment between annual tests. The components of the Company’s goodwill by an operating segment at June 30, 2017 and September 30, 2016 are as follows (in thousands): Brooks Semiconductor Brooks Solutions Life Science Group Systems Other Total Gross goodwill, at September 30, 2016 $ 655,781 $ 135,301 $ 26,014 $ 817,096 Accumulated goodwill impairments (588,944) — (26,014) (614,958) Goodwill, net of accumulated impairments, at September 30, 2016 66,837 135,301 — 202,138 Acquisitions and adjustments (56) 8,527 — 8,471 Gross goodwill, at June 30, 2017 655,725 143,828 26,014 825,567 Accumulated goodwill impairments (588,944) — (26,014) (614,958) Goodwill, net of accumulated impairments, at June 30, 2017 $ 66,781 $ 143,828 $ — $ 210,609 During the nine months ended June 30, 2017, the Company recorded a goodwill increase of $8.5 million primarily related to the acquisition of Cool Lab which represented the excess of the consideration transferred over the fair value of the net assets acquired. Please refer to the Note 4 "Acquisitions" for further information on this transaction. The components of the Company’s identifiable intangible assets as of June 30, 2017 and September 30, 2016 are as follows (in thousands): June 30, 2017 September 30, 2016 Accumulated Net Book Accumulated Net Book Cost Amortization Value Cost Amortization Value Patents $ 9,028 $ 7,724 $ 1,304 $ 7,808 $ 7,486 $ 322 Completed technology 60,745 53,931 6,814 60,485 51,018 9,467 Trademarks and trade names 9,142 4,776 4,366 9,142 4,204 4,938 Customer relationships 119,260 56,286 62,974 114,263 47,147 67,116 $ 198,175 $ 122,717 $ 75,458 $ 191,698 $ 109,855 $ 81,843 Amortization expense for intangible assets was $4.3 million and $3.8 million, respectively, during the three months ended June 30, 2017 and 2016 and $12.7 million and $11.1 million, respectively, during the nine months ended June 30, 2017 and 2016. Estimated future amortization expense for the intangible assets for the remainder of fiscal year 2017 and the subsequent four fiscal years is as follows (in thousands): Fiscal year ended September 30, 2017 $ 3,970 2018 15,693 2019 15,468 2020 14,156 2021 8,253 Thereafter 17,918 $ 75,458

Equity Method Investments

Equity Method Investments	9 Months Ended
	Jun. 30, 2017
Equity Method Investments and Joint Ventures [Abstract]
Equity Method Investments	6. Equity Method Investments The Company accounts for certain of its investments using the equity method of accounting and records its proportionate share of the investee’s earnings (losses) in its results of operations with a corresponding increase (decrease) in the carrying value of the investment. BioCision, LLC At September 30, 2016, the Company held a 20% equity interest in BioCision, a privately-held company based in Larkspur, California, which was accounted for as an equity method investment. The carrying value of the investment in BioCision was $1.7 million at September 30, 2016. During the three and nine months ended June 30, 2016, the Company recorded a loss associated with BioCision of $0.3 million and $0.7 million, respectively. At September 30, 2016, the Company held a term loan receivable from BioCision and five-year convertible debt securities with a warrant agreement to purchase BioCision’s preferred units. The convertible debt securities and the warrant were recorded at fair value during each reporting period, and the remeasurement gains and losses were recognized as a component of "Other loss, net" in the Company’s unaudited Consolidated Statements of Operations. The fair value of the convertible debt securities and the warrant was $5.8 million and less than $0.1 million, respectively, at September 30, 2016. During the nine months ended June 30, 2016, the Company recognized remeasurement gains of $0.5 million related to these financial instruments. Please refer to Note 17, “Fair Value Measurements” for further information on the valuation techniques and inputs used in fair value measurements of the convertible debt securities and the warrant. The term loan with an aggregate principal amount of $1.5 million bore an annual interest rate of 10% and was provided to BioCision to support its working capital requirements. At September 30, 2016, the term loan was recorded at its carrying value of $1.5 million and included in "Other assets" in the Company’s unaudited Consolidated Balance Sheets. Please refer to Note 8, "Equity Method and Other Investments" to the Company’s consolidated financial statements included in the 2016 Annual Report on Form 10‑K for further information on these financial instruments. On November 28, 2016, BioCision established Cool Lab as its subsidiary upon transferring certain assets related to cell cryopreservation solutions with net carrying values of $0.9 million, in which the Company acquired a 100% equity interest on that date for an aggregate purchase price of $15.2 million. The purchase price consisted of a cash payment of $4.8 million, a liability to the seller of $0.1 million, which has been satisfied, and non-cash consideration of $10.3 million measured at fair value on the acquisition date which was comprised of: (i) the redeemable fair value of the existing 20% equity ownership interest in BioCision of $3.1 million, (ii) the convertible debt securities of BioCision and warrants of $5.6 million to purchase BioCision’s preferred units, and (iii) the term notes of BioCision of $1.6 million including accrued interest. Carrying value of the equity method investment in BioCision was $1.2 million on November 28, 2016 and reflected BioCision’s losses of $0.5 million recorded from October 1, 2016 through the acquisition date. The Company has traditionally recorded the income and losses related to the equity method investment in BioCision one quarter in arrears. During the first quarter of fiscal year 2017, the Company recorded two additional months of activity in the carrying value of the investment as a result of its settlement. The Company deemed the amount of $0.2 million related to two additional months of activity to be insignificant. The equity method investment in BioCision was measured at fair value of $3.1 million at the acquisition date, and as a result the Company recognized a gain of $1.8 million upon the redemption of the equity method investment in its unaudited Consolidated Statements of Operations during the nine months ended June 30, 2017. On November 28, 2016, convertible debt, warrant and the term loan with carrying values of $5.8 million, less than $0.1 million and $1.6 million, respectively, were measured at their fair values of $5.6 million, less than $0.1 million and $1.6 million, respectively. As a result of such measurement, the Company recognized an aggregate loss of $0.2 million upon the settlement of these financial instruments in "Other loss, net" in its unaudited Consolidated Statements of Operations during the nine months ended June 30, 2017. Please refer to Note 4, "Acquisitions" and Note 17, "Fair Value Measurements" for further information on the acquisition transaction and the valuation techniques and inputs used in fair value measurements. ULVAC Cryogenics, Inc. The Company and ULVAC Corporation of Chigasaki, Japan each own a 50% stake in the joint venture, ULVAC Cryogenics, Inc (“UCI”). UCI manufactures and sells cryogenic vacuum pumps, principally to ULVAC Corporation. The carrying value of the investment in UCI was $32.6 million and $25.6 million, respectively, at June 30, 2017 and September 30, 2016. During the three months ended June 30, 2017 and 2016, the Company recorded income of $2.5 million and $0.7 million, respectively, representing its proportionate share of UCI’s earnings. During the nine months ended June 30, 2017 and 2016, the Company recorded income of $7.7 million and $2.0 million, respectively, representing its proportionate share of UCI’s earnings. Management fee payments received by the Company from UCI were $0.3 million and $0.2 million, respectively, during the three months ended June 30, 2017 and 2016. Management fee payments received by the Company from UCI were $0.8 million and $0.6 million, respectively, during the nine months ended June 30, 2017 and 2016. During the nine months ended June 30, 2017 and 2016, the Company incurred charges from UCI’s for products or services of $0.2 million each. Such charges were insignificant during the three months ended June 30, 2017 and 2016. At June 30, 2017 and September 30, 2016, the Company owed UCI $0.1 million in connection with accounts payable for unpaid products and services.

Line of Credit

Line of Credit	9 Months Ended
	Jun. 30, 2017
Debt Disclosure [Abstract]
Line of Credit	7. Line of Credit The Company maintains a five-year senior secured revolving line of credit (the "line of credit"), with Wells Fargo Bank, N.A. ("Wells Fargo"), that provides for up to $75 million of borrowing capacity, subject to borrowing base availability, as defined in the agreement governing the line of credit. There were no amounts outstanding under the line of credit as of June 30, 2017 and September 30, 2016. During the three and nine months ended June 30, 2017, the Company incurred less than $0.1 million and $0.1 million, respectively, in fees related to the unused portion of the line of credit commitment amount. Such fees were insignificant during the three and nine months ended June 30, 2016. The line of credit contains certain customary representations and warranties, a financial covenant, affirmative and negative covenants, as well as events of default. The Company was in compliance with the line of credit covenants as of June 30, 2017 and September 30, 2016. Please refer to Note 11, "Line of Credit" to the Company’s consolidated financial statements included in the 2016 Annual Report on Form 10‑K for further information on the line of credit arrangement.

Income Taxes

Income Taxes	9 Months Ended
	Jun. 30, 2017
Income Tax Disclosure [Abstract]
Income Taxes	8. Income Taxes During the three and nine months ended June 30, 2017, the Company recorded an income tax provision of $3.7 million and $9.9 million, respectively, which was driven primarily by foreign income. Tax provision recorded during the nine months ended June 30, 2017 was partially offset by $0.9 million of tax benefits related to the reduction of reserves for unrecognized tax benefits resulting from the expiration of statutes of limitations. During the three and nine months ended June 30, 2016, the Company recorded an income tax provision of $0.2 million and $75.1 million, respectively. The income tax provision of $0.2 million recorded during the third quarter of fiscal year 2016 was driven primarily by global income generated during the period, partially offset by $0.3 million of tax benefits related to the reduction of reserves for unrecognized tax benefits resulting from the expiration of statues of limitations. The tax provision of $75.1 million recorded during the nine months ended June 30, 2016 was driven primarily by the change in the valuation allowance against U.S. net deferred tax assets recognized during the second quarter of fiscal year 2016. Partially offsetting the valuation allowance provision were benefits related to pre-tax losses in the U.S., the reinstatement of the U.S. research and development tax credit retroactive to January 1, 2015, and reductions of reserves for unrecognized tax benefits resulting from the expiration of the statute of limitations. The Company evaluates the realizability of its deferred tax assets by tax-paying component and assesses the need for a valuation allowance on an annual and quarterly basis. The Company evaluates the profitability of each tax-paying component on a historic cumulative basis and on a forward looking basis in the course of performing this analysis. The Company evaluated all positive and negative evidence in concluding it was appropriate to establish a full valuation allowance against U.S. net deferred tax assets during the second quarter of fiscal year 2016. The Company maintained such allowance at June 30, 2017 and will continue to maintain it until there is sufficient positive evidence to support the reversal of all or some portion of these allowances. Please refer to Note 12, "Income Taxes" to the Company’s consolidated financial statements included in the 2016 Annual Report on Form 10‑K for further information on the valuation allowance. The Company is subject to U.S. federal income tax and various state, local and international income taxes in various jurisdictions. The amount of income taxes paid is subject to the Company’s interpretation of applicable tax laws in the jurisdictions in which it files tax returns. In the normal course of business, the Company is subject to income tax audits in various global jurisdictions in which it operates. The years subject to examination vary for the U.S. and international jurisdictions, with the earliest tax year being 2010. Based on the outcome of these examinations or the expiration of statutes of limitations for specific jurisdictions, it is reasonably possible that the related unrecognized tax benefits could change from those recorded in the Company’s unaudited Consolidated Balance Sheets. The Company currently anticipates that it is reasonably possible that the unrecognized tax benefits will be reduced by approximately $0.5 million within the next twelve months.

Other Balance Sheet Information

Other Balance Sheet Information	9 Months Ended
	Jun. 30, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Other Balance Sheet Information	9. Other Balance Sheet Information The following is a summary of accounts receivable at June 30, 2017 and September 30, 2016 (in thousands): June 30, September 30, 2017 2016 Accounts receivable $ 122,394 $ 108,713 Less allowance for doubtful accounts (1,514) (2,241) Less allowance for sales returns (128) (100) Accounts receivable, net $ 120,752 $ 106,372 The following is a summary of inventories at June 30, 2017 and September 30, 2016 (in thousands): June 30, September 30, 2017 2016 Inventories Raw materials and purchased parts $ 72,820 $ 60,979 Work-in-process 11,273 16,090 Finished goods 21,211 15,503 Total inventories $ 105,304 $ 92,572 Reserves for excess and obsolete inventory were $23.9 million and $24.8 million, respectively, at June 30, 2017 and September 30, 2016. During the nine months ended June 30, 2017 and the fiscal year ended September 30, 2016, the Company had cumulative capitalized direct costs of $4.4 million and $3.7 million, respectively, associated with development of software for its internal use which are included within "Property, plant and equipment, net" in the accompanying unaudited Consolidated Balance Sheets. During the nine months ended June 30, 2017, the Company capitalized direct costs of $0.8 million associated with development of software for its internal use. Deferred financing costs of $0.6 million and $0.7 million, respectively, at June 30, 2017 and September 30, 2016 are associated with obtaining the line of credit financing and presented within "Other assets" in the accompanying unaudited Consolidated Balance Sheets. Amortization expense incurred during the three and nine months ended June 30, 2017 was less than $0.1 million and $0.1 million, respectively, and included in interest expense in the accompanying unaudited Consolidated Statements of Operations. Such expenses were insiginficant during the three and nine months ended June 30, 2016. Please refer to Note 7, “Line of Credit” for further information on this arrangement. A note receivable of $0.2 million at June 30, 2017 and September 30, 2016 is recorded at carrying value and included in "Other assets" in the accompanying unaudited Consolidated Balance Sheets. The note had an initial value of $3.0 million and a stated interest rate of 9% upon its origination in fiscal year 2012 and was provided by the Company to a strategic partner (the “Borrower”) to support its future product development and other working capital requirements. Prior to fiscal year 2017, the Company amended the terms of the note due to the subordination of its security interest in the assets of the Borrower to the new lender and recognized cumulative impairment charges of $3.4 million as a result of making a determination that a recovery of all amounts due from the loan was not probable. No triggering events indicating additional impairment of the note receivable occurred during the three and nine months ended June 30, 2017. Please refer to Note 9, "Loan Receivable" to the Company’s consolidated financial statements included in the 2016 Annual Report on Form 10‑K for further information on the loan. The Company determined that the Borrower represented a variable interest entity since the level of equity investment at risk was not sufficient for the entity to finance its activities without additional financial support. However, the Company did not qualify as the primary beneficiary since it would not absorb the majority of the expected losses from the Borrower and did not have the power to direct the Borrower’s product research, development and marketing activities that have the most significant impact on its economic performance. The Company has no future contractual funding commitments to the Borrower and, as a result, the Company’s exposure to loss is limited to the outstanding principal and interest due on the loan. During the nine months ended June 30, 2017, the Company adopted the Accounting Standards Update 2015‑02, Consolidation (Topic 810): Amendments to the Consolidation Analysis, and concluded that it does not qualify as the primary beneficiary since it doesn’t have the power to direct the Borrower’s activities that most significantly impact its economic performance. The adoption of the guidance did not have an impact on the Company’s financial position and the results of operations since it concluded that it does not have a controlling financial interest in Borrower . The Company establishes reserves for estimated cost of product warranties based on historical information. Product warranty reserves are recorded at the time product revenue is recognized, and retrofit accruals are recorded at the time retrofit programs are established. The Company’s warranty obligation is affected by product failure rates, utilization levels, material usage, service delivery costs incurred in correcting a product failure and supplier warranties on parts delivered to the Company. The following is a summary of product warranty and retrofit activity on a gross basis for the three and nine months ended June 30, 2017 and 2016 (in thousands): Activity -Three Months Ended June 30, 2017 Balance Balance March 31, June 30, 2017 Accruals Costs Incurred 2017 $ 7,073 $ 2,440 $ (1,867) $ 7,646 Activity -Three Months Ended June 30, 2016 Balance Balance March 31, June 30, 2016 Accruals Costs Incurred 2016 $ 5,735 $ 2,279 $ (2,059) $ 5,955 Activity -Nine Months Ended June 30, 2017 Balance Balance September 30, June 30, 2016 Accruals Costs Incurred 2017 $ 6,324 $ 7,656 $ (6,334) $ 7,646 Activity -Nine Months Ended June 30, 2016 Balance Balance September 30, June 30, 2015 Accruals Costs Incurred 2016 $ 6,089 $ 6,989 $ (7,123) $ 5,955

Derivative Instruments

Derivative Instruments	9 Months Ended
	Jun. 30, 2017
Derivative Instruments and Hedging Activities Disclosure [Abstract]
Derivative Instruments	10. Derivative Instruments The Company has transactions and balances denominated in currencies other than the U.S. dollar. Most of these transactions or balances are denominated in Euros, British Pounds and a variety of Asian currencies. These transactions and balances, including short-term advances between the Company and its subsidiaries, subject the Company’s operations to exposure from exchange rate fluctuations. The impact of currency exchange rate movement can be positive or negative in any period. The Company mitigates the impact of potential currency transaction gains and losses on short-term intercompany advances through timely settlement of each transaction, generally within 30 days. The Company also enters into foreign exchange contracts to reduce its exposure to currency fluctuations. Under forward contract arrangements, the Company typically agrees to purchase a fixed amount of U.S. dollars in exchange for a fixed amount of a foreign currency on specified dates with maturities of three months or less. These transactions do not qualify for hedge accounting. Net gains and losses related to these contracts are recorded as a component of "Other loss, net" in the accompanying unaudited Consolidated Statements of Operations and are as follows for the three and nine months ended June 30, 2017 and 2016 (in thousands): Three Months Ended Nine Months Ended June 30, June 30, 2017 2016 2017 2016 Realized gains (losses) on derivatives not designated as hedging instruments $ 147 $ 233 $ (450) $ 1,230 The Company had the following notional amounts outstanding under foreign currency contracts that do not qualify for hedge accounting at June 30, 2017 and September 30, 2016 (in thousands): June 30, 2017: Notional Amount Notional Amount Fair Value of Fair Value of Buy Currency of Buy Currency Sell Currency Maturity of Sell Currency Assets Liabilities Japanese Yen 445,000 U.S. Dollar July 2017 3,980 $ — $ (13) British Pound 1,470 U.S. Dollar July 2017 1,906 — (16) Korean Won 4,193,000 U.S. Dollar July 2017 3,679 — (10) U.S. Dollar 5,860 Chinese Yuan July 2017 40,000 — (20) Euro 11,600 U.S. Dollar July 2017 13,229 — (53) British Pound 164 Norwegian Krone July 2017 1,800 2 — Singapore Dollar 620 U.S. Dollar July 2017 449 — (1) U.S. Dollar 213 Israeli Shekel July 2017 748 1 — Euro 18,513 British Pound July 2017 16,280 99 — $ 102 $ (113) September 30, 2016: Notional Amount Notional Amount Fair Value of Fair Value of Buy Currency of Buy Currency Sell Currency Maturity of Sell Currency Assets Liabilities British Pound 190 Swedish Krona October 2016 2,100 $ 1 $ — Japanese Yen 124,000 U.S. Dollar October 2016 1,229 — — U.S. Dollar 6,107 British Pound October 2016 4,710 2 — Euro 13,300 U.S. Dollar October 2016 14,976 — (40) U.S. Dollar 5,815 Chinese Yuan October 2016 39,000 — (33) Korean Won 2,488,000 U.S. Dollar October 2016 2,255 1 — Euro 7,482 British Pound October 2016 6,500 — (23) U.S. Dollar 311 Israeli Shekel October 2016 1,169 1 — Singapore Dollar 360 U.S. Dollar October 2016 265 — — U.S. Dollar 210 Taiwanese Dollar October 2016 6,600 — — British Pound 171 Norwegian Krone October 2016 1,800 — — $ 5 $ (96) The fair values of the forward contracts described above are recorded in the Company’s accompanying unaudited Consolidated Balance Sheets as "Prepaid expenses and other current assets" and "Accrued expenses and other current liabilities". Stock Warrant The stock warrant was less than $0.1 million at September 30, 2016. The BioCision warrant agreement contained net share settlement provisions, which permitted the Company to pay the warrant exercise price using shares issuable under the warrant (“cashless exercise”). The value of the stock warrant fluctuated primarily in relation to the value of BioCision’s underlying securities, either providing an appreciation in value or potentially expiring with no value. Gains and losses on the revaluation of the stock warrant were recognized as a component of "Other loss, net" in the accompanying unaudited Consolidated Statements of Operations. During the first quarter of fiscal year 2017, the Company canceled the stock warrant as a portion of the non-cash consideration transferred for the acquisition of Cool Lab, which was measured at fair value on the acquisition date. There were no stock warrants held by the Company at June 30, 2017. Please refer to Note 4, "Acquisitions"; Note 6, "Equity Method Investments" and Note 17 “Fair Value Measurements” for further information on the acquisition of Cool Lab and the stock warrant.

Stock-Based Compensation

Stock-Based Compensation	9 Months Ended
	Jun. 30, 2017
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-Based Compensation	11. Stock-Based Compensation The Company may issue restricted stock units and restricted stock awards (collectively "restricted stock units") and stock options which vest upon the satisfaction of a performance condition and/or a service condition. In addition, the Company issues shares to participating employees pursuant to an employee stock purchase plan and unrestricted stock awards to its directors in accordance with its director compensation program. The following table reflects stock-based compensation expense recorded during the three and nine months ended June 30, 2017 and 2016 (in thousands): Three Months Ended June 30, Nine Months Ended June 30, 2017 2016 2017 2016 Restricted stock $ 4,044 $ 1,501 $ 10,634 $ 7,801 Employee stock purchase plan 153 136 447 405 Total stock-based compensation expense $ 4,197 $ 1,637 $ 11,081 $ 8,206 The fair value of restricted stock units is determined based on the number of shares granted and the closing price of the Company’s common stock quoted on NASDAQ on the date of grant. The Company recognizes stock-based compensation expense on a straight-line basis, net of estimated forfeitures, over the requisite service period. Additionally, the Company assesses the likelihood of achieving the performance goals against previously established performance targets in accordance with the Company’s long-term equity incentive plan for stock-based awards that vest upon or after the satisfaction of these goals. The Company grants restricted stock units that vest over a required service period and/or achievement of certain operating performance goals. Restricted stock units granted with performance goals may also have a required service period following the achievement of all or a portion of the goals. The following table reflects restricted stock units granted during the nine months ended June 30, 2017 and 2016: Time-Based Performance- Total Units Units Stock Grants Based Units Nine months ended June 30, 2017 1,008,570 377,213 43,019 Nine months ended June 30, 2016 1,679,591 734,250 85,091 Time-Based Grants Restricted stock units granted with a required service period typically have three year vesting schedules in which one-third of awards vest at the first anniversary of the grant date, one-third vest at the second anniversary of the grant date and one-third vest at the third anniversary of the grant date, subject to the award holders meeting service requirements. Stock Grants During the nine months ended June 30, 2017 and 2016, the Company granted 43,019 and 85,091 units to the members of the Company’s Board of Directors, including compensation-related units of 28,065 and 55,380, respectively. Compensation-related units granted during the nine months ended June 30, 2017 are subject to a one-year vesting period starting from the grant date. The units will vest on the date which is one day before the Company’s 2018 Annual Meeting of Stockholders. Compensation-related units granted during the nine months ended June 30, 2016 vested on the grant date upon their issuance. Certain members of the Board of Directors previously elected to defer receiving their annual awards of restricted shares of the Company stock and quarterly dividends until a future date. During the nine months ended June 30, 2017 and 2016, the Company granted 13,065 and 25,560 units, respectively, related to such deferred annual restricted share awards, as well as 1,889 and 4,151 units, respectively, related to deferred quarterly dividends. Annual restricted share awards granted during the nine months ended June 30, 2017 are subject to a one-year vesting period starting from the grant date. The units will vest on the date which is one day before the Company’s 2018 Annual Meeting of Stockholders, but certain holders have elected to defer the receipt of the Company shares until they attain a certain age or cease to provide services to the Company in their capacity as Board members. Annual restricted share awards granted during the nine months ended June 30, 2016 vested on the grant date upon their issuance, but the settlement was deferred by certain holders, for the same conditions as described above for grants in fiscal year 2017. The amount of deferred dividends granted during the nine months ended June 30, 2017 and 2016 was equal to the value of cash dividends that would be paid on the number of total deferred shares based on the closing price of the Company’s stock on the dividend record date. Such units vested upon their issuance, but the settlement was deferred by certain holders for the same conditions, as described above. Performance-Based Grants Performance-based restricted stock units are earned based on the achievement of performance criteria established by the Human Resources and Compensation Committee of the Board of Directors. The criteria for performance-based awards are weighted and have threshold, target and maximum performance goals. Performance-based awards granted in fiscal year 2017 allow participants to earn 100% of a targeted number of restricted stock units if the Company’s performance meets its target for each applicable financial metric, and up to a maximum of 200% of the restricted stock units if the Company’s performance for such metrics meets the maximum threshold. Performance below the minimum threshold for each financial metric results in award forfeitures. Performance goals will be measured over a three year period at the end of fiscal year 2019 to determine the number of units earned by recipients who continue to meet a service requirement. Units held by recipients who fail to meet the continued service requirement are forfeited. Earned units for recipients who continue to meet the service requirements vest on the date the Company’s Board of Directors determines the number of units earned, which will be approximately the third anniversary of the grant date. Performance-based awards granted in fiscal year 2016 also include provisions that allow participants to earn threshold, target and maximum awards ranging from 0% of the award for performance below the minimum threshold, 100% of the award for performance at target, and up to a maximum of 200% of the award if the Company achieves the maximum performance goals. Restricted Stock Unit Activity The following table summarizes restricted stock unit activity for the nine months ended June 30, 2017: Weighted Average Grant-Date Shares Fair Value Outstanding at September 30, 2016 2,489,076 $ 10.79 Granted 1,008,570 14.32 Vested (911,738) 10.51 Forfeited (79,699) 11.66 Outstanding at June 30, 2017 2,506,209 $ 12.52 The weighted average grant date fair value of restricted stock units granted during the three months ended June 30, 2017 and 2016 was $25.21 and $9.58, respectively. The weighted average grant date fair value of restricted stock units granted during the nine months ended June 30, 2017 and 2016 was $14.32 and $10.84, respectively. The fair value of restricted stock units vested during the three months ended June 30, 2017 and 2016 was $2.9 million and $0.3 million, respectively. The fair value of restricted stock units vested during the nine months ended June 30, 2017 and 2016 was $14.8 million and $14.3 million, respectively. During the nine months ended June 30, 2017 and 2016, the Company remitted $4.6 million and $4.4 million, respectively, for withholding taxes on vested restricted stock units, of which $0.1 million and $4.3 million, respectively, was paid by the Company. During the nine months ended June 30, 2017 and 2016, the Company received $4.6 million and $0.1 million, respectively, in cash proceeds from employees to satisfy their tax obligations as a result of share issuances. As of June 30, 2017, the unrecognized compensation cost related to restricted stock units that are expected to vest is $20.5 million and will be recognized over an estimated weighted average service period of approximately 1.7 years. Employee Stock Purchase Plan The Company maintains an Employee Stock Purchase Plan that allows its employees to purchase shares of common stock at a price equal to 85% of the fair market value of the Company’s stock at the beginning or the end of the semi-annual period, whichever is lower. During the three and nine months ended June 30, 2017, the Company issued 90,681 shares under the employee stock purchase plan for $1.0 million. The Company issued 118,548 shares under the employee stock purchase plan for $0.9 million during the corresponding periods of the prior fiscal year.

Earnings per Share

Earnings per Share	9 Months Ended
	Jun. 30, 2017
Earnings Per Share [Abstract]
Earnings per Share	12. Earnings per Share The calculations of basic and diluted net income (loss) per share and basic and diluted weighted average shares outstanding are as follows for the three and nine months ended June 30, 2017 and 2016 (in thousands, except per share data): Three Months Ended Nine Months Ended June 30, June 30, 2017 2016 2017 2016 Net income (loss) $ 17,350 $ 8,564 $ 45,226 $ (80,022) Weighted average common shares outstanding used in computing basic earnings (losses) per share 69,711 68,628 69,496 68,437 Dilutive common stock options and restricted stock units 694 538 702 — Weighted average common shares outstanding used in computing diluted earnings (losses) per share 70,405 69,166 70,198 68,437 Basic net income (loss) per share $ $ $ $ Diluted net income (loss) per share $ $ $ $ During the three and nine months ended June 30, 2017, there were no antidilutive restricted stock units excluded from the computation of diluted earnings per share. During the three months ended June 30, 2016, 50,000 restricted stock units were excluded from the computation of diluted earnings per share as their effect was anti-dilutive based on the treasury stock method. During the nine months ended June 30, 2016, 991,000 shares were excluded from the computation of diluted earnings per share as a result of a net loss incurred during the period.

Restructuring Charges

Restructuring Charges	9 Months Ended
	Jun. 30, 2017
Restructuring and Related Activities [Abstract]
Restructuring Charges	13. Restructuring Charges Three Months Ended June 30, 2017 During the three months ended June 30, 2017, the Company recorded restructuring charges of $0.8 million related to severance attributable primarily to the Brooks Semiconductor Solutions Group segment. Such costs included $0.6 million of charges related to the actions initiated during fiscal year 2017 and $0.2 million of charges related to the actions initiated prior to fiscal year 2017. During fiscal year 2017, the Company initiated a restructuring action to streamline service operations in order to optimize the cost structure and improve productivity. Total severance costs expected to be incurred in connection with this action are $1.5 million, of which $0.9 million were recognized prior to the third quarter of fiscal year 2017 and $0.6 million were recognized during the three months ended June 30, 2017. This restructuring action has been substantially completed as of June 30, 2017. Accrued restructuring costs related to this action were $0.8 million at June 30, 2017 and are expected to be paid within the next twelve months from cash flows generated from operating activities. Prior to fiscal year 2017, the Company initiated a restructuring action within the Brooks Semiconductor Solutions Group segment to consolidate the Company’s Jena, Germany repair facility into the Chelmsford, Massachusetts repair operation as a part of the Company’s strategy to reduce global footprint and streamline the cost structure. Total severance costs expected to be incurred in connection with this action are $2.5 million, of which: (i) $1.8 million were recognized prior to fiscal year 2017, (ii) $0.5 million were recognized during fiscal year 2017, including $0.2 million during the three months ended June 30, 2017, and (iii) $0.2 million are expected to be recognized in future periods. This restructuring action has been substantially completed as of June 30, 2017. Accrued restructuring costs related to this action were $0.9 million at June 30, 2017 and are expected to be paid within the next twelve months from cash flows generated from operating activities. Please refer to Note 17, "Restructuring and Other Charges" to the Company’s consolidated financial statements included in the 2016 Annual Report on Form 10‑K for further information on this restructuring initiative. Nine Months Ended June 30, 2017 During the nine months ended June 30, 2017, the Company recorded restructuring charges of $2.7 million related to severance, of which $2.2 million were attributable to the Brooks Semiconductor Solutions Group segment, $0.2 million were attributable to the Brooks Life Science Systems segment and $0.3 million were attributable to the company-wide restructuring action initiated prior to fiscal year 2017. The restructuring charges of $2.2 million attributable to the Brooks Semiconductor Solutions Group segment consisted of $1.5 million of charges related to the actions initiated during fiscal year 2017 to streamline service operations, as described above, and $0.7 million of charges related to the actions initiated prior to fiscal year 2017. Restructuring charges of $0.7 million consisted of $0.5 million attributable to the consolidation of the Jena, Germany repair facility into the Chelmsford, Massachusetts repair operation, as described above, and $0.2 million related to the integration of Contact Co., Ltd. ("Contact") after its acquisition by the Company, including the closure and transfer of its Mistelgau, Germany manufacturing operations to a contract manufacturer, and other cost reductions to improve profitability and competitiveness. Total restructuring costs incurred in connection with this action are approximately $3.2 million, of which approximately $3.0 million were recognized prior to fiscal year 2017 and $0.2 million were recognized during the nine months ended June 30, 2017. This restructuring action was substantially completed as of June 30, 2017 and is not expected to result in any significant additional restructuring charges in future periods. There were no accrued restructuring costs from this action at June 30, 2017. Prior to fiscal year 2017, the Company initiated a restructuring action to streamline its business operations as part of a company-wide initiative to improve profitability and competitiveness which is expected to benefit both segments. Total severance costs incurred in connection with this action were $6.1 million, of which $5.8 million were recognized prior to fiscal year 2017 and $0.3 million were recognized during the nine months ended June, 30, 2017. Severance costs incurred in connection with this action were attributable to the elimination of positions across the Company, including certain senior management positions. This restructuring action was substantially completed as of June 30, 2017 and is not expected to result in any additional restructuring charges in future periods. There were no accrued restructuring costs related to this action at June 30, 2017. Three Months Ended June 30, 2016 During the three months ended June 30, 2016, the Company recorded restructuring charges of $1.0 million related to severance which were attributable to actions initiated prior to the third quarter of fiscal year 2016. Such charges were comprised of $0.3 million of costs attributable to the Brooks Life Science Systems segment and $0.6 million of costs related to the Company-wide restructuring actions, as described above. The Brooks Life Science Systems restructuring initiatives included several actions that were primarily related to streamlining the segment’s management structure, integrating BioStorage, and the closure of the segment’s Spokane, Washington facility in March 2016. Total severance costs incurred in connection with these initiatives were $2.8 million, of which $2.4 million was recognized prior to the third quarter of fiscal year 2016, and $0.3 million were recognized during the three months ended June 30, 2016. There were no accrued restructuring costs from these initiatives at June 30, 2017. Nine Months Ended June 30, 2016 During the nine months ended June 30, 2016, the Company recorded restructuring charges of $9.8 million related to severance, which consisted of $8.5 million of charges related to restructuring actions initiated during the nine months ended June 30, 2016 and $1.2 million of charges related to restructuring actions intiated prior to fiscal year 2016. The charges of $8.5 million were comprised primarily of $2.8 million of costs attributable to the restructuring initiatives within the Brooks Life Science Systems segment and $5.8 million of costs related to the company-wide restructuring action, as described above. The charges of $1.2 million were attributable to the Brooks Semiconductor Solutions Group segment and related to the integration of Contact, as well as closure and transfer of the Mistelgau, Germany manufacturing operations to a contract manufacturer, as described above. The following is a summary of activity related to the Company’s restructuring charges for the three and nine months ended June 30, 2017 and 2016 (in thousands): Activity -Three Months Ended June 30, 2017 Balance Balance March 31, June 30, 2017 Expenses Payments 2017 Total restructuring liabilities related to workforce termination benefits $ 2,044 $ 828 $ (1,182) $ 1,690 Activity -Three Months Ended June 30, 2016 Balance Balance March 31, June 30, 2016 Expenses Payments 2016 Facility and other contract termination costs $ 96 $ — $ (96) $ — Workforce-related termination benefits 7,293 996 (2,500) 5,789 Total restructuring liabilities $ 7,389 $ 996 $ (2,596) $ 5,789 Activity -Nine Months Ended June 30, 2017 Balance Balance September 30, June 30, 2016 Expenses Payments 2017 Total restructuring liabilities related to workforce termination benefits $ 5,939 $ 2,663 $ (6,912) $ 1,690 Activity -Nine Months Ended June 30, 2016 Balance Balance September 30, June 30, 2015 Expenses Payments 2016 Facility and other contract termination costs $ 433 $ 25 $ (458) $ — Workforce-related termination benefits 1,640 9,782 (5,633) 5,789 Total restructuring liabilities $ 2,073 $ 9,807 $ (6,091) $ 5,789 Accrued restructuring costs of $1.7 million at June 30, 2017 are expected to be paid within the next twelve months.

Employee Benefit Plans

Employee Benefit Plans	9 Months Ended
	Jun. 30, 2017
Compensation and Retirement Disclosure [Abstract]
Employee Benefit Plans	14. Employee Benefit Plans The Company has two active defined benefit pension plans (collectively, the “Plans”). The Plans cover substantially all of the Company’s employees in Switzerland and Taiwan. Retirement benefits are generally earned based on the years of service and the level of compensation during active employment, but the level of benefits varies within the Plans. Eligibility is determined in accordance with local statutory requirements. The components of the Company’s net pension cost for the three and nine months ended June 30, 2017 and 2016 are as follows (in thousands): Three Months Ended Nine Months Ended June 30, June 30, 2017 2016 2017 2016 Service cost $ 68 $ 138 $ 202 $ 410 Interest cost 7 18 21 54 Amortization of losses 2 4 6 12 Expected return on plan assets (33) (41) (99) (120) Net periodic pension cost $ 44 $ 119 $ 130 $ 356

Segment Information

Segment Information	9 Months Ended
	Jun. 30, 2017
Segment Reporting [Abstract]
Segment Information	15. Segment Information Operating segments are defined as components of an enterprise that engage in business activities for which discrete financial information is available and regularly reviewed by the chief operating decision maker in deciding how to allocate resources and assess performance. The Company’s Chief Executive Officer is the Company’s chief operating decision maker. Prior to the third quarter of fiscal year 2016, the Company had three operating and reportable segments that consisted of Brooks Product Solutions, Brooks Global Services and Brooks Life Science Systems. During the third quarter of fiscal year 2016, the Company reorganized its previous reporting structure into two operating and reportable segments consisting of: (i) Brooks Semiconductor Solutions Group; and (ii) Brooks Life Science Systems and reported its financial results for the periods then ended based on the revised segment structure. Please refer to Note 20, "Segment and Geographic Information" to the Company’s Consolidated Financial Statements included in the 2016 Annual Report on Form 10‑K for further information on the segments realignment, operating segments’ description and accounting policies. The following is the summary of the financial information for the Company’s operating and reportable segments for the three and nine months ended June 30, 2017 and 2016 (in thousands): Brooks Brooks Semiconductor Life Science Solutions Group Systems Total Three Months Ended June 30, 2017: Revenue Products $ 124,681 $ 17,276 $ 141,957 Services 20,280 19,480 39,760 Segment revenue $ 144,961 $ 36,756 $ 181,717 Gross profit $ 58,083 $ 13,489 $ 71,572 Segment operating income 26,188 1,134 27,322 Depreciation expense 1,192 1,134 2,326 Three Months Ended June 30, 2016: Revenue Products $ 99,254 $ 12,342 $ 111,596 Services 19,179 16,759 35,938 Segment revenue $ 118,433 $ 29,101 $ 147,534 Gross profit $ 42,904 $ 11,259 $ 54,163 Segment operating income (loss) 13,119 (736) 12,383 Depreciation expense 1,448 1,018 2,466 Nine Months Ended June 30, 2017: Revenue Products $ 349,710 $ 46,974 $ 396,684 Services 56,532 57,789 114,321 Segment revenue $ 406,242 $ 104,763 $ 511,005 Gross profit $ 154,877 $ 38,162 $ 193,039 Segment operating income 63,562 2,535 66,097 Depreciation expense 3,786 3,269 7,055 Nine Months Ended June 30, 2016: Revenue Products $ 268,671 $ 33,567 $ 302,238 Services 57,657 42,875 100,532 Segment revenue $ 326,328 $ 76,442 $ 402,770 Gross profit $ 114,506 $ 27,011 $ 141,517 Segment operating income (loss) 22,717 (7,555) 15,162 Depreciation expense 3,375 2,452 5,827 Assets: June 30, 2017 $ 330,746 $ 262,250 $ 592,996 September 30, 2016 317,717 247,735 565,452 The following is a reconciliation of the Company’s operating and reportable segments’ operating income and segment assets to the corresponding amounts presented in the accompanying unaudited Consolidated Balance Sheets and Consolidated Statements of Operations for the three and nine months ended June 30, 2017 and 2016 (in thousands): Three Months Ended Nine Months Ended June 30, June 30, 2017 2016 2017 2016 Segment operating income $ 27,322 $ 12,383 $ 66,097 $ 15,162 Amortization of acquired intangible assets 3,278 2,754 9,636 8,056 Restructuring charges 828 996 2,663 9,807 Other unallocated corporate expenses 4,446 139 7,066 3,464 Total operating income (loss) $ 18,770 $ 8,494 $ 46,732 $ (6,165) June 30, September 30, 2017 2016 Segment assets $ 592,996 $ 565,452 Cash, cash equivalents and marketable securities 119,658 91,221 Deferred tax assets 1,460 1,982 Equity method investments 32,606 27,250 Other unallocated corporate net assets 51 — Total assets $ 746,771 $ 685,905

Significant Customers

Significant Customers	9 Months Ended
	Jun. 30, 2017
Risks and Uncertainties [Abstract]
Significant Customers	16. Significant Customers During the three months ended June 30, 2017 and 2016, the Company had one customer that accounted for 10% or more of its consolidated revenue, at 11% and 10% , respectively. During each of the nine months ended June 30, 2017 and 2016, the Company had one customer that accounted for 10% of its consolidated revenue. As of September 30, 2016, the Company had one customer that accounted for 11% of the Company’s total receivables. There were no such customers as of June 30, 2017. For purposes of determining the percentage of revenue generated from any of the Company’s original equipment manufacturer (the "OEM") customers, the Company does not include revenue from products sold to contract manufacturer customers who in turn sell to the OEM’s. If the Company included revenue from products sold to contract manufacturer customers supporting the Company’s OEM customers, the percentage of the Company’s total revenue derived from certain OEM customers would be higher.

Fair Value Measurements

Fair Value Measurements	9 Months Ended
	Jun. 30, 2017
Fair Value Disclosures [Abstract]
Fair Value Measurements	17. Fair Value Measurements The fair value measurement guidance establishes a fair value hierarchy that requires an entity to maximize the use of observable inputs and minimize the use of unobservable inputs when measuring fair value. The following levels of inputs may be used to measure fair value: Level 1 Inputs: Quoted prices in active markets for identical assets or liabilities as of the reporting date. Active markets are those in which transactions for the asset and liability occur in sufficient frequency and volume to provide pricing information on an ongoing basis. Level 2 Inputs: Observable inputs other than prices included in Level 1, including quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities. Level 3 Inputs: Unobservable inputs that are significant to the fair value of the assets or liabilities and reflect an entity’s own assumptions in pricing assets or liabilities since they are supported by little or no market activity. The following tables summarize assets and liabilities measured and recorded at fair value on a recurring basis in the accompanying unaudited Consolidated Balance Sheets as of June 30, 2017 and September 30, 2016 (in thousands): Fair Value Measurements at Reporting Date Using Quoted Prices in Significant Active Markets for Significant Other Unobservable June 30, Identical Assets Observable Inputs Inputs Description 2017 (Level 1) (Level 2) (Level 3) Assets: Cash equivalents $ 45 $ — $ 45 $ — Available-for-sale securities 2,577 — 2,577 — Foreign exchange contracts 102 — 102 — Total Assets $ 2,724 $ — $ 2,724 $ — Liabilities: Foreign exchange contracts $ 113 $ — $ 113 $ — Total Liabilities $ 113 $ — $ 113 $ — The convertible debt securities and the stock warrant were included in "Other assets" in the accompanying Consolidated Balance Sheets at September 30, 2016. During the nine months ended June 30, 2017, the Company settled the convertible debt securities and the stock warrant as a part of the non-cash consideration for the Company’s acquisition of Cool Lab completed on November 28, 2016. The convertible debt securities and the stock warrant were measured at fair value on the acquisition date as a portion of the consideration transferred to the seller. A loss of $0.2 million on settlement of these financial instruments was recorded in the "Other loss, net" in the Company’s unaudited Consolidated Statements of Operations for the nine months ended June 30, 2017. Please refer to Note 6, "Equity Method Investments" for further information on the convertible debt securities and the stock warrant and Note 4 "Acquisitions" for the acquisition of Cool Lab. Fair Value Measurements at Reporting Date Using Quoted Prices in Significant Active Markets for Significant Other Unobservable September 30, Identical Assets Observable Inputs Inputs Description 2016 (Level 1) (Level 2) (Level 3) Assets: Cash equivalents $ 143 $ 98 $ 45 $ — Available-for-sale securities 6,135 — 6,135 — Foreign exchange contracts 5 — 5 — Convertible debt securities 5,774 — — 5,774 Stock warrant 45 — — 45 Total Assets $ 12,102 $ 98 $ 6,185 $ 5,819 Liabilities: Contingent consideration $ 500 $ — $ — $ 500 Foreign exchange contracts 97 — 97 — $ 597 $ — $ 97 $ 500 Cash Equivalents Cash equivalents of $0.1 million at September 30, 2016 consist of Money Market Funds and are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices in active markets. Cash equivalents of less than $0.1 million each at June 30, 2017 and September 30, 2016 consist primarily of Bank Certificate of Deposits and are classified within Level 2 of the fair value hierarchy because they are not actively traded. Available-For-Sale Securities Available-for-sale securities of $2.6 million and $6.1 million, respectively, at June 30, 2017 and September 30, 2016 consist of Municipal Securities, U.S. Corporate Securities and Other Debt Securities. The securities are valued using matrix pricing and benchmarking and classified within Level 2 of the fair value hierarchy because they are not actively traded. Matrix pricing is a mathematical technique used to value securities by relying on the securities’ relationship to other benchmark quoted prices. Foreign Exchange Contracts Foreign exchange contract assets and liabilities amounted to $0.1 million each at June 30, 2017. Foreign exchange contract assets and liabilities amounted to less than $0.1 million and $0.1 million, respectively, at September 30, 2016. Foreign exchange contract assets and liabilities are measured and reported at fair value based on observable market inputs and classified within Level 2 of the fair value hierarchy due to a lack of an active market for these contracts. Convertible Debt Securities At September 30, 2016, convertible debt securities of $5.8 million were measured at fair value and classified within Level 3 of the fair value hierarchy. During the nine months ended June 30, 2017, the Company settled the convertible debt securities as a part of the non-cash consideration for the Company’s acquisition of Cool Lab. The convertible debt securities were measured at fair value of $5.6 million on the acquisition date which was determined based on the probability weighted average Discounted Cash Flow (the "DCF") approach and a Monte Carlo simulation model. The DCF approach was utilized for the instrument’s variable conversion price scenarios for which fair value was determined based on probability weighted average method utilizing various outcomes for the instrument’s expected payout. The fair value for each outcome was computed based on the present value of cash flows associated with the expected payout discounted at the risk-adjusted discount rate. The key inputs used in the DCF approach included a risk-adjusted discount rate of 23% and the time of the instrument’s payout, which ranged between 1.5 years and 3.2 years. The Monte Carlo simulation model was utilized for the instrument’s fixed conversion price scenarios. The fair value of the instrument was computed for the period from the valuation date through the expected payoff date based on multiple scenarios. The key inputs used in the Monte-Carlo approach consisted of: (i) risk free rate, which was used for the scenarios in which the instrument’s conversion value was greater than its fixed payoff value, and ranged between 0.96% and 1.39%, (ii) risk-adjusted discount rate of 23%, which was used for the scenarios in which the instrument’s conversion value was less than its fixed payoff value, (iii) expected payoff period, which ranged between 1.50 years and 3.06 years, (iv) underlying stock price estimated at $1.76, and (v) underlying stock volatility of 55%, which was calculated based on security-specific volatility. A loss of $0.2 million on the settlement of convertible debt securities with a fair value of $5.6 million and a carrying value of $5.8 million on November 28, 2016 was recognized within "Other loss, net" in the Company’s unaudited Consolidated Statements of Operations during the nine months ended June 30, 2017. Please refer to Note 6, "Equity Method Investments" for further information on the convertible debt securities and Note 4 "Acquisitions" for the acquisition of Cool Lab. Stock Warrant Stock warrant valued at less than $0.1 million at September 30, 2016 was classified within Level 3 of the fair value hierarchy and measured at fair value based on the Black-Scholes model. The Black-Scholes model applied to the warrant incorporated the constant price variation of the underlying asset, the time value of money, the warrant’s strike price and the time until the warrant’s expiration date. The fair value of the warrant was determined utilizing a five year equity volatility percentage based on an average equity volatility derived from comparable public companies. During the first quarter of fiscal year 2017, the Company canceled the stock warrant as part of the non-cash consideration for the Company’s acquisition of Cool Lab and measured the stock warrant at fair value of less than $0.1 million on the acquisition date. The fair value of the warrant was determined based on the option pricing approach that treats various classes of securities in a company’s capital structure as call options on the total equity value of the company. Contingent Consideration Contingent consideration liability of $0.5 million at September 30, 2016 was classified within Level 3 of the fair value hierarchy and measured at fair value based on the probability-weighted average discounted cash flow model utilizing potential outcomes related to achievement of certain specified targets and events. The fair value measurement of the contingent consideration was based on probabilities assigned to each potential outcome and the discount rate. During the nine months ended June 30, 2017, the Company settled the liability and remitted a cash payment of $0.5 million to the sellers of Contact as a remaining part of the acquisition purchase price. Please refer to Note 4 “Acquisitions” to the Company’s consolidated financial statements included in the 2016 Annual Report on Form 10‑K for further information on the contingent consideration liability. The carrying amounts of accounts receivable and accounts payable approximate their fair value due to their short-term nature. The following table presents the reconciliation of the assets and liabilities measured and recorded at fair value on a recurring basis using significant unobservable inputs (Level 3) (in thousands): Convertible Stock Contingent Debt Securities Warrants Consideration Total Balance at September 30, 2016 $ 5,774 $ 45 $ 500 $ 6,319 Change in fair value (194) (37) — (231) Settlements (5,580) (8) (500) (6,088) Balance at June 30, 2017 $ — $ — $ — $ — Nonrecurring Fair Value Measurements The Company holds certain assets that are measured at fair value on a nonrecurring basis in periods subsequent to initial recognition. A note receivable of $0.2 million at each of June 30, 2017 and September 30, 2016 is recorded at carrying value and included in "Other assets" in the accompanying unaudited Consolidated Balance Sheets. Please refer to Note 9, "Other Balance Sheet Information" for further information on the loan. A loan receivable of $1.5 million at September 30, 2016 was recorded at carrying value and included in "Other assets" in the accompanying unaudited Consolidated Balance Sheets. During the nine months ended June 30, 2017, the Company settled the loan as part of the non-cash consideration for the Company’s acquisition of Cool Lab and remeasured it at fair value of $1.6 million on the acquisition date. Fair value of the loan was classified within Level 3 of the fair value hierarchy and determined based on the market approach utilizing a loan settlement value, including its principal and accrued interest, in a similar transaction in a non-observable market. The carrying value of the loan was $1.6 million on the acquisition date and included the loan’s principal and accrued interest. Please refer to Note 6, "Equity Method Investments" for further information on the loan and Note 4 "Acquisitions" for the acquisition of Cool Lab. The equity method investment in BioCision of $1.7 million at September 30, 2016 was recorded at carrying value in the accompanying unaudited Consolidated Balance Sheets. During the nine months ended June 30, 2017, the Company redeemed the equity method investment in BioCision as part of the non-cash consideration for the Company’s acquisition of Cool Lab. Fair value of the equity method investment in BioCision of $3.1 million was classified within Level 3 of the fair value hierarchy and measured based on the option pricing approach which treats various classes of securities in a company’s capital structure as call options on the total equity value of the company. The key inputs used in the option pricing approach consisted of: (i) total equity value of BioCision estimated at $6.5 million; (ii) equity volatility estimated at 80%; (iii) time to liquidity event estimated at 1.5 years; and (iv) risk free rate of 0.96%. Please refer to Note 6, "Equity Method Investments" for further information on the convertible debt securities and Note 4 "Acquisitions" for the acquisition of Cool Lab. Certain non-financial assets, including goodwill, finite-lived intangible assets and other long-lived assets, are measured at fair value on a non-recurring basis when there is an indication of impairment. Please refer to the Note 2, "Summary of Significant Accounting Policies" to the Company’s consolidated financial statements included in the 2016 Annual Report on Form 10‑K for further information on the valuation techniques used in developing these measurements.

Commitments and Contingencies

Commitments and Contingencies	9 Months Ended
	Jun. 30, 2017
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	18. Commitments and Contingencies Operating Leases During the nine months ended June 30, 2017, the Company entered into a new lease agreement for the existing 85,000 square feet of space in Indianapolis, Indiana which accommodates its sample storage, sales and support functions for the Brooks Life Science Systems segment. The original lease expires in July 2017. The new lease for such space commences on August 1, 2017 and expires on September 30, 2023. Additionally, the Company executed another new lease agreement for an additional 13,000 square feet of space within the aforementioned facility which commences on March 1, 2019 and expires on September 30, 2023. The new leases may be extended at the Company’s option for three additional terms of five years each subject to the terms and conditions of the lease. The non-cancelable obligations under the new leases total $2.4 million. Letters of Credit At June 30, 2017 and September 30, 2016, the Company had approximately $3.4 million and $2.0 million, respectively, of letters of credit outstanding related primarily to customer advances and other performance obligations. These arrangements guarantee the refund of advance payments received from our customers in the event that the product is not delivered or warranty obligations are not fulfilled in accordance with the contract terms. These obligations could be called by the beneficiaries at any time before the expiration date of the particular letter of credit if the Company fails to meet certain contractual requirements. None of these obligations were called during the nine months ended June 30, 2017 and the fiscal year ended September 30, 2016, and the Company currently does not anticipate any of these obligations to be called in the near future. Purchase Commitments The Company has non-cancellable contracts and purchase orders for inventory of $112.8 million and $101.4 million, respectively, at June 30, 2017 and September 30, 2016. Contingencies During fiscal year 2016, the Company discovered that it inadvertently failed to register on Form S‑8 with the Securities and Exchange Commission certain shares of common stock previously authorized for issuance by the Company’s Board of Directors and stockholders under the Company’s 1995 Employee Stock Purchase Plan, as amended (the “ESPP”). As a result, certain purchasers of common stock under the ESPP may have the right to rescind their purchases for an amount equal to the purchase price paid for the shares, plus interest from the date of purchase, limited to the shares purchased in the last twelve months, which is the applicable federal statute of limitations, and still held by the original purchasers. These shares have been treated as issued and outstanding for financial reporting purposes. As of June 30, 2017, there were approximately 36,531 shares of common stock issued under the ESPP and held by the original purchasers of such shares that may be subject to these rescission rights which expire by statute of limitations on July 31, 2017. The shares were originally purchased for $8.02 per share. If holders of all of these shares seek to rescind their purchases, the Company could be required to make aggregate payments of up to approximately $0.3 million, which includes estimated statutory interest. The Company may also be subject to civil and other penalties by regulatory authorities as a result of the potential failure to register these shares. The Company does not believe that the failure to register the shares on a Form S‑8 or a potential rescission offer, if any, will have a material impact on its consolidated financial statements. The Company is subject to various legal proceedings, both asserted and unasserted, that arise in the ordinary course of business. The Company cannot predict the ultimate outcome of such legal proceedings or in certain instances provide reasonable ranges of potential losses. However, as of the date of this report, the Company believes that none of these claims will have a material adverse effect on its consolidated financial position or results of operations. In the event of unexpected subsequent developments and given the inherent unpredictability of these legal proceedings, there can be no assurance that the Company’s assessment of any claim will reflect the ultimate outcome, and an adverse outcome in certain matters could, from time to time, have a material adverse effect on the Company’s consolidated financial position or results of operations in particular quarterly or annual periods.

Subsequent Events

Subsequent Events	9 Months Ended
	Jun. 30, 2017
Subsequent Events [Abstract]
Subsequent Events	19. Subsequent Events On July 5, 2017, the Company entered into an Asset Purchase Agreement with Pacific Bio-Material Management, Inc. (“PBMMI”) and Novare, LLC, a wholly owned subsidiary of PBMMI (collectively, the “Sellers”), pursuant to which the Company acquired substantially all of the assets and liabilities of the Sellers’ business related to providing storage, transportation, management, and cold chain logistics of biological materials. Total cash payment made by the Company was $34.3 million, net of cash acquired, and is subject to working capital adjustments. The acquisition is expected to expand the Company’s existing capabilities with respect to sample management and integrated cold chain storage and transportation solutions within the Brooks Life Science Systems segment. The Company expects to report the results of operations for this acquisition within the results of Brooks Life Science Systems segment starting from the acquisition date. The Company has not presented a purchase price allocation related to fair values of assets acquired and liabilities assumed, as well as proforma information summary for its consolidated results of operations for the three and nine months ended June 30, 2017 and 2016 as if the acquisition occurred on October 1, 2015 because the initial accounting for the acquisition was incomplete on the financial statements issuance date. On August 1, 2017, the Company’s Board of Directors declared a cash dividend of $0.10 per share payable on September 29, 2017 to common stockholders of record as of September 8, 2017. Dividends are declared at the discretion of the Company’s Board of Directors and depend on the Company’s actual cash flows from operations, its financial condition and capital requirements and any other factors the Company’s Board of Directors may consider relevant. Future dividend declarations, as well as the record and payment dates for such dividends, will be determined by the Company’s Board of Directors on a quarterly basis.

Summary of Significant Accoun27

Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Jun. 30, 2017
Accounting Policies [Abstract]
Foreign Currency Translation	Foreign Currency Translation Certain transactions of the Company and its subsidiaries are denominated in currencies other than their functional currency. Foreign currency exchange losses generated from the settlement and remeasurement of these transactions are recognized in earnings and presented within “Other loss, net” in the Company’s unaudited Consolidated Statements of Operations. Net foreign currency transaction and remeasurement losses totaled $0.7 million and $0.5 million, respectively, during the three months ended June 30, 2017 and 2016 and $1.6 million and $1.5 million, respectively, during the nine months ended June 30, 2017 and 2016.
Use of Estimates	Use of Estimates The preparation of unaudited consolidated financial statements in conformity with GAAP requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the unaudited consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Significant estimates are associated with accounts receivable, inventories, goodwill, intangible assets other than goodwill, long-lived assets, derivative financial instruments, deferred income taxes, warranty obligations, revenue recognized using the percentage of completion method, pension obligations and stock-based compensation expense. The Company bases its estimates on historical experience and various other assumptions, including in certain circumstances, future projections that management believes to be reasonable under the circumstances. Although the Company regularly assesses these estimates, actual results could differ from those estimates. Changes in estimates are recorded in the period in which they occur and become known.
Recently Issued Accounting Pronouncements	Recently Issued Accounting Pronouncements In January 2017, the Financial Accounting Standards Board (the "FASB") issued an amendment to the accounting guidance related to goodwill impairment testing which eliminates the requirement to calculate the fair value of individual assets and liabilities of a reporting unit to measure goodwill impairment. In accordance with the provisions of the newly issued guidance, an entity should perform its goodwill impairment test by comparing the fair value of the reporting unit with its carrying value and recognize an impairment charge for the amount by which the carrying amount exceeds the reporting unit’s fair value, up to the amount of goodwill allocated to that reporting unit. The guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2019 and should be adopted prospectively. Early adoption of the newly issued guidance is permitted for interim or annual goodwill impairment tests performed after January 1, 2017. The Company performs its annual goodwill impairment assessment on April 1 st of each fiscal year. The Company adopted the guidance during the third quarter of fiscal year 2017. The adoption of the guidance did not have an impact on the Company’s financial position or results of operations. No triggering events indicating goodwill impairment occurred during the three and nine months ended June 30, 2017. Please refer to Note 5, “Goodwill and Intangible Assets” for further discussion. In January 2017, the FASB issued an amendment to the accounting guidance on business combinations to clarify the definition of a business when assessing whether a set of transferred assets and activities represents a business. Such set of transferred assets and activities does not represent a business if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or a group of similar identifiable assets. If the threshold is not met, entities need to evaluate whether the set of assets and activities meets the requirement that a business includes, at a minimum, an input and a substantive process that together significantly contribute to the ability to create outputs. The guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2017 and should be adopted prospectively. Early adoption of the newly issued guidance is permitted. The Company is currently evaluating the impact of this guidance on its financial position and results of operations. In February 2016, the FASB issued new accounting guidance for reporting lease transactions. In accordance with the provisions of the newly issued guidance, a lessee should recognize at the inception of the arrangement a right-of-use asset and a corresponding lease liability initially measured at the present value of lease payments over the lease term. For finance leases, interest on a lease liability should be recognized separately from the amortization of the right-of-use asset, while for operating leases, total lease costs are recorded on a straight-line basis over the lease term. For leases with a term of twelve months or less, a lessee is permitted to make an accounting policy election by class of underlying assets to forgo a recognition of right-of-use assets and corresponding lease liabilities and record a lease expense on a straight-line basis. Entities should determine at the inception of the arrangement whether a contract represents a lease or contains a lease which is defined as a right to control the use of identified property for a period of time in exchange for consideration. Additionally, entities should separate the lease components from the non-lease components and allocate the contract consideration on a relative standalone price basis in accordance with provisions of ASC Topic 606, Revenue from Contracts with Customers . The guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2018 and should be adopted via a modified retrospective approach with certain optional practical expedients that entities may elect to apply. The Company expects to adopt the guidance during the first quarter of fiscal year 2020 and is currently evaluating the impact of this guidance on its financial position and results of operations. In June 2016, the FASB issued new accounting guidance for reporting credit losses. The new guidance introduces a new "expected loss" impairment model that applies to most financial assets measured at amortized cost and certain other instruments, including trade and other receivables, loans, held-to-maturity debt securities and other financial assets. Entities are required to estimate expected credit losses over the life of financial assets and record an allowance against the assets’ amortized cost basis to present them at the amount expected to be collected. Additionally, the guidance amends the impairment model for available for sale debt securities and requires entities to determine whether all or a portion of the unrealized loss on such debt security is a credit loss. The guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2019. Early adoption of the newly issued guidance is permitted for fiscal years, and interim periods within those years, beginning after December 15, 2018. The standard should be applied as a cumulative-effect adjustment to retained earnings as of the beginning of the first reporting period in which the guidance is effective. The Company expects to adopt the guidance during the first quarter of fiscal year 2021 and is currently evaluating the impact of this guidance on its financial position and results of operations. In February 2015, the FASB issued an amendment to the accounting guidance for consolidations of financial statements by changing the analysis that a reporting entity must perform to determine whether it should consolidate certain types of variable interest entities. The guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2015. The guidance can be adopted either via a full retrospective approach or a modified retrospective approach by recording a cumulative-effect adjustment to beginning equity in the period of adoption. The Company adopted the guidance during the first quarter of fiscal year 2017. The adoption of the guidance did not have an impact on the Company’s financial position or results of operations. Please refer to Note 9, "Other Balance Sheet Information" for further discussion. In August 2014, the FASB issued new accounting guidance related to evaluation of relevant conditions or events that raise substantial doubt about the entity’s ability to continue as a going concern within one year after the financial statements issuance date. The guidance is effective for fiscal years ending after December 15, 2016, and for annual periods and interim periods thereafter. The Company expects to adopt the guidance during the fourth quarter of fiscal year 2017. Early adoption of the newly issued guidance is permitted. The adoption of the guidance is not expected to have an impact on the Company’s financial position or results of operations. In May 2014, the FASB issued new accounting guidance for reporting revenue recognition. The guidance provides for the recognition of revenue when promised goods or services are transferred to customers in an amount that reflects the consideration that is expected to be received for those goods or services. A five-step process set forth in the guidance may require more judgment and estimation within the revenue recognition process than the current GAAP, including identifying performance obligations in the contract, estimating the amount of variable consideration to include in the transaction price and allocating the transaction price to each separate performance obligation. The guidance was initially effective for fiscal years, and interim periods within those years, beginning after December 15, 2016. In August 2015, the FASB issued an amendment deferring the effective date of the guidance by one year. The guidance should be adopted retrospectively either for each reporting period presented or via recognizing the cumulative effect at the date of the initial application. Early adoption is permitted only as of annual reporting periods, including the interim periods, beginning after December 15, 2016. The Company expects to adopt the guidance during the first quarter of fiscal year 2019. The Company has initiated the evaluation of the potential impact of adopting the new guidance on its financial position and results of operations, but has not yet completed such assessment or determined the transition method that will be used to adopt the new guidance.

Marketable Securities (Tables)

Marketable Securities (Tables)	9 Months Ended
	Jun. 30, 2017
Investments, Debt and Equity Securities [Abstract]
Summary of Marketable Securities Including Accrued Interest Receivable	The following is a summary of the amortized cost and the fair value, including accrued interest receivable, as well as unrealized holding gains (losses) on the short-term and long-term marketable securities as of June 30, 2017 and September 30, 2016 (in thousands): Gross Gross Amortized Unrealized Unrealized Cost Gains Losses Fair Value June 30, 2017 : Corporate securities $ 2,565 $ — $ — $ 2,565 Other debt securities 12 — — 12 $ 2,577 $ — $ — $ 2,577 September 30, 2016 : Corporate securities $ 2,394 $ — $ — $ 2,394 Other debt securities 39 — — 39 Municipal securities 3,704 1 (3) 3,702 $ 6,137 $ 1 $ (3) $ 6,135
Fair Value of Marketable Securities by Contractual Maturity	The fair values of the marketable securities by contractual maturities at June 30, 2017 are presented below (in thousands): Fair Value Due in one year or less $ 12 Due after ten years 2,565 Total marketable securities $ 2,577

Acquisitions (Tables)

Acquisitions (Tables)	9 Months Ended
	Jun. 30, 2017
Business Combinations [Abstract]
Amounts of Assets and Liabilities at Fair Value as of Acquisition Date	The preliminary amounts recorded were as follows (in thousands): Fair Value of Assets Liabilities Inventory $ 1,283 Intangible assets 6,100 Goodwill 8,527 Accrued liabilities (30) Other liabilities (686) Total purchase price $ 15,194
Pro Forma Information	The following unaudited pro forma financial information represents a summary of the consolidated results of operations for the Company and BioStorage for the three and nine months ended June 30, 2016 as if the acquisition of BioStorage occurred on October 1, 2014 (in thousands): Three Months Ended Nine Months Ended June 30, 2016 June 30, 2016 Revenue $ 147,534 $ 413,816 Net income (loss) 9,163 (74,024) Basic income (loss) per share $ 0.13 $ (1.08) Diluted income (loss) per share $ 0.13 $ (1.08) Weighted average shares outstanding used in computing net income (loss) per share: Basic 68,628 68,437 Diluted 69,166 68,437

Goodwill and Intangible Assets

Goodwill and Intangible Assets (Tables)	9 Months Ended
	Jun. 30, 2017
Goodwill and Intangible Assets Disclosure [Abstract]
Components of Goodwill by Business Segment	The components of the Company’s goodwill by an operating segment at June 30, 2017 and September 30, 2016 are as follows (in thousands): Brooks Semiconductor Brooks Solutions Life Science Group Systems Other Total Gross goodwill, at September 30, 2016 $ 655,781 $ 135,301 $ 26,014 $ 817,096 Accumulated goodwill impairments (588,944) — (26,014) (614,958) Goodwill, net of accumulated impairments, at September 30, 2016 66,837 135,301 — 202,138 Acquisitions and adjustments (56) 8,527 — 8,471 Gross goodwill, at June 30, 2017 655,725 143,828 26,014 825,567 Accumulated goodwill impairments (588,944) — (26,014) (614,958) Goodwill, net of accumulated impairments, at June 30, 2017 $ 66,781 $ 143,828 $ — $ 210,609
Components of Identifiable Intangible Assets	The components of the Company’s identifiable intangible assets as of June 30, 2017 and September 30, 2016 are as follows (in thousands): June 30, 2017 September 30, 2016 Accumulated Net Book Accumulated Net Book Cost Amortization Value Cost Amortization Value Patents $ 9,028 $ 7,724 $ 1,304 $ 7,808 $ 7,486 $ 322 Completed technology 60,745 53,931 6,814 60,485 51,018 9,467 Trademarks and trade names 9,142 4,776 4,366 9,142 4,204 4,938 Customer relationships 119,260 56,286 62,974 114,263 47,147 67,116 $ 198,175 $ 122,717 $ 75,458 $ 191,698 $ 109,855 $ 81,843
Schedule of Future Amortization Expense	Estimated future amortization expense for the intangible assets for the remainder of fiscal year 2017 and the subsequent four fiscal years is as follows (in thousands): Fiscal year ended September 30, 2017 $ 3,970 2018 15,693 2019 15,468 2020 14,156 2021 8,253 Thereafter 17,918 $ 75,458

Other Balance Sheet Informati31

Other Balance Sheet Information (Tables)	9 Months Ended
	Jun. 30, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Summary of Accounts Receivable	The following is a summary of accounts receivable at June 30, 2017 and September 30, 2016 (in thousands): June 30, September 30, 2017 2016 Accounts receivable $ 122,394 $ 108,713 Less allowance for doubtful accounts (1,514) (2,241) Less allowance for sales returns (128) (100) Accounts receivable, net $ 120,752 $ 106,372
Summary of Inventories	The following is a summary of inventories at June 30, 2017 and September 30, 2016 (in thousands): June 30, September 30, 2017 2016 Inventories Raw materials and purchased parts $ 72,820 $ 60,979 Work-in-process 11,273 16,090 Finished goods 21,211 15,503 Total inventories $ 105,304 $ 92,572
Product Warranty and Retrofit Activity on Gross Basis	The following is a summary of product warranty and retrofit activity on a gross basis for the three and nine months ended June 30, 2017 and 2016 (in thousands): Activity -Three Months Ended June 30, 2017 Balance Balance March 31, June 30, 2017 Accruals Costs Incurred 2017 $ 7,073 $ 2,440 $ (1,867) $ 7,646 Activity -Three Months Ended June 30, 2016 Balance Balance March 31, June 30, 2016 Accruals Costs Incurred 2016 $ 5,735 $ 2,279 $ (2,059) $ 5,955 Activity -Nine Months Ended June 30, 2017 Balance Balance September 30, June 30, 2016 Accruals Costs Incurred 2017 $ 6,324 $ 7,656 $ (6,334) $ 7,646 Activity -Nine Months Ended June 30, 2016 Balance Balance September 30, June 30, 2015 Accruals Costs Incurred 2016 $ 6,089 $ 6,989 $ (7,123) $ 5,955

Derivative Instruments (Tables)

Derivative Instruments (Tables)	9 Months Ended
	Jun. 30, 2017
Derivative Instruments and Hedging Activities Disclosure [Abstract]
Schedule of Net Gains and Losses Realized on Derivative Instruments	Net gains and losses related to these contracts are recorded as a component of "Other loss, net" in the accompanying unaudited Consolidated Statements of Operations and are as follows for the three and nine months ended June 30, 2017 and 2016 (in thousands): Three Months Ended Nine Months Ended June 30, June 30, 2017 2016 2017 2016 Realized gains (losses) on derivatives not designated as hedging instruments $ 147 $ 233 $ (450) $ 1,230
Notional Amounts Outstanding under Foreign Currency Contracts	The Company had the following notional amounts outstanding under foreign currency contracts that do not qualify for hedge accounting at June 30, 2017 and September 30, 2016 (in thousands): June 30, 2017: Notional Amount Notional Amount Fair Value of Fair Value of Buy Currency of Buy Currency Sell Currency Maturity of Sell Currency Assets Liabilities Japanese Yen 445,000 U.S. Dollar July 2017 3,980 $ — $ (13) British Pound 1,470 U.S. Dollar July 2017 1,906 — (16) Korean Won 4,193,000 U.S. Dollar July 2017 3,679 — (10) U.S. Dollar 5,860 Chinese Yuan July 2017 40,000 — (20) Euro 11,600 U.S. Dollar July 2017 13,229 — (53) British Pound 164 Norwegian Krone July 2017 1,800 2 — Singapore Dollar 620 U.S. Dollar July 2017 449 — (1) U.S. Dollar 213 Israeli Shekel July 2017 748 1 — Euro 18,513 British Pound July 2017 16,280 99 — $ 102 $ (113) September 30, 2016: Notional Amount Notional Amount Fair Value of Fair Value of Buy Currency of Buy Currency Sell Currency Maturity of Sell Currency Assets Liabilities British Pound 190 Swedish Krona October 2016 2,100 $ 1 $ — Japanese Yen 124,000 U.S. Dollar October 2016 1,229 — — U.S. Dollar 6,107 British Pound October 2016 4,710 2 — Euro 13,300 U.S. Dollar October 2016 14,976 — (40) U.S. Dollar 5,815 Chinese Yuan October 2016 39,000 — (33) Korean Won 2,488,000 U.S. Dollar October 2016 2,255 1 — Euro 7,482 British Pound October 2016 6,500 — (23) U.S. Dollar 311 Israeli Shekel October 2016 1,169 1 — Singapore Dollar 360 U.S. Dollar October 2016 265 — — U.S. Dollar 210 Taiwanese Dollar October 2016 6,600 — — British Pound 171 Norwegian Krone October 2016 1,800 — — $ 5 $ (96)

Stock-Based Compensation (Table

Stock-Based Compensation (Tables)	9 Months Ended
	Jun. 30, 2017
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-Based Compensation Expense	The following table reflects stock-based compensation expense recorded during the three and nine months ended June 30, 2017 and 2016 (in thousands): Three Months Ended June 30, Nine Months Ended June 30, 2017 2016 2017 2016 Restricted stock $ 4,044 $ 1,501 $ 10,634 $ 7,801 Employee stock purchase plan 153 136 447 405 Total stock-based compensation expense $ 4,197 $ 1,637 $ 11,081 $ 8,206
Status of Restricted Stock Activity and Changes	The following table summarizes restricted stock unit activity for the six months ended March 31, 2017: Weighted Average Grant-Date Shares Fair Value Outstanding at September 30, 2016 2,489,076 $ 10.79 Granted 1,008,570 $ 14.32 Vested (911,738) $ 10.51 Forfeited (79,699) $ 11.66 Outstanding at June 30, 2017 2,506,209 $ 12.52 The following table reflects restricted stock units granted during the six months ended March 31, 2017 and 2016: Time-Based Performance- Total Units Units Stock Grants Based Units Nine months ended June 30, 2017 1,008,570 377,213 43,019 Nine months ended June 30, 2016 1,679,591 734,250 85,091

Earnings per Share (Tables)

Earnings per Share (Tables)	9 Months Ended
	Jun. 30, 2017
Earnings Per Share [Abstract]
Reconciliation of Weighted Average Common Shares Outstanding for Purposes of Calculating Basic and Diluted Earnings Per Share	The calculations of basic and diluted net income (loss) per share and basic and diluted weighted average shares outstanding are as follows for the three and nine months ended June 30, 2017 and 2016 (in thousands, except per share data): Three Months Ended Nine Months Ended June 30, June 30, 2017 2016 2017 2016 Net income (loss) $ 17,350 $ 8,564 $ 45,226 $ (80,022) Weighted average common shares outstanding used in computing basic earnings (losses) per share 69,711 68,628 69,496 68,437 Dilutive common stock options and restricted stock units 694 538 702 — Weighted average common shares outstanding used in computing diluted earnings (losses) per share 70,405 69,166 70,198 68,437 Basic net income (loss) per share $ $ $ $ Diluted net income (loss) per share $ $ $ $

Restructuring Charges (Tables)

Restructuring Charges (Tables)	9 Months Ended
	Jun. 30, 2017
Restructuring and Related Activities [Abstract]
Activity Related to Restructuring Accruals	The following is a summary of activity related to the Company’s restructuring charges for the three and nine months ended June 30, 2017 and 2016 (in thousands): Activity -Three Months Ended June 30, 2017 Balance Balance March 31, June 30, 2017 Expenses Payments 2017 Total restructuring liabilities related to workforce termination benefits $ 2,044 $ 828 $ (1,182) $ 1,690 Activity -Three Months Ended June 30, 2016 Balance Balance March 31, June 30, 2016 Expenses Payments 2016 Facility and other contract termination costs $ 96 $ — $ (96) $ — Workforce-related termination benefits 7,293 996 (2,500) 5,789 Total restructuring liabilities $ 7,389 $ 996 $ (2,596) $ 5,789 Activity -Nine Months Ended June 30, 2017 Balance Balance September 30, June 30, 2016 Expenses Payments 2017 Total restructuring liabilities related to workforce termination benefits $ 5,939 $ 2,663 $ (6,912) $ 1,690 Activity -Nine Months Ended June 30, 2016 Balance Balance September 30, June 30, 2015 Expenses Payments 2016 Facility and other contract termination costs $ 433 $ 25 $ (458) $ — Workforce-related termination benefits 1,640 9,782 (5,633) 5,789 Total restructuring liabilities $ 2,073 $ 9,807 $ (6,091) $ 5,789

Employee Benefit Plans (Tables)

Employee Benefit Plans (Tables)	9 Months Ended
	Jun. 30, 2017
Compensation and Retirement Disclosure [Abstract]
Components of Net Pension Cost	The components of the Company’s net pension cost for the three and nine months ended June 30, 2017 and 2016 are as follows (in thousands): Three Months Ended Nine Months Ended June 30, June 30, 2017 2016 2017 2016 Service cost $ 68 $ 138 $ 202 $ 410 Interest cost 7 18 21 54 Amortization of losses 2 4 6 12 Expected return on plan assets (33) (41) (99) (120) Net periodic pension cost $ 44 $ 119 $ 130 $ 356

Segment Information (Tables)

Segment Information (Tables)	9 Months Ended
	Jun. 30, 2017
Segment Reporting [Abstract]
Financial Information for Business Segments	The following is the summary of the financial information for the Company’s operating and reportable segments for the three and nine months ended June 30, 2017 and 2016 (in thousands): Brooks Brooks Semiconductor Life Science Solutions Group Systems Total Three Months Ended June 30, 2017: Revenue Products $ 124,681 $ 17,276 $ 141,957 Services 20,280 19,480 39,760 Segment revenue $ 144,961 $ 36,756 $ 181,717 Gross profit $ 58,083 $ 13,489 $ 71,572 Segment operating income 26,188 1,134 27,322 Depreciation expense 1,192 1,134 2,326 Three Months Ended June 30, 2016: Revenue Products $ 99,254 $ 12,342 $ 111,596 Services 19,179 16,759 35,938 Segment revenue $ 118,433 $ 29,101 $ 147,534 Gross profit $ 42,904 $ 11,259 $ 54,163 Segment operating income (loss) 13,119 (736) 12,383 Depreciation expense 1,448 1,018 2,466 Nine Months Ended June 30, 2017: Revenue Products $ 349,710 $ 46,974 $ 396,684 Services 56,532 57,789 114,321 Segment revenue $ 406,242 $ 104,763 $ 511,005 Gross profit $ 154,877 $ 38,162 $ 193,039 Segment operating income 63,562 2,535 66,097 Depreciation expense 3,786 3,269 7,055 Nine Months Ended June 30, 2016: Revenue Products $ 268,671 $ 33,567 $ 302,238 Services 57,657 42,875 100,532 Segment revenue $ 326,328 $ 76,442 $ 402,770 Gross profit $ 114,506 $ 27,011 $ 141,517 Segment operating income (loss) 22,717 (7,555) 15,162 Depreciation expense 3,375 2,452 5,827 Assets: June 30, 2017 $ 330,746 $ 262,250 $ 592,996 September 30, 2016 317,717 247,735 565,452
Reconciliation of Reportable Segment Operating Income (Loss) to Corresponding Consolidated Amounts	The following is a reconciliation of the Company’s operating and reportable segments’ operating income and segment assets to the corresponding amounts presented in the accompanying unaudited Consolidated Balance Sheets and Consolidated Statements of Operations for the three and nine months ended June 30, 2017 and 2016 (in thousands): Three Months Ended Nine Months Ended June 30, June 30, 2017 2016 2017 2016 Segment operating income $ 27,322 $ 12,383 $ 66,097 $ 15,162 Amortization of acquired intangible assets 3,278 2,754 9,636 8,056 Restructuring charges 828 996 2,663 9,807 Other unallocated corporate expenses 4,446 139 7,066 3,464 Total operating income (loss) $ 18,770 $ 8,494 $ 46,732 $ (6,165)
Reconciliation of Reportable Segment Assets to Corresponding Consolidated Amounts	June 30, September 30, 2017 2016 Segment assets $ 592,996 $ 565,452 Cash, cash equivalents and marketable securities 119,658 91,221 Deferred tax assets 1,460 1,982 Equity method investments 32,606 27,250 Other unallocated corporate net assets 51 — Total assets $ 746,771 $ 685,905

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	9 Months Ended
	Jun. 30, 2017
Fair Value Disclosures [Abstract]
Assets and Liabilities Measured at Fair Value on Recurring Basis	The following tables summarize assets and liabilities measured and recorded at fair value on a recurring basis in the accompanying unaudited Consolidated Balance Sheets as of June 30, 2017 and September 30, 2016 (in thousands): Fair Value Measurements at Reporting Date Using Quoted Prices in Significant Active Markets for Significant Other Unobservable June 30, Identical Assets Observable Inputs Inputs Description 2017 (Level 1) (Level 2) (Level 3) Assets: Cash equivalents $ 45 $ — $ 45 $ — Available-for-sale securities 2,577 — 2,577 — Foreign exchange contracts 102 — 102 — Total Assets $ 2,724 $ — $ 2,724 $ — Liabilities: Foreign exchange contracts 113 — 113 — Total Liabilities $ 113 $ — $ 113 $ — Fair Value Measurements at Reporting Date Using Quoted Prices in Significant Active Markets for Significant Other Unobservable September 30, Identical Assets Observable Inputs Inputs Description 2016 (Level 1) (Level 2) (Level 3) Assets: Cash equivalents $ 143 $ 98 $ 45 $ — Available-for-sale securities 6,135 — 6,135 — Foreign exchange contracts 5 — 5 — Convertible debt securities 5,774 — — 5,774 Stock warrant 45 — — 45 Total Assets $ 12,102 $ 98 $ 6,185 $ 5,819 Liabilities: Contingent consideration $ 500 $ — $ — $ 500 Foreign exchange contracts 97 — 97 — $ 597 $ — $ 97 $ 500
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation	The following table presents the reconciliation of the assets and liabilities measured and recorded at fair value on a recurring basis using significant unobservable inputs (Level 3) (in thousands): Convertible Stock Contingent Debt Securities Warrants Consideration Total Balance at September 30, 2016 $ 5,774 $ 45 $ 500 $ 6,319 Change in fair value (194) (37) — (231) Settlements (5,580) (8) (500) (6,088) Balance at June 30, 2017 $ — $ — $ — $ —

Summary of Significant Accoun39

Summary of Significant Accounting Policies (Details) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Accounting Policies [Abstract]
Foreign currency transaction and remeasurement loss	$ 0.7	$ 0.5	$ 1.6	$ 1.5

Marketable Securities - General

Marketable Securities - General Information (Details) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Schedule of Available-for-sale Securities [Line Items]
Marketable securities sold during period, fair value	$ 3.6	$ 0	$ 3.6	$ 127.6
Marketable securities sold during period, amortized cost basis	3.6	$ 0	3.6	127.7
Net realized losses				0.2
Proceeds from sale of marketable securities			3.5	127
Reclassification unrealized net holding losses				$ 0.2
Unrealized losses on available for sale securities presented as a component of accumulated other comprehensive income	0		0
Maximum
Schedule of Available-for-sale Securities [Line Items]
Net realized losses	$ 0.1		0.1
Reclassification unrealized net holding losses			$ 0.1

Marketable Securities - Summary

Marketable Securities - Summary of Amortized Cost and Fair Value (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 2,577	$ 6,137
Gross Unrealized Gains		1
Gross Unrealized Losses		(3)
Fair Value	2,577	6,135
Corporate securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	2,565	2,394
Fair Value	2,565	2,394
Other debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	12	39
Fair Value	$ 12	39
Municipal securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost		3,704
Gross Unrealized Gains		1
Gross Unrealized Losses		(3)
Fair Value		$ 3,702

Marketable Securities - Fair Va

Marketable Securities - Fair Value of Marketable Securities by Contractual Maturity (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Investments, Debt and Equity Securities [Abstract]
Due in one year or less	$ 12
Due after ten years	2,565
Fair Value	$ 2,577	$ 6,135

Marketable Securities - Unreali

Marketable Securities - Unrealized Loss Position (Details) - USD ($) $ in Millions	Jun. 30, 2017	Sep. 30, 2016
Investments, Debt and Equity Securities [Abstract]
Fair value of marketable securities in unrealized loss position	$ 0	$ 2.5

Acquisitions - Ownership Inform

Acquisitions - Ownership Information (Details) $ in Millions	Nov. 28, 2016USD ($)
Cool Lab, LLC
Business Acquisition [Line Items]
Percentage of voting interests acquired (as a percent)	100.00%
BioCision, LLC
Business Acquisition [Line Items]
Equity interest in acquiree, percentage (as a percent)	20.00%
BioCision, LLC | Cool Lab, LLC
Business Acquisition [Line Items]
Net carrying value of assets transferred	$ 0.9

Acquisitions - Purchase Conside

Acquisitions - Purchase Consideration (Details) - USD ($) $ in Thousands	Nov. 28, 2016	Jun. 30, 2017
Business Acquisition [Line Items]
Non-cash consideration transferred		$ 10,348
Cool Lab, LLC
Business Acquisition [Line Items]
Total purchase price	$ 15,200
Payments to acquire businesses	4,800
Liabilities incurred	100
Non-cash consideration transferred	10,300
Equity method investments, fair value disclosure	3,100
Convertible debt securities and warrants	5,600
Term notes, fair value disclosure	1,600
Aggregate carrying value	$ 8,600
Gain of fair value measurement included in earnings		$ 1,600

Acquisitions - Amounts of Asset

Acquisitions - Amounts of Assets and Liabilities at Fair Value as of Acquisition Date (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Business Acquisition [Line Items]
Goodwill	$ 210,609	$ 202,138
Cool Lab, LLC
Business Acquisition [Line Items]
Inventory	1,283
Intangible assets	6,100
Goodwill	8,527
Accrued liabilities	(30)
Other liabilities	(686)
Total purchase price	$ 15,194

Acquisitions - Intangible Asset

Acquisitions - Intangible Assets Acquired (Details) - Cool Lab, LLC $ in Millions	Nov. 28, 2016USD ($)
Acquired Finite-Lived Intangible Assets [Line Items]
Weighted average useful life of intangible assets (in years)	5 years 6 months
Customer Relationships, Certain Customer
Acquired Finite-Lived Intangible Assets [Line Items]
Finite-lived intangible assets acquired	$ 3.6
Weighted average useful life of intangible assets (in years)	3 years
Completed Technology
Acquired Finite-Lived Intangible Assets [Line Items]
Finite-lived intangible assets acquired	$ 1.2
Weighted average useful life of intangible assets (in years)	8 years
Other Customer Relationship
Acquired Finite-Lived Intangible Assets [Line Items]
Finite-lived intangible assets acquired	$ 1.3
Weighted average useful life of intangible assets (in years)	10 years

Acquisitions - Escrow (Details)

Acquisitions - Escrow (Details) - BioStorage Technologies, Inc. - USD ($) $ in Millions	Jun. 30, 2017	Sep. 30, 2016	Nov. 30, 2015
Business Acquisition [Line Items]
Escrow deposit	$ 0		$ 5.4
Escrow reserve			2.9
Escrow deposit for acquiree's employees retention obligations	$ 0	$ 0.1	$ 2.5

Acquisitions - General Informat

Acquisitions - General Information (Details) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016	Nov. 28, 2016	Sep. 30, 2016	Nov. 30, 2015
Business Acquisition [Line Items]
Amortization of acquired intangible assets	$ 4.3	$ 3.8	$ 12.7	$ 11.1
Acquisition related costs			0.2	3.2
Cool Lab, LLC
Business Acquisition [Line Items]
Liabilities arising from contingencies, amount recognized	0.7		0.7		$ 0.7
Actual revenues	1.1		2.5
Actual net income (loss)			(0.3)
Inventory step up	0.1		0.4
Amortization of acquired intangible assets	0.4		0.8
BioStorage Technologies, Inc.
Business Acquisition [Line Items]
Actual revenues	15.3	12.4	46	30.3
Actual net income (loss)	2.4	1.1	6	0.3
Amortization of acquired intangible assets	1.1	0.9	3.4	2
Escrow deposit for acquiree's employees retention obligations	0		0			$ 0.1	$ 2.5
Compensation expense	0	0.3	0.1	$ 0.7
Selling, General and Administrative Expenses | Cool Lab, LLC
Business Acquisition [Line Items]
Acquisition related costs	0.1		$ 0.4
Selling, General and Administrative Expenses | BioStorage Technologies, Inc.
Business Acquisition [Line Items]
Acquisition related costs	0.1	$ 0.1
Prepaid Expenses and Other Current Assets
Business Acquisition [Line Items]
Escrow deposit for acquiree's employees retention obligations							$ 2.5
Maximum | Cool Lab, LLC
Business Acquisition [Line Items]
Actual net income (loss)	$ (0.1)

Acquisitions - Pro Forma Inform

Acquisitions - Pro Forma Information - Tabular Disclosure (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended	9 Months Ended
	Jun. 30, 2016	Jun. 30, 2016
Business Combinations [Abstract]
Revenue	$ 147,534	$ 413,816
Net income (loss)	$ 9,163	$ (74,024)
Basic income (loss) per share (in dollars per share)	$ 0.13	$ (1.08)
Diluted income (loss) per share (in dollars per share)	$ 0.13	$ (1.08)
Basic (in shares)	68,628	68,437
Diluted (in shares)	69,166	68,437

Acquisitions - Pro Forma Info51

Acquisitions - Pro Forma Information - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Business Acquisition [Line Items]
Income tax provision	$ 3,680	$ 220	$ 9,900	$ 75,070
Pro Forma | BioStorage Technologies, Inc.
Business Acquisition [Line Items]
Aggregate amortization and depreciation expense				600
Income tax provision				$ 500

Goodwill and Intangible Asset52

Goodwill and Intangible Assets - Goodwill Impairment Test (Details)	9 Months Ended
	Jun. 30, 2017item
Goodwill and Intangible Assets Disclosure [Abstract]
Number of reporting units	5
Number of reporting units for which qualitative assessment was conducted	3
Number of reporting units for which quantitative assessment was conducted	2

Goodwill and Intangible Asset53

Goodwill and Intangible Assets - Components of Goodwill by Operating Segment (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Goodwill [Line Items]
Gross goodwill	$ 825,567	$ 817,096
Accumulated goodwill impairments	(614,958)	(614,958)
Goodwill, net of accumulated impairments	210,609	202,138
Brooks Semiconductor Solutions Group
Goodwill [Line Items]
Gross goodwill	655,725	655,781
Accumulated goodwill impairments	(588,944)	(588,944)
Goodwill, net of accumulated impairments	66,781	66,837
Brooks Life Science Systems
Goodwill [Line Items]
Gross goodwill	143,828	135,301
Goodwill, net of accumulated impairments	143,828	135,301
Other
Goodwill [Line Items]
Gross goodwill	26,014	26,014
Accumulated goodwill impairments	$ (26,014)	$ (26,014)

Goodwill and Intangible Asset54

Goodwill and Intangible Assets - Goodwill Roll Forward (Details) $ in Thousands	9 Months Ended
	Jun. 30, 2017USD ($)
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	$ 202,138
Acquisitions and adjustments	8,471
Goodwill, net of accumulated impairments, ending balance	210,609
Brooks Semiconductor Solutions Group
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	66,837
Acquisitions and adjustments	(56)
Goodwill, net of accumulated impairments, ending balance	66,781
Brooks Life Science Systems
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	135,301
Acquisitions and adjustments	8,527
Goodwill, net of accumulated impairments, ending balance	$ 143,828

Goodwill and Intangible Asset55

Goodwill and Intangible Assets - Goodwill Acquired (Details) $ in Millions	9 Months Ended
	Jun. 30, 2017USD ($)
Cool Lab, LLC
Goodwill [Line Items]
Goodwill acquired during period	$ 8.5

Goodwill and Intangible Asset56

Goodwill and Intangible Assets - Components of Identifiable Intangible Assets (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Finite-Lived Intangible Assets [Line Items]
Cost	$ 198,175	$ 191,698
Accumulated Amortization	122,717	109,855
Net Book Value	75,458	81,843
Patents
Finite-Lived Intangible Assets [Line Items]
Cost	9,028	7,808
Accumulated Amortization	7,724	7,486
Net Book Value	1,304	322
Completed Technology
Finite-Lived Intangible Assets [Line Items]
Cost	60,745	60,485
Accumulated Amortization	53,931	51,018
Net Book Value	6,814	9,467
Trademarks and Trade Names
Finite-Lived Intangible Assets [Line Items]
Cost	9,142	9,142
Accumulated Amortization	4,776	4,204
Net Book Value	4,366	4,938
Customer Relationships
Finite-Lived Intangible Assets [Line Items]
Cost	119,260	114,263
Accumulated Amortization	56,286	47,147
Net Book Value	$ 62,974	$ 67,116

Goodwill and Intangible Asset57

Goodwill and Intangible Assets - Amortization Expense (Details) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Goodwill and Intangible Assets Disclosure [Abstract]
Amortization expense for intangible assets	$ 4.3	$ 3.8	$ 12.7	$ 11.1

Goodwill and Intangible Asset58

Goodwill and Intangible Assets - Estimated Future Amortization Expense of Intangible Assets (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Goodwill and Intangible Assets Disclosure [Abstract]
2,017	$ 3,970
2,018	15,693
2,019	15,468
2,020	14,156
2,021	8,253
Thereafter	17,918
Net Book Value	$ 75,458	$ 81,843

Equity Method Investments - Bio

Equity Method Investments - BioCision, LLC (Details) - USD ($) $ in Thousands	Nov. 28, 2016	Nov. 28, 2016	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016	Sep. 30, 2016
Schedule of Equity Method Investments [Line Items]
Equity method investments			$ 32,628		$ 32,628		$ 27,273
Equity in earnings of equity method investments			2,530	$ 379	7,249	$ 1,248
Non-cash consideration transferred					10,348
Gain on settlement of equity method investment					1,847
BioCision, LLC
Schedule of Equity Method Investments [Line Items]
Joint venture interest, percentage							20.00%
Equity method investments	$ 1,200	$ 1,200					$ 1,700
Equity in earnings of equity method investments		$ (500)		$ (300)		(700)
Recognized measurement gains						$ 500
Annual interest rate (percent)							10.00%
Equity interest in acquiree, percentage (as a percent)	20.00%	20.00%
Equity in earnings of equity method investments, adjustment		$ 200
BioCision, LLC | Maximum
Schedule of Equity Method Investments [Line Items]
Stock warrant							$ 100
Convertible Debt Securities
Schedule of Equity Method Investments [Line Items]
Convertible debt securities, carrying value	$ 5,800	5,800
Convertible Debt Securities | BioCision, LLC
Schedule of Equity Method Investments [Line Items]
Investment maturity period							5 years
Convertible debt securities							$ 5,800
Other Assets
Schedule of Equity Method Investments [Line Items]
Loan receivable, carrying value	$ 1,600	$ 1,600					1,500
Other Assets | BioCision, LLC
Schedule of Equity Method Investments [Line Items]
Loan receivable, carrying value							1,500
Loan receivable							1,500
Other Income
Schedule of Equity Method Investments [Line Items]
Loss on settlement of financial instruments					200
Other Income | BioCision, LLC
Schedule of Equity Method Investments [Line Items]
Gain on settlement of equity method investment					1,800
Cool Lab, LLC
Schedule of Equity Method Investments [Line Items]
Percentage of voting interests acquired (as a percent)	100.00%	100.00%
Total purchase price	$ 15,200
Payments to acquire businesses	4,800
Liabilities incurred	100
Non-cash consideration transferred	10,300
Equity method investments, fair value disclosure	3,100
Convertible debt securities and warrants	5,600
Term notes, fair value disclosure	1,600
Loan receivable, carrying value	1,600	$ 1,600
Cool Lab, LLC | BioCision, LLC
Schedule of Equity Method Investments [Line Items]
Net carrying value of assets transferred	900
Cool Lab, LLC | Convertible Debt Securities
Schedule of Equity Method Investments [Line Items]
Convertible debt securities	5,600	5,600
Convertible debt securities, carrying value	5,800	5,800
Significant Unobservable Inputs (Level 3) | Cool Lab, LLC
Schedule of Equity Method Investments [Line Items]
Loan receivable, fair value	1,600	1,600
Warrants
Schedule of Equity Method Investments [Line Items]
Stock warrant			$ 0		0
Loss on settlement of financial instruments					$ 37
Warrants | Maximum
Schedule of Equity Method Investments [Line Items]
Stock warrant							$ 100
Warrants | Cool Lab, LLC | Maximum
Schedule of Equity Method Investments [Line Items]
Stock warrant	100	100
Warrants | Significant Unobservable Inputs (Level 3) | Cool Lab, LLC | Maximum
Schedule of Equity Method Investments [Line Items]
Stock warrant	$ 100	$ 100

Equity Method Investments - ULV

Equity Method Investments - ULVAC Cryogenics, Inc. (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016	Sep. 30, 2016
Schedule of Equity Method Investments [Line Items]
Equity method investments	$ 32,628		$ 32,628		$ 27,273
Equity in earnings of equity method investments	$ 2,530	$ 379	$ 7,249	$ 1,248
Ulvac Cryogenics Incorporated
Schedule of Equity Method Investments [Line Items]
Joint venture interest, percentage	50.00%		50.00%
Equity method investments	$ 32,600		$ 32,600		25,600
Equity in earnings of equity method investments	2,500	700	7,700	2,000
Management fee payments received	300	$ 200	800	600
Charges incurred from related parties			200	$ 200
Accounts payable for unpaid products and services (less than)	$ 100		$ 100		$ 100

Line of Credit (Details)

Line of Credit (Details) - Wells Fargo Bank, N.A. - Line of Credit - Revolving Credit Facility - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Jun. 30, 2017	Jun. 30, 2017	Sep. 30, 2016
Line of Credit Facility [Line Items]
Debt instrument, term (in years)		5 years
Line of credit, maximum borrowing capacity	$ 75,000	$ 75,000
Outstanding line of credit	0	0	$ 0
Maximum
Line of Credit Facility [Line Items]
Unused portion commitment fee, value (less than)	$ 100	$ 100

Income Taxes (Details)

Income Taxes (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Income Tax Disclosure [Abstract]
Income tax provision	$ 3,680	$ 220	$ 9,900	$ 75,070
Reductions in unrecognized tax benefits from expiration		$ 300	900
Anticipated unrecognized tax benefit reduction during next twelve months	$ 500		$ 500

Other Balance Sheet Informati63

Other Balance Sheet Information - Summary of Account Receivable (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Valuation and Qualifying Accounts Disclosure [Line Items]
Accounts receivable	$ 122,394	$ 108,713
Less allowance for doubtful accounts	(1,514)	(2,241)
Accounts receivable, net	120,752	106,372
Allowance for Sales Returns
Valuation and Qualifying Accounts Disclosure [Line Items]
Less allowance for sales returns	$ (128)	$ (100)

Other Balance Sheet Informati64

Other Balance Sheet Information - Summary of Inventories (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Raw materials and purchased parts	$ 72,820	$ 60,979
Work-in-process	11,273	16,090
Finished goods	21,211	15,503
Inventory, net	105,304	92,572
Reserves for excess and obsolete inventory	$ 23,900	$ 24,800

Other Balance Sheet Informati65

Other Balance Sheet Information - Capitalized Direct Costs (Details) - USD ($) $ in Millions	9 Months Ended
	Jun. 30, 2017	Sep. 30, 2016
Property, Plant and Equipment [Line Items]
Capitalized computer software costs	$ 0.8
Property, Plant and Equipment
Property, Plant and Equipment [Line Items]
Capitalized computer software, gross	$ 4.4	$ 3.7

Other Balance Sheet Informati66

Other Balance Sheet Information - Deferred Financing Costs (Details) - USD ($) $ in Millions	3 Months Ended	9 Months Ended
	Jun. 30, 2017	Jun. 30, 2017	Sep. 30, 2016
Other Assets
Line of Credit Facility [Line Items]
Deferred finance costs, net	$ 0.6	$ 0.6	$ 0.7
Interest Expense
Line of Credit Facility [Line Items]
Amortization		$ 0.1
Interest Expense | Maximum
Line of Credit Facility [Line Items]
Amortization	$ 0.1

Other Balance Sheet Informati67

Other Balance Sheet Information - Note Receivable (Details) - USD ($) $ in Millions	12 Months Ended
	Sep. 30, 2016	Jun. 30, 2017	Sep. 30, 2012
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Note receivable, face value	$ 0.2	$ 0.2
Initial value of notes receivable			$ 3
Note receivable, interest rate			9.00%
Impairment charge	$ 3.4

Other Balance Sheet Informati68

Other Balance Sheet Information - Product Warranty and Retrofit Activity on Gross Basis (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Beginning Balance	$ 7,073	$ 5,735	$ 6,324	$ 6,089
Accruals	2,440	2,279	7,656	6,989
Costs Incurred	(1,867)	(2,059)	(6,334)	(7,123)
Ending Balance	$ 7,646	$ 5,955	$ 7,646	$ 5,955

Derivative Instruments - Realiz

Derivative Instruments - Realized Gains (Losses) on Derivative Instruments (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Derivative Instruments and Hedging Activities Disclosure [Abstract]
Realized gains (losses) on derivative instruments not designated as hedging instruments	$ 147	$ 233	$ (450)	$ 1,230

Derivative Instruments - Notion

Derivative Instruments - Notional Amounts Outstanding under Foreign Currency Contracts - Notional Amount of Buy Currency (Details) - Not Designated as Hedging Instrument - Long € in Thousands, ₩ in Thousands, ¥ in Thousands, £ in Thousands, SGD in Thousands, $ in Thousands

Jun. 30, 2017SGD

Jun. 30, 2017JPY (¥)

Jun. 30, 2017EUR (€)

Jun. 30, 2017KRW (₩)

Jun. 30, 2017GBP (£)

Jun. 30, 2017USD ($)

Sep. 30, 2016SGD

Sep. 30, 2016JPY (¥)

Sep. 30, 2016EUR (€)

Sep. 30, 2016KRW (₩)

Sep. 30, 2016GBP (£)

Sep. 30, 2016USD ($)

Foreign Currency Contract, Buy Japanese Yen, Sell United States Dollar, Maturing July 2017

Derivative [Line Items]

Notional Amount | ¥

¥ 445,000

Foreign Currency Contract, Buy British Pound, Sell United States Dollar, Maturing July 2017

Derivative [Line Items]

Notional Amount | £

£ 1,470

Foreign Currency Contract, Buy Korean Won, Sell United States Dollar, Maturing July 2017

Derivative [Line Items]

Notional Amount | ₩

₩ 4,193,000

Foreign Currency Contract, Buy United States Dollar, Sell Chinese Yuan, Maturing July 2017

Derivative [Line Items]

Notional Amount

$ 5,860

Foreign Currency Contract, Buy Euro, Sell United States Dollar, Maturing July 2017

Derivative [Line Items]

Notional Amount | €

€ 11,600

Foreign Currency Contract, Buy British Pound, Sell Norwegian Krone, Maturing July 2017

Derivative [Line Items]

Notional Amount | £

£ 164

Foreign Currency Contract, Buy Singapore Dollar, Sell United States Dollar, Maturing July 2017

Derivative [Line Items]

Notional Amount | SGD

SGD 620

Foreign Currency Contract, Buy United States Dollar, Sell Israeli Shekel, Maturing July 2017

Derivative [Line Items]

Notional Amount

$ 213

Foreign Currency Contract, Buy Euro Sell British Pound, Maturing July 2017

Derivative [Line Items]

Notional Amount | €

€ 18,513

Foreign Currency Contract, Buy British Pound, Sell Swedish Krona, Maturing October 2016

Derivative [Line Items]

Notional Amount | £

£ 190

Foreign Currency Contract, Buy Japanese Yen, Sell United States Dollar, Maturing October 2016

Derivative [Line Items]

Notional Amount | ¥

¥ 124,000

Foreign Currency Contract, Buy United States Dollar, Sell British Pound, Maturing October 2016

Derivative [Line Items]

Notional Amount

$ 6,107

Foreign Currency Contract, Buy Euro, Sell United States Dollar, Maturing October 2016

Derivative [Line Items]

Notional Amount | €

€ 13,300

Foreign Currency Contract, Buy United States Dollar, Sell Chinese Yuan, Maturing October 2016

Derivative [Line Items]

Notional Amount

5,815

Foreign Currency Contract, Buy Korean Won, Sell United States Dollar, Maturing October 2016

Derivative [Line Items]

Notional Amount | ₩

₩ 2,488,000

Foreign Currency Contract, Buy Euro, Sell British Pound, Maturing October 2016

Derivative [Line Items]

Notional Amount | €

€ 7,482

Foreign Currency Contract, Buy United States Dollar, Sell Israeli Shekel, Maturing October 2016

Derivative [Line Items]

Notional Amount

311

Foreign Currency Contract, Buy Singapore Dollar, Sell United States Dollar, Maturing October 2016

Derivative [Line Items]

Notional Amount | SGD

SGD 360

Foreign Currency Contract, Buy United States Dollar, Sell Taiwanese Dollar, Maturing October 2016

Derivative [Line Items]

Notional Amount

$ 210

Foreign Currency Contract, Buy British Pound, Sell Norwegian Krone, Maturing October 2016

Derivative [Line Items]

Notional Amount | £

£ 171

Derivative Instruments - Noti71

Derivative Instruments - Notional Amounts Outstanding under Foreign Currency Contracts - Notional Amount of Sell Currency (Details) - Not Designated as Hedging Instrument - Short ₪ in Thousands, ₩ in Thousands, ¥ in Thousands, £ in Thousands, TWD in Thousands, NOK in Thousands, $ in Thousands

Jun. 30, 2017ILS (₪)

Jun. 30, 2017CNY (¥)

Jun. 30, 2017NOK

Jun. 30, 2017GBP (£)

Jun. 30, 2017USD ($)

Sep. 30, 2016TWD

Sep. 30, 2016ILS (₪)

Sep. 30, 2016CNY (¥)

Sep. 30, 2016KRW (₩)

Sep. 30, 2016NOK

Sep. 30, 2016GBP (£)

Sep. 30, 2016USD ($)

Foreign Currency Contract, Buy Japanese Yen, Sell United States Dollar, Maturing July 2017

Derivative [Line Items]

Notional Amount

$ 3,980

Foreign Currency Contract, Buy British Pound, Sell United States Dollar, Maturing July 2017

Derivative [Line Items]

Notional Amount

1,906

Foreign Currency Contract, Buy Korean Won, Sell United States Dollar, Maturing July 2017

Derivative [Line Items]

Notional Amount

3,679

Foreign Currency Contract, Buy United States Dollar, Sell Chinese Yuan, Maturing July 2017

Derivative [Line Items]

Notional Amount | ¥

¥ 40,000

Foreign Currency Contract, Buy Euro, Sell United States Dollar, Maturing July 2017

Derivative [Line Items]

Notional Amount

13,229

Foreign Currency Contract, Buy British Pound, Sell Norwegian Krone, Maturing July 2017

Derivative [Line Items]

Notional Amount | NOK

NOK 1,800

Foreign Currency Contract, Buy Singapore Dollar, Sell United States Dollar, Maturing July 2017

Derivative [Line Items]

Notional Amount

$ 449

Foreign Currency Contract, Buy United States Dollar, Sell Israeli Shekel, Maturing July 2017

Derivative [Line Items]

Notional Amount | ₪

₪ 748

Foreign Currency Contract, Buy Euro Sell British Pound, Maturing July 2017

Derivative [Line Items]

Notional Amount | £

£ 16,280

Foreign Currency Contract, Buy British Pound, Sell Swedish Krona, Maturing October 2016

Derivative [Line Items]

Notional Amount | ₩

₩ 2,100

Foreign Currency Contract, Buy Japanese Yen, Sell United States Dollar, Maturing October 2016

Derivative [Line Items]

Notional Amount

$ 1,229

Foreign Currency Contract, Buy United States Dollar, Sell British Pound, Maturing October 2016

Derivative [Line Items]

Notional Amount | £

£ 4,710

Foreign Currency Contract, Buy Euro, Sell United States Dollar, Maturing October 2016

Derivative [Line Items]

Notional Amount

14,976

Foreign Currency Contract, Buy United States Dollar, Sell Chinese Yuan, Maturing October 2016

Derivative [Line Items]

Notional Amount | ¥

¥ 39,000

Foreign Currency Contract, Buy Korean Won, Sell United States Dollar, Maturing October 2016

Derivative [Line Items]

Notional Amount

2,255

Foreign Currency Contract, Buy Euro, Sell British Pound, Maturing October 2016

Derivative [Line Items]

Notional Amount | £

£ 6,500

Foreign Currency Contract, Buy United States Dollar, Sell Israeli Shekel, Maturing October 2016

Derivative [Line Items]

Notional Amount | ₪

₪ 1,169

Foreign Currency Contract, Buy Singapore Dollar, Sell United States Dollar, Maturing October 2016

Derivative [Line Items]

Notional Amount

$ 265

Foreign Currency Contract, Buy United States Dollar, Sell Taiwanese Dollar, Maturing October 2016

Derivative [Line Items]

Notional Amount | TWD

TWD 6,600

Foreign Currency Contract, Buy British Pound, Sell Norwegian Krone, Maturing October 2016

Derivative [Line Items]

Notional Amount | NOK

NOK 1,800

Derivative Instruments - Noti72

Derivative Instruments - Notional Amounts Outstanding under Foreign Currency Contracts - Fair Value of Assets (Details) - Not Designated as Hedging Instrument - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Foreign Exchange Contract
Derivative [Line Items]
Fair Value of Assets	$ 102	$ 5
Foreign Currency Contract, Buy British Pound, Sell Norwegian Krone, Maturing July 2017
Derivative [Line Items]
Fair Value of Assets	2
Foreign Currency Contract, Buy United States Dollar, Sell Israeli Shekel, Maturing July 2017
Derivative [Line Items]
Fair Value of Assets	1
Foreign Currency Contract, Buy Euro Sell British Pound, Maturing July 2017
Derivative [Line Items]
Fair Value of Assets	$ 99
Foreign Currency Contract, Buy British Pound, Sell Swedish Krona, Maturing October 2016
Derivative [Line Items]
Fair Value of Assets		1
Foreign Currency Contract, Buy United States Dollar, Sell British Pound, Maturing October 2016
Derivative [Line Items]
Fair Value of Assets		2
Foreign Currency Contract, Buy Korean Won, Sell United States Dollar, Maturing October 2016
Derivative [Line Items]
Fair Value of Assets		1
Foreign Currency Contract, Buy United States Dollar, Sell Israeli Shekel, Maturing October 2016
Derivative [Line Items]
Fair Value of Assets		$ 1

Derivative Instruments - Noti73

Derivative Instruments - Notional Amounts Outstanding under Foreign Currency Contracts - Fair Value of Liabilities (Details) - Not Designated as Hedging Instrument - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Foreign Exchange Contract
Derivative [Line Items]
Fair Value of Liabilities	$ (113)	$ (96)
Foreign Currency Contract, Buy Japanese Yen, Sell United States Dollar, Maturing July 2017
Derivative [Line Items]
Fair Value of Liabilities	(13)
Foreign Currency Contract, Buy British Pound, Sell United States Dollar, Maturing July 2017
Derivative [Line Items]
Fair Value of Liabilities	(16)
Foreign Currency Contract, Buy Korean Won, Sell United States Dollar, Maturing July 2017
Derivative [Line Items]
Fair Value of Liabilities	(10)
Foreign Currency Contract, Buy United States Dollar, Sell Chinese Yuan, Maturing July 2017
Derivative [Line Items]
Fair Value of Liabilities	(20)
Foreign Currency Contract, Buy Euro, Sell United States Dollar, Maturing July 2017
Derivative [Line Items]
Fair Value of Liabilities	(53)
Foreign Currency Contract, Buy Singapore Dollar, Sell United States Dollar, Maturing July 2017
Derivative [Line Items]
Fair Value of Liabilities	$ (1)
Foreign Currency Contract, Buy Euro, Sell United States Dollar, Maturing October 2016
Derivative [Line Items]
Fair Value of Liabilities		(40)
Foreign Currency Contract, Buy United States Dollar, Sell Chinese Yuan, Maturing October 2016
Derivative [Line Items]
Fair Value of Liabilities		(33)
Foreign Currency Contract, Buy Euro, Sell British Pound, Maturing October 2016
Derivative [Line Items]
Fair Value of Liabilities		$ (23)

Derivative Instruments - Stock

Derivative Instruments - Stock Warrant (Details) - Warrants - USD ($) $ in Millions	Jun. 30, 2017	Sep. 30, 2016
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Stock warrant	$ 0
Maximum
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Stock warrant		$ 0.1

Stock-Based Compensation - Stoc

Stock-Based Compensation - Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	$ 4,197	$ 1,637	$ 11,081	$ 8,206
Restricted Stock Units (RSUs)
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	4,044	1,501	10,634	7,801
Employee Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	$ 153	$ 136	$ 447	$ 405

Stock-Based Compensation - Rest

Stock-Based Compensation - Restricted Stock Units Granted (Details) - shares	9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Restricted Stock Units (RSUs)
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Granted (in shares)	1,008,570	1,679,591
Restricted Stock, Time Based Shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Granted (in shares)	377,213	734,250
Board of Director Units
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Granted (in shares)	43,019	85,091
Restricted Stock, Performance Based Shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Granted (in shares)	588,338	860,250

Stock-Based Compensation - Time

Stock-Based Compensation - Time-Based Grants (Details) - Restricted Stock, Time Based Shares	9 Months Ended
	Jun. 30, 2017
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting period (in years)	3 years
Share-based Compensation Award, Tranche One
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting percentage (as a percent)	33.33%
Share-based Compensation Award, Tranche Two
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting percentage (as a percent)	33.33%
Share-based Compensation Award, Tranche Three
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting percentage (as a percent)	33.33%

Stock-Based Compensation - St78

Stock-Based Compensation - Stock Grants (Details) - shares	9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Board of Director Units
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Granted (in shares)	43,019	85,091
Board of Director Units, Compensation Related Units
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Granted (in shares)	28,065	55,380
Award vesting period (in years)	1 year
Board of Director Units, Deferred Annual Awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Granted (in shares)	13,065,000	25,560,000
Board of Director Units, Deferred Quarterly Dividends
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Granted (in shares)	1,889,000	4,151,000

Stock-Based Compensation - Perf

Stock-Based Compensation - Performance-Based Grants (Details) - Restricted Stock, Performance Based Shares	9 Months Ended	12 Months Ended
	Jun. 30, 2017	Sep. 30, 2016
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Performance-based awards granted, percentage, minimum (as a percent)		0.00%
Performance-based awards granted, percentage (as a percent)	100.00%	100.00%
Performance-based awards granted, percentage, maximum threshold met (as a percent)	200.00%	200.00%
Performance goal measurement period (in years)	3 years

Stock-Based Compensation - Re80

Stock-Based Compensation - Restricted Stock Unit Activity - Tabular Disclosure (Details) - Restricted Stock Units (RSUs) - $ / shares	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Shares
Outstanding at beginning of period (in shares)			2,489,076
Granted (in shares)			1,008,570	1,679,591
Vested (in shares)			(911,738)
Forfeited (in shares)			(79,699)
Outstanding at end of period (in shares)	2,506,209		2,506,209
Weighted Average Grant-Date Fair Value
Outstanding at beginning of period (in dollars per share)			$ 10.79
Granted (in dollars per share)	$ 25.21	$ 9.58	14.32	$ 10.84
Vested (in dollars per share)			10.51
Forfeited (in dollars per share)			11.66
Outstanding at end of period (in dollars per share)	$ 12.52		$ 12.52

Stock-Based Compensation - Re81

Stock-Based Compensation - Restricted Stock Unit Activity - Additional Information (Details) - Restricted Stock Units (RSUs) - USD ($) $ / shares in Units, $ in Millions	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Granted (in dollars per share)	$ 25.21	$ 9.58	$ 14.32	$ 10.84
Fair value of restricted stock awards vested	$ 2.9	$ 0.3	$ 14.8	$ 14.3
Withholding taxes remitted			4.6	4.4
Withholding taxes paid			0.1	4.3
Proceeds from employees to satisfy tax obligation			$ 4.6	$ 0.1

Stock-Based Compensation - Re82

Stock-Based Compensation - Restricted Stock Unit Activity - Unrecognized Compensation Cost (Details) - Restricted Stock Units (RSUs) $ in Millions	9 Months Ended
	Jun. 30, 2017USD ($)
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized compensation cost	$ 20.5
Unrecognized compensation cost, estimated weighted average amortization period	1 year 8 months 12 days

Stock-Based Compensation - Empl

Stock-Based Compensation - Employee Stock Purchase Plan (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares issued under employee stock purchase plan (in shares)	90,681	118,548	90,681	118,548
Proceeds from issuance of shares under employee stock purchase plan			$ 960	$ 948
Employee Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Purchase price of common stock (as a percent)			85.00%
Proceeds from issuance of shares under employee stock purchase plan	$ 1,000		$ 1,000	$ 900

Earnings per Share - Tabular Di

Earnings per Share - Tabular Disclosure (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Earnings Per Share [Abstract]
Net (loss) income	$ 17,350	$ 8,564	$ 45,226	$ (80,022)
Weighted average common shares outstanding used in computing basic earnings (losses) per share	69,711	68,628	69,496	68,437
Dilutive common stock options and restricted stock units	694	538	702
Weighted average common shares outstanding used in computing diluted earnings (losses) per share	70,405	69,166	70,198	68,437
Basic net income (loss) per share (in dollars per share)	$ 0.25	$ 0.12	$ 0.65	$ (1.17)
Diluted net income (loss) per share (in dollars per share)	$ 0.25	$ 0.12	$ 0.64	$ (1.17)

Earnings per Share - Anti-dilut

Earnings per Share - Anti-dilutive Securities (Details) - shares	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from computation of diluted earnings per share				991,000
Restricted Stock Units (RSUs)
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from computation of diluted earnings per share	0	50,000	0

Restructuring Charges - General

Restructuring Charges - General Information (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended		9 Months Ended		12 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Mar. 31, 2017	Mar. 31, 2016	Jun. 30, 2017	Jun. 30, 2016	Sep. 30, 2016	Sep. 30, 2015
Restructuring Cost and Reserve [Line Items]
Restructuring charges		$ 996				$ 9,807
Restructuring reserve		5,789		$ 7,389		5,789		$ 2,073
Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges	$ 828	996			$ 2,663	9,782
Restructuring reserve	1,690	5,789	$ 2,044	7,293	1,690	5,789	$ 5,939	1,640
Facilities and other contract termination costs
Restructuring Cost and Reserve [Line Items]
Restructuring charges						25
Restructuring reserve		0		96		0		$ 433
Brooks Life Science Systems | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges		300			200
Brooks Semiconductor Solutions Group
Restructuring Cost and Reserve [Line Items]
Restructuring charges					2,200
Brooks Semiconductor Solutions Group | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges					2,200
Streamline Service Operations, Initiated Fiscal Year 2017
Restructuring Cost and Reserve [Line Items]
Restructuring charges	600
Restructuring reserve	800				800
Streamline Service Operations, Initiated Fiscal Year 2017 | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges			$ 900
Restructuring expected cost	1,500				1,500
Streamline Service Operations, Initiated Fiscal Year 2017 | Brooks Semiconductor Solutions Group
Restructuring Cost and Reserve [Line Items]
Restructuring charges	600				1,500
Reduce Global Footprint and Streamline Cost Structure, Initiated Fiscal Year 2016
Restructuring Cost and Reserve [Line Items]
Restructuring charges	200				500
Restructuring reserve	900				900
Reduce Global Footprint and Streamline Cost Structure, Initiated Fiscal Year 2016 | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges	200				500		1,800
Restructuring expected cost	2,500				2,500
Restructuring expected cost remaining	200				200
Reduce Global Footprint and Streamline Cost Structure, Initiated Fiscal Year 2016 | Brooks Semiconductor Solutions Group
Restructuring Cost and Reserve [Line Items]
Restructuring charges					700
Reduce Global Footprint and Streamline Cost Structure, Initiated Fiscal Year 2016 | Brooks Semiconductor Solutions Group | Facilities and other contract termination costs
Restructuring Cost and Reserve [Line Items]
Restructuring charges					700
Actions Initiated Prior to Fiscal Year 2017 | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges					300
Actions Initiated Prior to Fiscal Year 2016
Restructuring Cost and Reserve [Line Items]
Restructuring reserve	0				0
Actions Initiated Prior to Fiscal Year 2016 | Brooks Semiconductor Solutions Group
Restructuring Cost and Reserve [Line Items]
Restructuring charges					200		3,000
Restructuring cost incurred to date	3,200				3,200
Actions Initiated Prior to Fiscal Year 2016 | Brooks Semiconductor Solutions Group | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges					200
Streamline Business Operations, Initiated Prior to Fiscal Year 2017
Restructuring Cost and Reserve [Line Items]
Restructuring reserve	0				0
Streamline Business Operations, Initiated Prior to Fiscal Year 2017 | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges		600			300	5,800	$ 5,800
Restructuring cost incurred to date	$ 6,100				$ 6,100
Streamlining Segment Structure, Integrating Acquisition, and Facility Closure, Initiated in Fiscal Year 2016 | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges						1,200
Restructuring reserve		0				0
Streamlining Segment Structure, Integrating Acquisition, and Facility Closure, Initiated in Fiscal Year 2016 | Brooks Life Science Systems | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges		300		$ 2,400
Restructuring expected cost remaining		2,800				2,800
Streamlining Segment Structure, Integrating Acquisition, and Facility Closure, Initiated in Fiscal Year 2016 | Brooks Semiconductor Solutions Group
Restructuring Cost and Reserve [Line Items]
Restructuring charges						1,200
Actions Initiated During June 2016 | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring charges						8,500
Actions Initiated During June 2016 | Brooks Life Science Systems | Workforce-related termination benefits
Restructuring Cost and Reserve [Line Items]
Restructuring expected cost		$ 2,800				$ 2,800

Restructuring Charges - Activit

Restructuring Charges - Activity Related to Restructuring Accruals (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended		9 Months Ended		12 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Mar. 31, 2017	Mar. 31, 2016	Jun. 30, 2017	Jun. 30, 2016	Sep. 30, 2016
Restructuring Reserve [Roll Forward]
Beginning Balance		$ 7,389		$ 2,073		$ 2,073	$ 2,073
Expenses		996				9,807
Payments		(2,596)				(6,091)
Ending Balance		5,789		7,389		5,789
Facilities and other contract termination costs
Restructuring Reserve [Roll Forward]
Beginning Balance		96		433		433	433
Expenses						25
Payments		(96)				(458)
Ending Balance		0		96		0
Workforce-related termination benefits
Restructuring Reserve [Roll Forward]
Beginning Balance	$ 2,044	7,293	$ 5,939	1,640	$ 5,939	1,640	1,640
Expenses	828	996			2,663	9,782
Payments	(1,182)	(2,500)			(6,912)	(5,633)
Ending Balance	$ 1,690	$ 5,789	$ 2,044	$ 7,293	$ 1,690	$ 5,789	$ 5,939

Employee Benefit Plans - Narrat

Employee Benefit Plans - Narrative (Details)	9 Months Ended
	Jun. 30, 2017plan
Compensation and Retirement Disclosure [Abstract]
Defined benefit pension plan, number of plans	2

Employee Benefit Plans - Compon

Employee Benefit Plans - Components of Net Pension Cost (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Compensation and Retirement Disclosure [Abstract]
Service cost	$ 68	$ 138	$ 202	$ 410
Interest cost	7	18	21	54
Amortization of net losses	2	4	6	12
Expected return on assets	(33)	(41)	(99)	(120)
Net periodic pension cost	$ 44	$ 119	$ 130	$ 356

Segment Information - General I

Segment Information - General Information (Details) - segment	3 Months Ended	9 Months Ended
	Jun. 30, 2016	Jun. 30, 2016
Segment Reporting [Abstract]
Number of operating segments	2	3
Number of reportable segments	2	3

Segment Information - Financial

Segment Information - Financial Information for Business Segments (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016	Sep. 30, 2016
Revenue
Products	$ 141,957	$ 111,596	$ 396,684	$ 302,238
Services	39,760	35,938	114,321	100,532
Total revenue	181,717	147,534	511,005	402,770
Gross profit	71,572	54,163	193,039	141,517
Segment operating income (loss)	18,770	8,494	46,732	(6,165)
Total assets	746,771		746,771		$ 685,905
Brooks Semiconductor Solutions Group
Revenue
Products	124,681	99,254	349,710	268,671
Services	20,280	19,179	56,532	57,657
Total revenue	144,961	118,433	406,242	326,328
Gross profit	58,083	42,904	154,877	114,506
Brooks Life Science Systems
Revenue
Products	17,276	12,342	46,974	33,567
Services	19,480	16,759	57,789	42,875
Total revenue	36,756	29,101	104,763	76,442
Gross profit	13,489	11,259	38,162	27,011
Operating Segments
Revenue
Segment operating income (loss)	27,322	12,383	66,097	15,162
Depreciation expense	2,326	2,466	7,055	5,827
Total assets	592,996		592,996		565,452
Operating Segments | Brooks Semiconductor Solutions Group
Revenue
Segment operating income (loss)	26,188	13,119	63,562	22,717
Depreciation expense	1,192	1,448	3,786	3,375
Total assets	330,746		330,746		317,717
Operating Segments | Brooks Life Science Systems
Revenue
Segment operating income (loss)	1,134	(736)	2,535	(7,555)
Depreciation expense	1,134	$ 1,018	3,269	$ 2,452
Total assets	$ 262,250		$ 262,250		$ 247,735

Segment Information - Reconcili

Segment Information - Reconciliation of Reportable Segment Operating Income (Loss) to Corresponding Consolidated Amounts (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Segment Reporting Information [Line Items]
Amortization of acquired intangible assets	$ 4,300	$ 3,800	$ 12,700	$ 11,100
Restructuring charges	828	996	2,663	9,807
Total operating income (loss)	18,770	8,494	46,732	(6,165)
Operating Segments
Segment Reporting Information [Line Items]
Total operating income (loss)	27,322	12,383	66,097	15,162
Segment Reconciling Items
Segment Reporting Information [Line Items]
Amortization of acquired intangible assets	3,278	2,754	9,636	8,056
Corporate, Non-Segment
Segment Reporting Information [Line Items]
Other unallocated corporate expenses	$ 4,446	$ 139	$ 7,066	$ 3,464

Segment Information - Reconci93

Segment Information - Reconciliation of Reportable Segment Assets to Corresponding Consolidated Amounts (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Segment Reporting Information [Line Items]
Assets	$ 746,771	$ 685,905
Cash, cash equivalents and marketable securities	119,658	91,221
Deferred tax assets	1,460	1,982
Equity method investments	32,628	27,273
Operating Segments
Segment Reporting Information [Line Items]
Assets	592,996	565,452
Segment Reconciling Items
Segment Reporting Information [Line Items]
Equity method investments	32,606	$ 27,250
Corporate, Non-Segment
Segment Reporting Information [Line Items]
Other unallocated corporate net assets	$ 51

Significant Customers (Details)

Significant Customers (Details)	3 Months Ended		9 Months Ended		12 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016	Sep. 30, 2016
Customer Concentration Risk | Sales Revenue, Net
Concentration Risk [Line Items]
Concentration risk, percentage (as a percent)	11.00%	10.00%	10.00%	10.00%
Credit Concentration Risk | Accounts Receivable
Concentration Risk [Line Items]
Concentration risk, percentage (as a percent)					11.00%

Fair Value Measurements - Asset

Fair Value Measurements - Assets and Liabilities Measured at Fair Value on Recurring Basis (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Nov. 28, 2016	Sep. 30, 2016
Assets:
Available-for-sale securities	$ 2,577		$ 6,135
Fair Value, Measurements, Recurring
Assets:
Cash equivalents	45		143
Available-for-sale securities	2,577		6,135
Foreign exchange contracts	102		5
Total Assets	2,724		12,102
Liabilities:
Contingent consideration			500
Foreign exchange contracts	113		97
Total Liabilities	113		597
Quoted Prices in Active Markets for Identical Assets (Level 1) | Fair Value, Measurements, Recurring
Assets:
Cash equivalents			98
Total Assets			98
Significant Other Observable Inputs (Level 2) | Fair Value, Measurements, Recurring
Assets:
Cash equivalents	45		45
Available-for-sale securities	2,577		6,135
Foreign exchange contracts	102		5
Total Assets	2,724		6,185
Liabilities:
Foreign exchange contracts	113		97
Total Liabilities	113		97
Significant Unobservable Inputs (Level 3) | Fair Value, Measurements, Recurring
Assets:
Total Assets			5,819
Liabilities:
Contingent consideration			500
Total Liabilities			500
Convertible Debt Securities | Fair Value, Measurements, Recurring
Assets:
Convertible debt securities			5,774
Convertible Debt Securities | Significant Unobservable Inputs (Level 3) | Fair Value, Measurements, Recurring
Assets:
Convertible debt securities		$ 5,600	5,774
Warrants
Assets:
Stock warrant	$ 0
Warrants | Fair Value, Measurements, Recurring
Assets:
Stock warrant			45
Warrants | Significant Unobservable Inputs (Level 3) | Fair Value, Measurements, Recurring
Assets:
Stock warrant			$ 45

Fair Value Measurements - Settl

Fair Value Measurements - Settlement of Convertible Debt Securities and Stock Warrant (Details) $ in Millions	9 Months Ended
	Jun. 30, 2017USD ($)
Other Nonoperating Income (Expense)
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Loss on settlement of financial instruments	$ 0.2

Fair Value Measurements - Cash

Fair Value Measurements - Cash Equivalents (Details) - Fair Value, Measurements, Recurring - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Assets:
Cash equivalents	$ 45	$ 143
Quoted Prices in Active Markets for Identical Assets (Level 1)
Assets:
Cash equivalents		98
Quoted Prices in Active Markets for Identical Assets (Level 1) | Money Market Funds
Assets:
Cash equivalents		100
Significant Other Observable Inputs (Level 2)
Assets:
Cash equivalents	45	45
Significant Other Observable Inputs (Level 2) | Certificates of Deposit | Maximum
Assets:
Cash equivalents	$ 100	$ 100

Fair Value Measurements - Avail

Fair Value Measurements - Available For Sale Securities (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Assets:
Available-for-sale securities	$ 2,577	$ 6,135
Fair Value, Measurements, Recurring
Assets:
Available-for-sale securities	2,577	6,135
Significant Other Observable Inputs (Level 2) | Fair Value, Measurements, Recurring
Assets:
Available-for-sale securities	$ 2,577	$ 6,135

Fair Value Measurements - Forei

Fair Value Measurements - Foreign Exchange Contracts (Details) - Fair Value, Measurements, Recurring - USD ($) $ in Thousands	Jun. 30, 2017	Sep. 30, 2016
Assets:
Foreign exchange contracts	$ 102	$ 5
Liabilities:
Foreign exchange contracts	113	97
Significant Other Observable Inputs (Level 2)
Assets:
Foreign exchange contracts	102	5
Liabilities:
Foreign exchange contracts	$ 113	$ 97

Fair Value Measurements - Conve

Fair Value Measurements - Convertible Debt Securities (Details) - USD ($) $ / shares in Units, $ in Thousands	Nov. 28, 2016	Jun. 30, 2017	Sep. 30, 2016
Convertible Debt Securities
Assets:
Discount rate (as a percent)		23.00%
Risk-adjusted discount rate (as a percent)		23.00%
Share price (in dollars per share)		$ 1.76
Expected volatility rate (as a percent)		55.00%
Convertible debt securities, carrying value	$ 5,800
Convertible Debt Securities | Fair Value, Measurements, Recurring
Assets:
Convertible debt securities			$ 5,774
Convertible Debt Securities | Significant Unobservable Inputs (Level 3) | Fair Value, Measurements, Recurring
Assets:
Convertible debt securities	5,600		$ 5,774
Minimum | Convertible Debt Securities
Assets:
Payout period (in years)		1 year 6 months
Risk free interest rate (as a percent)		0.96%
Expected payoff period (in years)		1 year 6 months
Maximum | Convertible Debt Securities
Assets:
Payout period (in years)		3 years 2 months 12 days
Risk free interest rate (as a percent)		1.39%
Expected payoff period (in years)		3 years 22 days
Other Nonoperating Income (Expense)
Assets:
Loss on settlement of financial instruments		$ 200
Other Nonoperating Income (Expense) | Convertible Debt Securities
Assets:
Loss on settlement of financial instruments	$ 200

Fair Value Measurements - Stock

Fair Value Measurements - Stock Warrant (Details) - Warrants - USD ($) $ in Thousands	Jun. 30, 2017	Nov. 28, 2016	Sep. 30, 2016
Assets:
Stock warrant	$ 0
Fair Value, Measurements, Recurring
Assets:
Stock warrant			$ 45
Significant Unobservable Inputs (Level 3) | Fair Value, Measurements, Recurring
Assets:
Stock warrant			45
Maximum
Assets:
Stock warrant			$ 100
Cool Lab, LLC | Maximum
Assets:
Stock warrant		$ 100
Cool Lab, LLC | Maximum | Significant Unobservable Inputs (Level 3)
Assets:
Stock warrant		100
Cool Lab, LLC | Maximum | Significant Unobservable Inputs (Level 3) | Fair Value, Measurements, Recurring
Assets:
Stock warrant		$ 100

Fair Value Measurements - Conti

Fair Value Measurements - Contingent Consideration (Details) - USD ($) $ in Thousands	9 Months Ended
	Jun. 30, 2017	Sep. 30, 2016
Fair Value, Measurements, Recurring
Liabilities:
Contingent consideration		$ 500
Significant Unobservable Inputs (Level 3) | Fair Value, Measurements, Recurring
Liabilities:
Contingent consideration		$ 500
Contact Co., Ltd
Liabilities:
Payment of contingent consideration	$ 500

Fair Value Measurements - Recon

Fair Value Measurements - Reconciliation of Assets and Liabilities Measured Using Significant Unobservable Inputs (Details) $ in Thousands	9 Months Ended
	Jun. 30, 2017USD ($)
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Total, balance at beginning of period	$ 6,319
Total, change in fair value	(231)
Total, settlements	(6,088)
Total, balance at end of period	0
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Balance at beginning of period	500
Change in fair value	0
Settlements	(500)
Balance at end of period	0
Convertible Debt Securities
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Balance at beginning of period	5,774
Change in fair value	(194)
Settlements	(5,580)
Balance at end of period	0
Warrants
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Balance at beginning of period	45
Change in fair value	(37)
Settlements	(8)
Balance at end of period	$ 0

Fair Value Measurements - Nonre

Fair Value Measurements - Nonrecurring Fair Value Measurements - Note Receivable (Details) - USD ($) $ in Millions	Jun. 30, 2017	Sep. 30, 2016
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Note receivable, face value	$ 0.2	$ 0.2
Other Assets
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Note receivable, face value	$ 0.2	$ 0.2

Fair Value Measurements - No105

Fair Value Measurements - Nonrecurring Fair Value Measurements - Loan Receivable (Details) - USD ($) $ in Millions	Nov. 28, 2016	Sep. 30, 2016
Fair Value, Measurements, Nonrecurring | Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Loan receivable, fair value	$ 1.6
Other Assets
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Loan receivable, carrying value	$ 1.6	$ 1.5

Fair Value Measurements - No106

Fair Value Measurements - Nonrecurring Fair Value Measurements - Equity Method Investment (Details) - USD ($) $ in Thousands	9 Months Ended
	Jun. 30, 2017	Nov. 28, 2016	Sep. 30, 2016
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Equity method investments	$ 32,628		$ 27,273
BioCision, LLC
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Equity method investments		$ 1,200	$ 1,700
Equity value	$ 6,500
BioCision, LLC | Equity Method Investments
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Expected volatility rate (as a percent)	80.00%
Expected payoff period (in years)	1 year 6 months
Risk free interest rate (as a percent)	0.96%
BioCision, LLC | Fair Value, Measurements, Nonrecurring | Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Equity method investments, fair value	$ 3,100

Commitments and Contingencies -

Commitments and Contingencies - Operating Leases (Details) $ in Millions	9 Months Ended
	Jun. 30, 2017USD ($)ft²
Property Subject to or Available for Operating Lease [Line Items]
Lease renewal term	5 years
Non-cancelable obligations, operating lease | $	$ 2.4
Lease Arrangement Expiring July 2017
Property Subject to or Available for Operating Lease [Line Items]
Area leased (in sq ft)	85,000
Lease Arrangement, March 2019 To September 2023
Property Subject to or Available for Operating Lease [Line Items]
Area leased (in sq ft)	13,000

Commitments and Contingencie108

Commitments and Contingencies - Letters of Credit (Details) - USD ($) $ in Millions	Jun. 30, 2017	Sep. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Outstanding letters of credit	$ 3.4	$ 2

Commitments and Contingencie109

Commitments and Contingencies - Purchase Commitments (Details) - USD ($) $ in Millions	Jun. 30, 2017	Sep. 30, 2016
Non-cancellable Contracts and Purchase Orders for Inventory
Other Commitments [Line Items]
Other Commitment	$ 112.8	$ 101.4

Commitments and Contingencie110

Commitments and Contingencies - Contingencies (Details) - USD ($) $ / shares in Units, $ in Millions	9 Months Ended
	Jun. 30, 2017	Sep. 30, 2016
Loss Contingency [Abstract]
Common stock, shares issued	83,216,169	82,220,270
Employee Stock Purchase Plan, Rescission Rights | Employee Stock
Loss Contingency [Abstract]
Common stock, shares issued	36,531
Share price (in dollars per share)	$ 8.02
Estimate of aggregate payments	$ 0.3

Subsequent Events (Details)

Subsequent Events (Details) - USD ($) $ / shares in Units, $ in Thousands	Aug. 01, 2017	Jul. 05, 2017	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Subsequent Event [Line Items]
Total cash payment					$ 5,346	$ 125,498
Cash dividend declared (USD per share)			$ 0.10	$ 0.10	$ 0.30	$ 0.30
Subsequent Event
Subsequent Event [Line Items]
Cash dividend declared (USD per share)	$ 0.10
Cash dividend declared, payment date	Sep. 29, 2017
Cash dividend declared, record date	Sep. 8, 2017
Subsequent Event | PBMMI and Novare
Subsequent Event [Line Items]
Total cash payment		$ 34,300