Azenta (AZTA) 10-Q 6 Feb 20 2020 Q1 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - $ / shares	3 Months Ended
	Dec. 31, 2019	Jan. 27, 2020
Cover [Abstract]
Entity Central Index Key	0000933974
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Dec. 31, 2019
Document Transition Report	false
Entity File Number	000-25434
Entity Registrant Name	BROOKS AUTOMATION, INC.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	04-3040660
Entity Address, Address Line One	15 Elizabeth Drive
Entity Address, City or Town	Chelmsford
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	01824
City Area Code	978
Local Phone Number	262-2400
Title of 12(b) Security	Common Stock, $0.01 par value
Entity Listing, Par Value Per Share	$ 0.01
Trading Symbol	BRKS
Security Exchange Name	NASDAQ
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		73,619,648
Current Fiscal Year End Date	--09-30
Document Fiscal Year Focus	2020
Document Fiscal Period Focus	Q1
Amendment Flag	false

CONSOLIDATED BALANCE SHEETS

CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Current assets
Cash and cash equivalents	$ 335,319	$ 301,642
Marketable securities	11,233	34,124
Accounts receivable, net	165,176	165,602
Inventories	105,181	99,445
Prepaid expenses and other current assets	46,560	46,332
Total current assets	663,469	647,145
Property, plant and equipment, net	105,296	100,669
Long-term marketable securities	3,039	2,845
Long-term deferred tax assets	6,004	5,064
Goodwill	490,370	488,602
Intangible assets, net	242,248	251,168
Other assets	48,532	20,506
Total assets	1,558,958	1,515,999
Current liabilities
Current portion of long-term debt	827	829
Accounts payable	65,306	58,919
Deferred revenue	29,042	29,435
Accrued warranty and retrofit costs	7,493	7,175
Accrued compensation and benefits	25,810	31,375
Accrued restructuring costs	844	1,040
Accrued income taxes payable	100,451	99,263
Accrued expenses and other current liabilities	53,179	44,234
Total current liabilities	282,952	272,270
Long-term debt	49,918	50,315
Long-term tax reserves	18,543	18,274
Long-term deferred tax liabilities	13,636	20,636
Long-term pension liabilities	5,397	5,338
Long-term operating lease liabilities	20,526
Other long-term liabilities	9,291	10,212
Total liabilities	400,263	377,045
Commitments and contingencies (Note 17)
Stockholders' Equity
Preferred stock, $0.01 par value - 1,000,000 shares authorized, no shares issued or outstanding
Common stock, $0.01 par value - 125,000,000 shares authorized, 87,080,017 shares issued and 73,618,148 shares outstanding at December 31, 2019, 85,759,700 shares issued and 72,297,831 shares outstanding at September 30, 2019	871	857
Additional paid-in capital	1,926,350	1,921,954
Accumulated other comprehensive income	13,154	3,511
Treasury stock, at cost- 13,461,869 shares	(200,956)	(200,956)
Accumulated deficit	(580,724)	(586,412)
Total stockholders' equity	1,158,695	1,138,954
Total liabilities and stockholders' equity	$ 1,558,958	$ 1,515,999

CONSOLIDATED BALANCE SHEETS (Pa

CONSOLIDATED BALANCE SHEETS (Parenthetical) - $ / shares	Dec. 31, 2019	Sep. 30, 2019
Preferred Stock, Number of Shares, Par Value and Other Disclosures [Abstract]
Preferred stock, par value (in dollars 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, Number of Shares, Par Value and Other Disclosures [Abstract]
Common stock, par value (in dollars per share)	$ 0.01	$ 0.01
Common stock, shares authorized	125,000,000	125,000,000
Common stock, shares issued	87,080,017	85,759,700
Common stock, shares outstanding	73,618,148	72,297,831
Treasury Stock, Number of Shares and Restriction Disclosures [Abstract]
Treasury stock, shares	13,461,869	13,461,869

CONSOLIDATED STATEMENTS OF OPER

CONSOLIDATED STATEMENTS OF OPERATIONS - USD ($) shares in Thousands, $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Revenue
Total revenue	$ 210,500	$ 179,368
Cost of revenue
Total cost of revenue	125,514	107,287
Gross profit	84,986	72,081
Operating expenses
Research and development	14,401	13,148
Selling, general and administrative	59,343	53,541
Restructuring charges	576	59
Total operating expenses	74,320	66,748
Operating income	10,666	5,333
Interest income	699	423
Interest expense	(737)	(5,290)
Other expenses, net	(417)	(30)
Income before income taxes	10,211	436
Income tax benefit	(2,963)	(5,830)
Income from continuing operations	13,174	6,266
(Loss) income from discontinued operations, net of tax	(117)	8,149
Net income	$ 13,057	$ 14,415
Basic net income per share:
Income from continuing operations	$ 0.18	$ 0.09
(Loss) income from discontinued operations, net of tax	0	0.11
Basic net income per share	0.18	0.20
Diluted net income per share:
Income from continuing operations	0.18	0.09
(Loss) income from discontinued operations, net of tax	0	0.11
Diluted net income per share	$ 0.18	$ 0.20
Weighted average shares used in computing net income per share:
Basic	72,972	71,450
Diluted	73,645	72,165
Products
Revenue
Total revenue	$ 131,862	$ 125,375
Cost of revenue
Total cost of revenue	79,971	74,574
Services
Revenue
Total revenue	78,638	53,993
Cost of revenue
Total cost of revenue	$ 45,543	$ 32,713

CONSOLIDATED STATEMENTS OF COMP

CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Statement of Comprehensive Income [Abstract]
Net income	$ 13,057	$ 14,415
Other comprehensive income, net of tax:
Foreign currency translation adjustments	9,645	1,677
Unrealized gains (losses) on marketable securities, net of tax effects of $0 and ($38) during the three months ended December 31, 2019 and 2018	10	(121)
Actuarial losses, net of tax effects of $1 and $2 during the three months ended December 31, 2019 and 2018	(12)	(9)
Total other comprehensive income, net of tax	9,643	1,547
Comprehensive income	$ 22,700	$ 15,962

CONSOLIDATED STATEMENTS OF CO_2

CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (Parenthetical) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Statement of Comprehensive Income [Abstract]
Unrealized gains (losses) on marketable securities, tax	$ 0	$ (38)
Actuarial (losses) gains	$ 1	$ 2

CONSOLIDATED STATEMENTS OF CASH

CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Cash flows from operating activities
Net income	$ 13,057	$ 14,415
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation and amortization	16,477	11,838
Stock-based compensation	4,410	4,467
Amortization of premium on marketable securities and deferred financing costs	67	235
Earnings of equity method investments		(1,772)
Deferred income taxes	(8,183)	(7,682)
Other losses on disposals of assets	126	6
Loss on sale of divestiture, net of tax	319
Changes in operating assets and liabilities, net of acquisitions and divestiture:
Accounts receivable	1,503	(13,826)
Inventories	(4,335)	(12,260)
Prepaid expenses and other assets	6,120	1,029
Accounts payable	5,255	7,932
Deferred revenue	(720)	6,385
Accrued warranty and retrofit costs	221	572
Accrued compensation and tax withholdings	(5,755)	(13,842)
Accrued restructuring costs	(203)	(181)
Accrued expenses and other liabilities	(2,616)	8,948
Net cash provided by operating activities	25,743	6,264
Cash flows from investing activities
Purchases of property, plant and equipment	(9,614)	(3,560)
Purchases of marketable securities	(10,742)	(1,290)
Sales of marketable securities		48,904
Maturities of marketable securities	33,584	2,557
Acquisitions, net of cash acquired		(445,210)
Net cash provided by (used in) investing activities	13,228	(398,599)
Cash flows from financing activities
Proceeds from term loans, net of discount		340,540
Principal payments on debt	(414)	(1,789)
Payments of capital leases	(319)	(121)
Common stock dividends paid	(7,369)	(7,208)
Net cash provided by (used in) financing activities	(8,102)	331,422
Effects of exchange rate changes on cash and cash equivalents	2,808	(1,004)
Net increase (decrease) in cash, cash equivalents and restricted cash	33,677	(61,917)
Cash, cash equivalents and restricted cash, beginning of period	305,171	197,708
Cash, cash equivalents and restricted cash, end of period	338,848	135,791
Supplemental disclosure of non-cash investing and financing activities:
Purchases of property, plant and equipment included in accounts payable	$ 2,622	1,717
Deferred financing costs included in accounts payable		$ 1,750

CONSOLIDATED STATEMENTS OF CA_2

CONSOLIDATED STATEMENTS OF CASH FLOWS (Parenthetical) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Reconciliation of cash, cash equivalents, and restricted cash to the consolidated balance sheets
Cash and cash equivalents	$ 335,319	$ 135,741
Restricted cash included in prepaid expenses and other current assets	3,529	50
Total cash, cash equivalents and restricted cash shown in the consolidated statements of cash flows	$ 338,848	$ 135,791
Restricted cash, location	us-gaap:PrepaidExpenseAndOtherAssetsCurrent	us-gaap:PrepaidExpenseAndOtherAssetsCurrent

CONSOLIDATED STATEMENTS OF CHAN

CONSOLIDATED STATEMENTS OF CHANGES IN EQUITY - USD ($) $ in Thousands	Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit	Treasury Stock	Total
Beginning Balance at Sep. 30, 2018	$ 841	$ 1,898,434	$ 13,587	$ (994,074)	$ (200,956)	$ 717,832
Beginning Balance (in shares) at Sep. 30, 2018	84,164,130
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Shares issued under restricted stock and purchase plans, net	$ 13	(13)
Shares issued under restricted stock and purchase plans, net (in shares)	1,252,908
Stock-based compensation		4,467				4,467
Common stock dividends declared, at $0.10 per share				(7,208)		(7,208)
Foreign currency translation adjustments			1,677			1,677
Changes in unrealized losses on marketable securities, net of tax effects of $0 and ($38) during the three months ended December 31, 2019 and 2018, respectively			(121)			(121)
Actuarial losses, net of tax effects of $1 and $2 during the three months ended December 31, 2019 and 2018			(9)			(9)
Cumulative effect of adoption of ASC 606				(858)		(858)
Net income				14,415		14,415
Ending Balance at Dec. 31, 2018	$ 854	1,902,888	15,134	(987,725)	(200,956)	730,195
Ending Balance (in shares) at Dec. 31, 2018	85,417,038
Beginning Balance at Sep. 30, 2019	$ 857	1,921,954	3,511	(586,412)	(200,956)	$ 1,138,954
Beginning Balance (in shares) at Sep. 30, 2019	85,759,700					72,297,831
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Shares issued under restricted stock and purchase plans, net	$ 14	(14)
Shares issued under restricted stock and purchase plans, net (in shares)	1,320,317
Stock-based compensation		4,410				$ 4,410
Common stock dividends declared, at $0.10 per share				(7,369)		(7,369)
Foreign currency translation adjustments			9,645			9,645
Changes in unrealized losses on marketable securities, net of tax effects of $0 and ($38) during the three months ended December 31, 2019 and 2018, respectively			10			10
Actuarial losses, net of tax effects of $1 and $2 during the three months ended December 31, 2019 and 2018			(12)			(12)
Net income				13,057		13,057
Ending Balance at Dec. 31, 2019	$ 871	$ 1,926,350	$ 13,154	$ (580,724)	$ (200,956)	$ 1,158,695
Ending Balance (in shares) at Dec. 31, 2019	87,080,017					73,618,148

CONSOLIDATED STATEMENTS OF CH_2

CONSOLIDATED STATEMENTS OF CHANGES IN EQUITY (Parenthetical) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Statement of Stockholders' Equity [Abstract]
Dividend declared per share (in dollars per share)	$ 0.10	$ 0.10
Changes in unrealized gains (losses) on marketable securities, tax	$ 0	$ (38)
Actuarial gain or loss arising in the year, tax	$ 1	$ 2

Basis of Presentation

Basis of Presentation	3 Months Ended
	Dec. 31, 2019
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 in 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, 2019 (the "2019 Annual Report on Form 10-K"). The accompanying Consolidated Balance Sheet as of September 30, 2019 was derived from the audited annual consolidated financial statements as of the period then ended. Discontinued Operations In the fourth quarter of fiscal year 2018, the Company entered into a definitive agreement to sell its semiconductor cryogenics business (the “Disposition”) to Edwards Vacuum LLC (a member of the Atlas Copco Group) (“Edwards”). The Company determined that the semiconductor cryogenics business met the “held for sale” criteria and the “discontinued operations” criteria in accordance with Financial Accounting Standard Boards (“FASB”) Accounting Standards Codification (“ASC”) 205, Presentation of Financial Statements, (“FASB ASC 205”) as of September 30, 2018. The Consolidated Balance Sheets and Consolidated Statements of Operations, and the notes to the Consolidated Financial Statements were restated for all periods presented to reflect the discontinuation of the semiconductor cryogenics business, in accordance with FASB ASC 205. The discussion in the notes to these Consolidated Financial Statements, unless otherwise noted, relate solely to the Company's continuing operations. Please refer to Note 3, “Discontinued Operations” for further information. On July 1, 2019, the Company completed the sale of the semiconductor cryogenics business for $661.1 million, which excludes $6.3 million retained by Edwards at closing as a result of the initial net working capital adjustments. Net cash proceeds from the sale were $553.1 million, after deducting estimated taxes payable and closing costs, which remains subject to adjustment for the final determination of working capital and other items. ​

Summary of Significant Accounti

Summary of Significant Accounting Policies	3 Months Ended
	Dec. 31, 2019
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies 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 recording accounts receivable, inventories, goodwill, intangible assets other than goodwill, long-lived assets, derivative financial instruments, deferred income taxes, warranty obligations, revenue recognized in accordance with the percentage of completion method, 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. 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 expenses, net” in the Company’s unaudited Consolidated Statements of Operations. Net foreign currency transaction and remeasurement losses totaled $0.7 million and $0.1 million, respectively, during the three months ended December 31, 2019 and 2018. 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. The Company enters into foreign exchange contracts to reduce its exposure to currency fluctuations. The forward contract arrangements that the Company enters into, typically mature in 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 expenses, net" in the accompanying unaudited Consolidated Statements of Operations and are as follows for the three months ended December 31, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ ​ ​ December 31, ​ ​ 2019 2018 Realized gains (losses) on derivatives not designated as hedging instruments ​ $ (3,668) ​ $ 2,977 ​ ​ The fair values of the forward contracts 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”. 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 described below due to a lack of an active market for these contracts. Fair Value Measurements The Company measures at fair value certain financial assets and liabilities, including cash equivalents and available for sale securities. FASB ASC 820, Fair Value Measurement and Disclosures Level 1 Inputs: Level 2 Inputs: Level 3 Inputs: As of December 31, the Company had no assets or liabilities measured and recorded at fair value on a recurring basis using Level 3 inputs. Leases The Company has operating leases for real estate and non-real estate and finance leases for non-real estate. The classification of a lease as operating or finance and the determination of the right-of-use asset (ROU asset) and lease liability are determined at lease inception. The ROU asset represents the Company’s right to use an underlying asset for the lease term and the lease liability represents the Company’s obligation to make lease payments arising from the lease. Operating lease ROU assets and liabilities are recognized at commencement date based on the present value of lease payments over the lease term. As most of the Company’s leases do not provide an implicit rate, an incremental borrowing rate is used based on the estimated rate of interest for collateralized borrowing over a similar term of the lease payments at commencement date. Lease terms may include options to extend or terminate the lease when it is reasonably certain that the option will be exercised. Lease expense is recognized on a straight-line basis over the lease term. The Company’s lease agreements may contain lease and non-lease components. Non-lease components primarily include payments for maintenance and utilities. Fixed payments for non-lease components are combined with lease payments and accounted for as a single lease component which increases the amount of the ROU asset and liability. The ROU asset for operating leases is included within Other assets and the ROU asset for finance leases is included within Property, plant, and equipment, net on the Consolidated Balance Sheets. The short-term lease liabilities for both operating leases and finance leases are included within Accrued expenses and other current liabilities. The long-term lease liabilities for operating leases and finance leases are included within Long-term operating lease liabilities, and Other long-term liabilities, respectively, on the Consolidated Balance Sheets. Recently Issued Accounting Pronouncements In December 2019, the FASB issued ASU 2019-12: Simplifying the Accounting for Income Taxes (Topic 740) is permitted. The Company is evaluating the impact of this ASU. ​ In August 2018, the FASB issued ASU 2018-15, Intangibles – Goodwill and Other – Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract In August 2018, the FASB issued ASU 2018-14, Disclosure Framework — Changes to the Disclosure Requirements for Defined Benefit Plans In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework - Changes to the Disclosure Requirements for Fair Value Measurement disclosure requirements related to fair value measurement. The amendments include new disclosure requirement for changes in unrealized gains or losses included in other comprehensive income for recurring Level 3 fair value measurements held at the end of the reporting period and the range and weighted average used to develop significant unobservable inputs for Level 3 fair value measurements. The amendments eliminated disclosure requirements for amount of and reasons for transfers between Level 1 and Level 2, valuation processes for Level 3 fair value measurements, and policy for timing of transfers between levels of the fair value hierarchy. In addition, the amendments modified certain disclosure requirement to provide clarification or to promote appropriate exercise of discretion by entities. ASU 2018-13 is effective for fiscal years beginning after December 15, 2019, including interim periods therein. Early adoption is permitted. The Company is currently evaluating the impact of this ASU. In June 2016, the FASB issued ASU 2016-13, Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments Codification Improvements to Topic 326, Financial Instruments - Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments Codification Improvements to Topic 326, Financial Instruments - Credit Losses Financial Instruments - Credit Losses (Topic 326): Targeted Transition Relief Financial Instruments - Overall Recently Adopted Accounting Pronouncements In July 2019, the FASB issued ASU 2019-07, Codification Updates to SEC Sections - Amendments to SEC Paragraphs Pursuant to SEC Final Rule Releases No. 33-10532, Disclosure Update and Simplification, and Nos. 33-10231 and 33-10442, Investment Company Reporting Modernization and Miscellaneous Updates (SEC Update) . ASU 2019-07 aligns the guidance in various SEC sections of the Codification with the requirements of certain SEC final rules. ASU 2019 -07 was effective immediately during the Company’s third quarter of fiscal 2020 and the adoption did not have any impact on our consolidated financial statements and related disclosures. ​ In March 2018, the FASB issued ASU 2018-02, Reclassification of Certain Tax Effects from Accumulated Other Comprehensive Income ​ In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842) modified retrospective million on its Consolidated Balance Sheets. There was no impact to the Company’s finance ROU asset and liability on October 1, 2019. The adoption of the standard does not impact the Consolidated Results of Operations or Consolidated Statement of Cash Flows. See Note 9, “Leases” for further information. 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 2019 Annual Report on Form 10-K. ​

Discontinued Operations

Discontinued Operations	3 Months Ended
	Dec. 31, 2019
Discontinued Operations and Disposal Groups [Abstract]
Discontinued Operations	3. Discontinued Operations On August 27, 2018, the Company entered into a definitive agreement to sell its semiconductor cryogenics business to Edwards for $675.0 million in cash, subject to adjustments. On July 1, 2019, the Company completed the sale of the semiconductor cryogenics business for $661.1 million, which excludes $6.3 million retained by Edwards at closing based on the initial adjustment for net working capital. Net proceeds from the sale were approximately $553.1 million, after deducting estimated taxes payable and closing costs, which remains subject to adjustment for the final determination of working capital and other items. The semiconductor cryogenics business consists of the CTI pump business, Polycold chiller business, the related services business and the Company's 50% share in Ulvac Cryogenics, Inc., a joint venture based in Japan. The semiconductor cryogenics business was originally acquired by the Company in its 2005 merger with Helix Technology Corporation. The operating results of the semiconductor cryogenics business had been included in the Brooks Semiconductor Solutions Group In connection with the closing of the Disposition on July 1, 2019, the Company and Edwards entered into a transition service agreement, a supply agreement, and lease agreements. The transition service agreement outlines the information technology, people, and facility support the Company will provide to Edwards for a period up to 9 months after transaction closing date. The supply agreement allows the Company to purchase CTI and Polycold goods at cost from Edwards up to an aggregate amount equal to $1.0 million during the one-year term after closing of the Disposition. The lease agreements provide facility space to Edwards free of charge for three years after the transaction closing date. Edwards will have the option to renew each lease at the then current market rates after the initial three-year lease term has ended. This Disposition is consistent with the Company’s long-standing strategy to increase shareholder value by accelerating the growth of its Life Sciences business with further acquisitions and strengthening its semiconductor automation business with opportunistic acquisitions. The Disposition met the "held for sale" criteria and the “discontinued operation” criteria in accordance with FASB ASC 205 as of September 30, 2018. As such, its operating results have been reported as a discontinued operation for all periods presented. The following table presents the financial results of discontinued operations (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, ​ ​ ​ ​ 2019 2018 ​ Revenue ​ ​ ​ ​ ​ ​ ​ ​ Products ​ ​ ​ $ - ​ $ 28,786 ​ Services ​ ​ ​ ​ - ​ ​ 10,538 ​ Total revenue ​ ​ ​ ​ - ​ ​ 39,324 ​ Cost of revenue ​ ​ ​ ​ ​ ​ ​ ​ ​ Products ​ ​ ​ ​ - ​ ​ 16,516 ​ Services ​ ​ ​ ​ - ​ ​ 6,049 ​ Total cost of revenue ​ ​ ​ ​ - ​ ​ 22,565 ​ Gross profit ​ ​ ​ ​ - ​ ​ 16,759 ​ Operating expenses ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development ​ ​ ​ ​ - ​ ​ 2,158 ​ Selling, general and administrative ​ ​ ​ ​ (257) ​ ​ 7,203 ​ Total operating expenses ​ ​ ​ ​ (257) ​ ​ 9,361 ​ Operating income ​ ​ ​ ​ 257 ​ ​ 7,398 ​ Other (loss) income, net ​ ​ ​ ​ (410) ​ ​ 289 ​ (Loss) income before income taxes and earnings of equity method investment ​ ​ ​ ​ (153) ​ ​ 7,687 ​ Income tax provision ​ ​ ​ ​ (36) ​ ​ 1,310 ​ (Loss) income before equity in earnings of equity method investment ​ ​ ​ ​ (117) ​ ​ 6,377 ​ Equity in earnings of equity method investment ​ ​ ​ ​ - ​ ​ 1,772 ​ Net (loss) income ​ ​ ​ $ (117) ​ $ 8,149 ​ ​ The table above reflects revenue for the three months ended December 31, 2018 in accordance with ASC 606. Results for the three months ended December 31, 2018 were not significantly impacted by the adoption of ASC 606. The following table presents the summarized financial information for Ulvac Cryogenics, Inc., the unconsolidated subsidiaries accounted for based on the equity method (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, ​ ​ ​ ​ ​ 2018 ​ Statements of Operations: ​ ​ ​ ​ ​ ​ ​ ​ Total revenue ​ ​ ​ ​ ​ ​ $ 22,299 ​ Gross profit ​ ​ ​ ​ ​ ​ ​ 8,928 ​ Operating Income ​ ​ ​ ​ ​ ​ ​ 5,124 ​ Net income ​ ​ ​ ​ ​ ​ ​ 3,496 ​ ​ ​ The following table presents the significant non-cash items and capital expenditures for the discontinued operations that are included in the Consolidated Statements of Cash Flows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, ​ ​ ​ ​ ​ ​ ​ 2018 ​ Depreciation and amortization ​ ​ ​ ​ ​ ​ $ 2 ​ Capital expenditures ​ ​ ​ ​ ​ ​ ​ 308 ​ Stock-based compensation ​ ​ ​ ​ ​ ​ ​ 291 ​ Earnings of equity method investment ​ ​ ​ ​ ​ ​ ​ (1,772) ​ ​

Marketable Securities

Marketable Securities	3 Months Ended
	Dec. 31, 2019
Investments, Debt and Equity Securities [Abstract]
Marketable Securities	4. 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. 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. 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 expenses, net" in the accompanying unaudited Consolidated Statements of Operations. There were no marketable securities sales during the three months ended December 31, 2019. During the three months ended December 31, 2018, the Company sold marketable securities with a fair value and amortized cost of $49.4 million and $49.5 million, respectively, and recognized net losses of $0.1 million. As a result, during this period, the Company collected cash proceeds of $48.9 million from the sale of marketable securities and reclassified net unrealized holding losses of $0.1 million from accumulated other comprehensive income into “Other expenses, net” in the accompanying unaudited Consolidated Statements of Operations as a result of these transactions. The following is a summary of the amortized cost and the fair value, including accrued interest receivable and unrealized holding gains (losses) on the short-term and long-term marketable securities as of December 31, 2019 and September 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Gross Gross ​ ​ ​ Amortized ​ Unrealized ​ Unrealized ​ ​ ​ ​ Cost ​ Losses ​ Gains ​ Fair Value December 31, 2019: ​ ​ ​ ​ U.S. Treasury securities and obligations of U.S. government agencies $ 6,696 ​ $ — ​ $ 1 $ 6,697 Bank certificates of deposits ​ ​ 500 ​ ​ — ​ ​ — ​ ​ 500 Corporate securities ​ ​ 4,519 ​ ​ — ​ ​ — ​ ​ 4,519 Municipal securities ​ 2,515 ​ ​ — ​ ​ — ​ 2,515 Other debt securities ​ 41 ​ ​ — ​ ​ — ​ 41 ​ ​ $ 14,271 ​ $ — ​ $ 1 ​ $ 14,272 September 30, 2019: ​ ​ ​ ​ U.S. Treasury securities and obligations of U.S. government agencies ​ $ 31,863 $ (2) $ 5 $ 31,866 Bank certificates of deposits ​ ​ 750 ​ ​ — ​ ​ — ​ ​ 750 Corporate securities ​ ​ 4,317 ​ ​ — ​ ​ 1 ​ ​ 4,318 Other debt securities ​ 35 ​ — ​ — ​ 35 ​ ​ $ 36,965 ​ $ (2) ​ $ 6 ​ $ 36,969 ​ The fair values of the marketable securities by contractual maturities at December 31, 2019 are presented below (in thousands): ​ ​ ​ ​ ​ Fair Value Due in one year or less ​ $ 11,233 Due after one year through five years ​ — Due after five years through ten years ​ ​ — Due after ten years ​ 3,039 Total marketable securities ​ $ 14,272 ​ 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 its fair value and recognizes the credit loss in earnings and the non-credit loss in accumulated other comprehensive income or loss. There were no securities in an unrealized loss position as of December 31, 2019. The aggregate fair value of the marketable securities in an unrealized loss position was $12.0 million as of September 30, 2019. Aggregate unrealized losses for these securities were insignificant as of September 30, 2019 and are presented in the table above. The securities in an unrealized loss position as of September 30, 2019 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. ​ Cash equivalents of $6.2 million at September 30, 2019 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 $37.2 million and $10.0 million, respectively, as of December 31, and September 30, 2019 consist primarily of treasury bills and agency bonds and are classified within Level 2 of the fair value hierarchy because they are not actively traded. Cash equivalents from level 1 and level 2 are recorded in “Cash and cash equivalents” within the accompanying unaudited Consolidated Balance Sheet.

Acquisitions

Acquisitions	3 Months Ended
	Dec. 31, 2019
Business Combinations [Abstract]
Acquisitions	5. Acquisitions Acquisition Completed in Fiscal Year 2019 Acquisition of the GENEWIZ Group On November 15, 2018, the Company acquired all the outstanding capital stock of GENEWIZ Group (“GENEWIZ”), a leading global genomics service provider headquartered in South Plainfield, New Jersey. GENEWIZ provides genomics services that enable research scientists to advance their discoveries within the pharmaceutical, academic, biotechnology, agriculture and other markets. It provides gene sequencing and synthesis services for more than 4,000 institutional customers worldwide supported by their global network of laboratories spanning the United States, China, Japan, Germany and the United Kingdom. This transaction has added a new and innovative platform which further enhances the Company’s core capabilities, and added even more value to samples that are under the Company’s care. The total cash purchase price for the acquisition was $442.7 million, net of cash acquired, which included a working capital settlement of $0.4 million. The Company used the proceeds of the incremental term loan described in Note 8, “Debt” to pay a portion of the purchase price. On the acquisition date, the Company paid $32.3 million to escrow accounts related to the satisfaction of the seller's indemnification obligations with respect to their representations and warranties and other indemnities. The Company also retained an amount equal to $1.5 million as collateral for any adjustment shortfall based on the final merger consideration calculation. During the fiscal year 2019, the final merger consideration was calculated to be $4.0 million less than the merger consideration paid at closing. To satisfy the shortfall, the Company reversed the $1.5 million liability associated with the holdback, received approval from the former shareholders to retain $0.7 million of funds the Company received on their behalf, and collected $1.8 million from the escrow accounts. ​ The Company recorded the assets acquired and liabilities assumed related to GENEWIZ at their fair values as of the acquisition date, from a market participant’s perspective. Fair value estimates are based on a complex series of judgments about future events and uncertainties and rely heavily on estimates and assumptions. The judgments used to determine the estimated fair value assigned to each class of assets acquired and liabilities assumed, as well as asset lives, can materially impact the Company’s results of operations. The following table presents the net purchase price and the fair values of the assets and liabilities of GENEWIZ (in thousands): ​ ​ ​ ​ ​ ​ Fair Value of ​ ​ Assets and ​ ​ Liabilities Accounts receivable (approximates contractual value) ​ $ 28,566 Inventories ​ 4,370 Prepaid expenses and other current assets ​ ​ 11,635 Property, plant and equipment ​ 36,379 Goodwill ​ 235,160 Intangible assets ​ 189,129 Other assets ​ ​ 15,998 Current portion of long-term debt ​ (3,170) Accounts payable ​ (6,522) Deferred revenue ​ (67) Accrued compensation and benefits ​ ​ (5,145) Other current liabilities ​ (10,073) Long-term debt ​ ​ (2,482) Long-term tax reserves ​ ​ (13,400) Long-term deferred tax liabilities ​ ​ (34,993) Other long-term liabilities ​ ​ (2,681) Total purchase price, net of cash acquired ​ $ 442,704 ​ The Company applied variations of the income approach to estimate the fair values of the intangible assets acquired. The identifiable intangible assets include customer relationships (excess earnings method) of $125.5 million with a useful life of 14 years , completed technology (relief from royalty method) of $44.5 million with useful lives from 10 to 15 years and trademarks (relief from royalty method) of $19.1 million with a useful life of 13 years . The intangible assets acquired are amortized over the total weighted average period of 13.3 years using methods that approximate the pattern in which the economic benefits are expected to be realized. ​ Goodwill of $235.2 million largely reflects the potential synergies and expansion of the Company’s core technologies and offerings in the Life Sciences business. The goodwill from this acquisition is reported within the Brooks Life Sciences segment and is not The revenues and net income from GENEWIZ recognized in the Company's consolidated results of operations were $40.0 million and $0.8 million, respectively for the three months ended December 31, 2019. The revenues and net income from GENEWIZ recognized in the Company’s consolidated results of operations were $16.4 million and $0.9 million, respectively during the period from the acquisition date to December 31, 2018. During the three months ended December 31, 2019, and the comparable reporting period since acquisition in fiscal year 2019, net income included $5.1 million and $1.6 million, respectively, related to amortization expense of acquired intangible assets. During the three months ended December 31, 2019 and 2018, the Company incurred less than $0.1 million and $6.3 million, respectively, in transaction costs, which were recorded in "Selling, general and administrative" expenses within the accompanying unaudited Consolidated Statements of Operations. The following unaudited pro forma information reflects the Company’s consolidated results of operations as if the acquisition had taken place on October 1, 2017. The unaudited pro forma information is not necessarily indicative of the results of operations that the Company would have reported had the transaction actually occurred at the beginning of these periods nor is it necessarily indicative of future results. The unaudited pro forma financial information does not reflect the impact of future events that may occur after the acquisition, including, but not limited to, anticipated costs savings from synergies or other operational improvements (in thousands). The pro forma amounts in below table were adjusted to reflect a correction made during the 2019 fiscal year, see the 2019 Annual Report on Form 10-K Note 4, “Acquisitions” for further information. ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, 2018 ​ ​ (pro forma) ​ ​ ​ ​ ​ Revenue $ 196,021 ​ Net income from continuing operations ​ 6,795 ​ ​ ​ The unaudited pro forma financial information presented in the table above includes adjustments for the application of the Company’s accounting policies, elimination of related party transactions, depreciation and amortization related to fair value adjustments to property, plant and equipment and intangible assets, and transaction costs, and interest expense on acquisition related debt. To present the Company’s consolidated results of operations as if the acquisition had taken place on October 1, 2017, the unaudited pro forma earnings for the three months ended December 31, 2018 has been adjusted to include the following additional expenses related to the acquisition: $1.6 million property, plant, and equipment, leases, and intangible asset step-up depreciation and amortization expense, $2.0 million interest expense related to financing activities and $42.1 million non-recurring compensation expenses and transaction costs.

Goodwill and Intangible Assets

Goodwill and Intangible Assets	3 Months Ended
	Dec. 31, 2019
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill and Intangible Assets	6. 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 events occur or circumstances change that would more likely than not reduce fair values of the reporting units below their carrying values, goodwill will be evaluated for impairment between annual tests. No triggering events indicating goodwill impairment occurred during the three months ended December 31, 2019. Please refer to Note 7, "Goodwill and Intangible Assets" to the Company's consolidated financial statements included in the 2019 Annual Report on Form 10-K for further information on the goodwill impairment testing performed during fiscal year 2019. The changes in the Company’s goodwill by reportable segment since September 30, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Brooks ​ ​ ​ ​ ​ ​ ​ ​ Semiconductor ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Solutions ​ Brooks ​ ​ ​ ​ ​ ​ ​ ​ Group ​ Life Sciences ​ Other ​ Total Gross goodwill, at September 30, 2019 ​ $ 636,791 ​ $ 440,755 ​ $ 26,014 ​ $ 1,103,560 Accumulated goodwill impairments ​ (588,944) ​ — ​ (26,014) ​ (614,958) Goodwill, net of accumulated impairments, at September 30, 2019 ​ 47,847 ​ 440,755 ​ — ​ 488,602 Acquisitions and adjustments ​ 35 ​ 1,733 ​ — ​ 1,768 Gross goodwill, at December 31, 2019 ​ ​ 636,826 ​ ​ 442,488 ​ ​ 26,014 ​ ​ 1,105,328 Accumulated goodwill impairments ​ (588,944) ​ — ​ (26,014) ​ (614,958) Goodwill, net of accumulated impairments, at December 31, 2019 ​ $ 47,882 ​ $ 442,488 ​ $ — ​ $ 490,370 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ During the three months ended December 31, 2019, the Company recorded a goodwill increase of $1.8 million primarily related to the impact of foreign currency translation adjustments. The components of the Company’s identifiable intangible assets as of December 31, 2019 and September 30, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ September 30, 2019 ​ ​ ​ ​ Accumulated ​ Net Book ​ ​ ​ Accumulated ​ Net Book ​ Cost Amortization Value Cost Amortization Value Patents ​ $ 5,302 ​ $ 4,702 ​ $ 600 ​ $ 5,302 ​ $ 4,628 ​ $ 674 Completed technology ​ 88,819 ​ 41,548 ​ 47,271 ​ 88,288 ​ 38,778 ​ 49,510 Trademarks and trade names ​ 25,424 ​ 6,689 ​ 18,735 ​ 25,340 ​ 5,807 ​ 19,533 Customer relationships ​ 267,087 ​ 91,474 ​ 175,613 ​ 265,450 ​ 84,047 ​ 181,403 Other intangibles ​ ​ 233 ​ ​ 204 ​ ​ 29 ​ ​ 231 ​ ​ 183 ​ ​ 48 ​ ​ $ 386,865 ​ $ 144,617 ​ $ 242,248 ​ $ 384,611 ​ $ 133,443 ​ $ 251,168 ​ Amortization expense for intangible assets was $10.6 million and $7.8 million, respectively, during the three months ended December 31, 2019 and 2018. Estimated future amortization expense for the intangible assets for the remainder of fiscal year 2020, the subsequent four fiscal years and thereafter is as follows (in thousands): ​ ​ ​ ​ Fiscal year ended September 30, ​ 2020 ​ $ 30,729 2021 ​ 37,494 2022 ​ 34,390 2023 ​ 31,267 2024 ​ 26,500 Thereafter ​ 81,868 ​ ​ $ 242,248 ​

Line of Credit

Line of Credit	3 Months Ended
	Dec. 31, 2019
Line of Credit
Line of Credit Facility [Line Items]
Line of Credit	7. Line of Credit The Company maintains a revolving line of credit under a credit agreement with Wells Fargo Bank, N.A. and JPMorgan Chase Bank, N.A. that provides for revolving credit facility of up to $75.0 million, subject to borrowing base availability, as defined in the credit agreement. The line of credit matures on October 4, 2022 and expires no less than 90 days prior to the term loan expiration. The proceeds from the line of credit are available for permitted acquisitions and general corporate purposes. ​ On October 4, 2017, the Company entered into a $200.0 million Senior Secured Term Loan Facility (the “term loan”) with Morgan Stanley Senior Funding, Inc., JPMorgan Chase Bank, N.A. and Wells Fargo Securities, LLC (collectively, the “lenders”). Coincident with the entry into the credit agreement for the term loan discussed in Note 8, “Debt” below, the Company amended certain terms and conditions of the credit agreement. Based on the amended terms of the credit agreement, the line of credit continues to provide for a revolving credit facility of up to $75.0 million, subject to borrowing base availability. Borrowing base availability under the amended credit agreement excludes collateral related to fixed assets and is redetermined periodically based on certain percentage of certain eligible U.S. assets, including accounts receivable and inventory. The sub-limits for letters of credit were reduced to $7.5 million under the amended terms of the credit agreement. All outstanding borrowings under the credit agreement are guaranteed by the Company and Brooks Life Sciences, Inc. (fka BioStorage Technologies, Inc.), the Company’s wholly-owned subsidiary (“guarantor”), and subordinated to the obligations under the term loan which are secured by a first priority lien on substantially all of the assets of the Company and the guarantor, other than accounts receivable and inventory. Please refer to Note 8, “Debt”, for further information on the term loan transaction. As of December 31, 2019, the Company had approximately $43.6 million available for borrowing under the line of credit. There were no amounts outstanding under the line of credit as of December 31, 2019 and September 30, 2019. The Company records commitment fees and other costs directly associated with obtaining line of credit facility as deferred financing costs which are presented within "Other assets" in the accompanying unaudited Consolidated Balance Sheets. Deferred financing costs were $0.3 million and $0.4 million, respectively, at December 31, 2019 and September 30, 2019. Such costs are amortized over the term of the related facility arrangement and are included in “Interest expense” in the accompanying unaudited Consolidated Statements of Operations. The line of credit contains certain customary representations and warranties, a financial covenant and affirmative and negative covenants as well as events of default. The Company was in compliance with the line of credit covenants as of December 31, 2019 and September 30, 2019. ​

Debt

Debt	3 Months Ended
	Dec. 31, 2019
Secured Debt
Debt Instrument [Line Items]
Debt	8. Debt Term Loans On October 4, 2017, the Company entered into a $200.0 million term loan with the lenders pursuant to the terms of a credit agreement. The term loan was issued at $197.6 million, or 98.8% of its par value, resulting in a discount of $2.4 million, or 1.2%, which represented loan origination fees paid at the closing. On November 15, 2018, the Company entered into an incremental amendment (the “First Amendment”) to the existing credit agreement. Under the First Amendment, the Company obtained an incremental term loan in an aggregate principal amount of $350.0 million. The proceeds of the incremental term loan were used to finance a portion of the purchase price for the Company’s acquisition of GENEWIZ. The incremental term loan was issued at $340.5 million, or 97.3% of its par value, resulting in a discount of $9.5 million, or 2.7%, which represented financing cost of the incremental term loan. Except as provided in the First Amendment, the incremental term loan was subject to the same terms and conditions as set forth in the existing credit agreement. On February 15, 2019, the Company entered into the second amendment to the credit agreement (the “Second Amendment”) and syndicated the incremental term loan to a group of new lenders which met the criteria of a debt extinguishment. The Company wrote off the carrying value of the incremental term loan of $340.1 million as of February 15, 2019 and recorded the syndicated incremental term loan at its present value for $349.1 million and a loss on debt extinguishment for $9.1 million. The syndicated incremental term loan was issued at $345.2 million, or 98.9% of its par value resulting in a discount of $4.0 million which represented financing costs which are presented as a reduction of the incremental term loan principal balance in the accompanying unaudited Consolidated Balance Sheets and was accreted over the life of the incremental term loan. Except as provided in the Second Amendment with respect to an increase of the applicable interest rates, the syndicated incremental term loan was subject to the same terms and conditions as the initial incremental term loan. On July 1, 2019, the Company completed the sale of its semiconductor cryogenics business and used $348.3 million of the proceeds from the Disposition to extinguish the outstanding balance of the incremental term loan. In addition, the Company used $147.0 million of the proceeds from the Disposition to extinguish a portion of the outstanding balance of the term loan. The Company recorded a loss on debt extinguishment of $5.2 million for the two term loans. The Company’s obligations under the term loan are also guaranteed by Brooks Life Sciences, Inc. (fka BioStorage Technologies, Inc.) as the guarantor, subject to the terms and conditions of the credit agreement. The Company and the guarantor granted the lenders a perfected first priority security interest in substantially all of the assets of the Company and the guarantor to secure the repayment of the term loan. The loan principal amount under the credit agreement may be increased by an aggregate amount equal to $75.0 million plus any voluntary repayments of the term loans plus any additional amount such that the secured leverage ratio of the Company is less than 3.00 to 1.00. Subject to certain conditions stated in the credit agreement, the Company may redeem the term loan at any time at its option without a significant premium or penalty, except for a repricing transaction, as defined in the credit agreement. The Company is required to redeem the term loan at the principal amount then outstanding upon occurrence of certain events, including (i) net proceeds received from the sale or other disposition of the Company’s or the guarantor’ assets, subject to certain limitations, (ii) casualty and condemnation proceeds received by the Company or the guarantor, subject to certain exceptions, (iii) net proceeds received by the Company or the guarantor from the issuance of debt or disqualified capital stock after October 4, 2017. Commencing on December 31, 2018, the Company was required to make principal payments equal to the excess cash flow amount, as defined in the credit agreement. Such prepayments are equal to 50% of the preceding year excess cash flow amount reduced by voluntary prepayments of the term loan, subject to certain limitations. The deferred financing costs are accreted over the term of the loan using the effective interest rate method and are included in “Interest expense” in the accompanying unaudited Consolidated Statements of Operations. At December 31, 2019, deferred financing costs were $0.5 million. The credit agreement contains certain customary representations and warranties, covenants and events of default. If any of the events of default occur and are not waived or cured within applicable grace periods, any unpaid amounts under the credit agreement will bear an annual interest rate at 2.00% above the rate otherwise applicable under the terms and conditions of such agreement. The credit agreement does not contain financial maintenance covenants. As of December 31, 2019, the Company was in compliance with all covenants and conditions under the credit agreement. In connection with the GENEWIZ acquisition, the Company assumed three five-year term loans for a total of $3.3 million and two one-year short term loans for a total of $3.2 million. The three five-year term loans were initiated during 2016 and mature in 2021. The principal payments are payable in eight installments equal to 12.5% of the initial principal amount of the term loans on December 14th and June 14th of each year. The three five-year term loans were secured by GENEWIZ to fund equipment procurement and new building related payments and the interest rates are equal to the LIBOR plus 3.1%. The two one-year term loans were secured by GENEWIZ to fund operations. Both of the one-year term loans were initiated in 2018 and matured in 2019. The interest rates of these two loans were 4.56% and 4.35%. There are no deferred financing costs related to either the five-year term loans or the one-year term loans. At December 31, 2019, the Company had an aggregate outstanding principal balance of $1.2 million for the three five-year term loans. Both of the During the three months ended December 31, 2019, the weighted average stated interest rate paid on all outstanding debt was 4.5%. During the three months ended December 31, 2019, the Company incurred aggregate interest expense of $0.6 million in connection with the borrowings, including less than $0.1 million of deferred financing costs amortization. The following are the future minimum principal payment obligations under all of the Company’s outstanding debt as of December 31, 2019 (in thousands): ​ ​ ​ ​ ​ ​ Amount Fiscal year ended September 30, ​ ​ ​ 2020 ​ $ 827 2021 ​ ​ 414 2022 ​ ​ — 2023 ​ ​ — 2024 ​ ​ — Thereafter ​ ​ 50,000 Total outstanding principal balance ​ ​ 51,241 Unamortized deferred financing costs ​ ​ (496) ​ ​ ​ 50,745 Current portion of long-term debt ​ ​ 827 Non-current portion of long-term debt ​ $ 49,918 ​ ​

Leases

Leases	3 Months Ended
	Dec. 31, 2019
Leases [Abstract]
Leases	9. Leases The Company has operating leases for real estate and non-real estate and finance leases for non-real estate in North America, Europe, and Asia. Non-real estate leases are primarily related to vehicles and office equipment. Lease expiration dates range between 2020 and 2039. The components of operating lease expense were as follows (in thousands): ​ ​ ​ ​ ​ Three Months Ended December 31, 2019 ​ ​ ​ Operating lease costs $ 2,122 Finance lease costs: ​ ​ Amortization of assets ​ 311 Interest on lease liabilities ​ 29 Total finance lease costs ​ 340 Variable lease costs ​ 406 Short-term lease costs ​ 164 Total lease costs $ 3,032 ​ Supplemental balance sheet information related to leases is as follows (in thousands, except lease term and discount rate): ​ ​ ​ ​ ​ ​ As of December 31, 2019 ​ Operating Leases: ​ ​ ​ Operating lease right-of-use assets $ 27,439 ​ ​ ​ ​ ​ Accrued expenses and other current liabilities $ 6,177 ​ Long-term operating lease liabilities ​ 20,526 ​ Total operating lease liabilities $ 26,703 ​ ​ ​ ​ ​ Finance Leases: ​ ​ ​ Property, plant and equipment, at cost $ 2,540 ​ Accumulated amortization ​ (311) ​ Property, plant and equipment, net $ 2,229 ​ ​ ​ ​ ​ Accrued expenses and other current liabilities $ 1,195 ​ Other long-term liabilities ​ 1,175 ​ Total finance lease liabilities $ 2,370 ​ ​ ​ ​ ​ Weighted average remaining lease term (in years): ​ ​ ​ Operating leases ​ 2.02 ​ Finance leases ​ 7.98 ​ ​ ​ ​ ​ Weighted average discount rate: ​ ​ ​ Operating leases ​ 4.7 % Finance leases ​ 4.1 % ​ Supplemental cash flow information related to operating leases was as follows (in thousands, unaudited): ​ ​ ​ ​ ​ Three Months Ended December 31, 2019 Cash paid for amounts included in measurement of liabilities: ​ ​ Operating cash flows from operating leases $ 1,807 Operating cash flows from finance leases ​ 29 Financing cash flows from finance leases ​ 290 ​ Future lease payments for operating and capital leases as of September 30, 2019 were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ Operating Leases ​ Capital Leases Fiscal year ended September 30, ​ ​ ​ ​ ​ 2020 $ 6,794 ​ $ 1,276 2021 ​ 5,520 ​ ​ 1,171 2022 ​ 3,904 ​ ​ 363 2023 ​ 3,110 ​ ​ - 2024 ​ 2,934 ​ ​ - Thereafter ​ 10,499 ​ ​ - Total future lease payments ​ 32,761 ​ ​ 2,810 Less imputed interest ​ (5,685) ​ ​ (150) Total lease liability balance $ 27,076 ​ $ 2,660 ​ ​ Future lease payments for operating and finance leases as of December 31, 2019 were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ Operating Leases ​ Finance Leases Fiscal year ended September 30, ​ ​ ​ ​ ​ 2020 $ 5,539 ​ $ 957 2021 ​ 5,827 ​ ​ 1,171 2022 ​ 4,182 ​ ​ 363 2023 ​ 3,151 ​ ​ - 2024 ​ 2,941 ​ ​ - Thereafter ​ 10,506 ​ ​ - Total future lease payments ​ 32,146 ​ ​ 2,491 Less imputed interest ​ (5,443) ​ ​ (121) Total lease liability balance $ 26,703 ​ $ 2,370 ​ ​ As of December 31, 2019, the Company has entered into leases that have not commenced with future lease payments of $8.2 million, excluding purchase options. These leases are not recorded on the Consolidated Balance Sheets. Lease commencement dates for these leases range between 2020 and 2030.

Income Taxes

Income Taxes	3 Months Ended
	Dec. 31, 2019
Income Tax Disclosure [Abstract]
Income Taxes	​ 10. Income Taxes The Company recorded an income tax benefit of $3.0 million during the three months ended December 31, 2019. The tax benefit was primarily driven by a $5.8 million stock compensation windfall benefit for tax deductions that exceeded the associated compensation expense, and a $0.5 million reduction in deferred tax liabilities related to the extension of a tax rate incentive in China. These discrete benefits were partially offset by the tax provision on earnings from operations during the period. The Company recorded an income tax benefit of $5.8 million, during the three months ended December 31, 2018. The tax benefit was primarily driven by a $3.7 million discrete benefit for stock compensation windfalls, $1.4 million of tax benefits related to the remeasurement of net U.S. deferred tax assets due to state tax rate changes, and a $1.1 million transition tax reduction. These discrete benefits were slightly offset by the tax provision on earnings from operations during the period. During 2018, the Internal Revenue Service issued proposed regulations on the federal toll charge and various other aspects of the Tax Cuts and Jobs Act. The Company finalized its analysis of the toll charge and related liabilities, including uncertain tax positions, during the three months ended December 31, 2018 pursuant to U.S. Securities and Exchange Commission (“SEC”) Staff Accounting Bulletin No. 118. As a result of the new guidance issued and additional work to complete the calculation of its federal toll charge, the Company reduced its provisional accrual for federal, state and foreign taxes by net $1.1 million during the three months ended December 31, 2018. The Company evaluates the realizability of its deferred tax assets by tax-paying component and assesses the need for a valuation allowance on a quarterly basis. The Company evaluates the profitability of each tax-paying component on a historic cumulative basis and a forward-looking basis while performing this analysis. The Company maintains a U.S. valuation allowance related to the realizability of certain state tax credits and net operating loss carry-forwards, as well as a valuation allowance against net deferred tax assets in certain foreign tax-paying components as of December 31, 2019. The Company maintains liabilities for uncertain tax positions. These liabilities involve judgment and estimation and are monitored based on the best information available. The Company recognizes interest related to unrecognized tax benefits as a component of the income tax expense or benefit. The Company recognized interest expense related to its unrecognized tax benefits of $0.3 million during the three months ended December 31, 2019. The Company is subject to U.S. federal income tax and 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 2011. 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 $0.2 million within the next twelve months.

Other Balance Sheet Information

Other Balance Sheet Information	3 Months Ended
	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Other Balance Sheet Information	11. Other Balance Sheet Information The following is a summary of accounts receivable at December 31, 2019 and September 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ September 30, ​ ​ 2019 2019 Accounts receivable ​ $ 168,851 ​ $ 169,317 ​ Less allowance for doubtful accounts ​ (3,592) ​ (3,644) ​ Less allowance for sales returns ​ (83) ​ (71) ​ Accounts receivable, net ​ $ 165,176 ​ $ 165,602 ​ ​ The following is a summary of inventories at December 31, 2019 and September 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ September 30, ​ ​ 2019 2019 Inventories ​ ​ Raw materials and purchased parts ​ $ 70,694 ​ $ 67,176 ​ Work-in-process ​ 13,625 ​ 13,684 ​ Finished goods ​ 20,862 ​ 18,585 ​ Total inventories ​ $ 105,181 ​ $ 99,445 ​ ​ Reserves for excess and obsolete inventory were $16.0 million and $16.3 million, respectively, at December 31, 2019 and September 30, 2019. At December 31, 2019 and September 30, 2019, the Company had cumulative capitalized direct costs of $12.5 million and $11.6 million, respectively, associated with the 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 three months ended December 31, 2019, the Company capitalized direct costs of $0.9 million associated with the development of software for its internal use. The Company establishes reserves for estimated costs 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 months ended December 31, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Activity -Three Months Ended December 31, 2019 Balance ​ ​ ​ ​ Balance September 30, ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Accruals ​ Costs Incurred ​ 2019 $ 7,175 ​ $ 2,479 ​ $ (2,161) ​ $ 7,493 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Activity -Three Months Ended December 31, 2018 Balance ​ ​ ​ ​ Balance September 30, ​ ​ ​ ​ ​ ​ ​ December 31, 2018 ​ Accruals ​ Costs Incurred ​ 2018 $ 6,340 ​ $ 2,355 ​ $ (1,844) ​ $ 6,851 ​ ​

Stock-Based Compensation

Stock-Based Compensation	3 Months Ended
	Dec. 31, 2019
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-Based Compensation	12. Stock-Based Compensation The Company may issue to eligible employees options to purchase shares of the Company’s stock, restricted stock and other equity incentives 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 stock awards, restricted stock awards and deferred stock and restricted stock units to its directors in accordance with its director compensation program. The following table reflects stock-based compensation expense recorded during the three months ended December 31, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, ​ ​ 2019 2018 Restricted stock units ​ $ 4,092 ​ $ 3,960 ​ Employee stock purchase plan ​ 318 ​ 216 ​ Total stock-based compensation expense ​ $ 4,410 ​ $ 4,176 ​ ​ 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 the Nasdaq Stock Market on the date of grant. For awards that vest based on service conditions, the Company recognizes stock-based compensation expense on a straight-line basis over the requisite service period. For awards that vest subject to performance conditions, the Company recognizes stock-based compensation expense ratably over the performance period if it is probable that performance condition will be met and adjusted for the probability percentage of achieving the performance goals. The Company makes estimates of stock award forfeitures and the number of awards expected to vest. The Company considers many factors in developing forfeiture estimates, including award types, employee classes and historical experience. Each quarter, the Company assesses the probability of achieving the performance goals. Current estimates may differ from actual results and future changes in estimates. 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 performance goals. The following table reflects restricted stock units, including stock awards, granted during the three months ended December 31, 2019 and 2018: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Time-Based Stock Performance- ​ ​ Total Units ​ Units ​ Grants ​ Based Units Three months ended December 31, 2019 377,212 155,461 181 221,570 Three months ended December 31, 2018 745,776 321,835 552 423,389 ​ Time-Based Grants Restricted stock units granted with a required service period typically have three-year vesting schedules in which one-third one-third one-third Stock Grants The stock awards granted to the members of the Company’s Board of Directors include stock awards, restricted stock awards and deferred stock and restricted stock units. Certain members of the Board of Directors have elected to defer receiving their annual stock awards and related quarterly dividends until they attain a certain age or cease to provide services as the Company’s Board members. Restricted stock awards granted in fiscal years 2018 are subject to a one-year vesting period, while the restricted stock awards granted in fiscal year 2019 were vested as of the grant date. 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 and approved by 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 2020, 2019 and 2018 allow participants to earn 100% of restricted stock units if the Company’s performance meets its target goal for each applicable financial metric, and up to a maximum of 200% if the Company’s performance for such metrics meets or exceeds the maximum or stretch goal. Performance below the minimum threshold for each financial metric results in award forfeiture. Performance goals will be measured over a three-year period for each year’s awards and at the end of the period to determine the number of units earned by recipients who continue to meet the service requirement. Around the third anniversary of each year awards’ grant date, the Company’s Board of Directors determines the number of units earned for participants who continue to meet the service requirements on the vest date. Restricted Stock Unit Activity The following table summarizes restricted stock unit activity for the three months ended December 31, 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted ​ ​ ​ ​ Average ​ ​ ​ ​ Grant-Date ​ ​ Shares ​ Fair Value Outstanding at September 30, 2019 1,782,726 ​ $ 24.63 Granted 377,212 ​ ​ 47.01 Vested (820,058) ​ ​ 26.35 Forfeited (26,264) ​ ​ 35.60 Outstanding at December 31, 2019 1,313,616 ​ ​ 35.07 ​ The weighted average grant date fair value of restricted stock units granted during the three months ended December 31, 2019 and 2018 was $47.01 and $30.49, respectively. The fair value of restricted stock units vested during the three months ended December 31, 2019 and 2018 was $38.5 million and $27.1 million, respectively. During the three months ended December 31, 2019 and 2018, the Company remitted $24.0 million and $14.2 million, respectively, collected from employees to satisfy their tax obligations as a result of share issuances. As of December 31, 2019, the unrecognized compensation cost related to restricted stock units that are expected to vest is $33.3 million and will be recognized over an estimated weighted average service period of approximately 2.0 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. There were no shares purchased by employees under the employee stock purchase plan during the three months ended December 31, 2019 and 2018.

Earnings per Share

Earnings per Share	3 Months Ended
	Dec. 31, 2019
Earnings Per Share [Abstract]
Earnings per Share	13. Earnings per Share The calculations of basic and diluted net income per share and basic and diluted weighted average shares outstanding are as follows for the three months ended December 31, 2019 and 2018 (in thousands, except per share data): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ ​ ​ December 31, ​ ​ 2019 2018 Income from continuing operations ​ $ 13,174 ​ $ 6,266 ​ (Loss) income from discontinued operations, net of tax ​ (117) ​ 8,149 ​ Net income ​ $ 13,057 ​ $ 14,415 ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average common shares outstanding used in computing basic earnings per share ​ 72,972 ​ 71,450 ​ Dilutive restricted stock units ​ 673 ​ 715 ​ Weighted average common shares outstanding used in computing diluted earnings per share ​ 73,645 ​ 72,165 ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic net income per share: ​ ​ ​ Income from continuing operations ​ $ 0.18 ​ $ 0.09 ​ (Loss) income from discontinued operations, net of tax ​ (0.00) ​ 0.11 ​ Basic net income per share ​ $ 0.18 ​ $ 0.20 ​ ​ ​ ​ ​ ​ ​ ​ ​ Diluted net income per share: ​ ​ ​ Income from continuing operations ​ $ 0.18 ​ $ 0.09 ​ (Loss) income from discontinued operations, net of tax ​ (0.00) ​ 0.11 ​ Diluted net income per share ​ $ 0.18 ​ $ 0.20 ​ Dividend declared per share ​ $ 0.10 ​ $ 0.10 ​ ​ During the three months ended December 31, 2019 and 2018, antidilutive restricted stock units of 158,058 and 261,384, respectively, were excluded from the computation of diluted earnings per share based on the treasury stock method.

Revenue from Contracts with Cus

Revenue from Contracts with Customers	3 Months Ended
	Dec. 31, 2019
Revenue from Contract with Customer [Abstract]
Revenue from Contracts with Customers	14. Revenue from Contracts with Customers Disaggregated Revenue The Company disaggregates revenue from contracts with customers in a manner that depicts how the nature, amount, timing, and uncertainty of revenue and cash flows are affected by economic factors. The Company disaggregates revenue based on the transfer of control of the underlying performance obligations, the geographic location in which customer orders are placed and by reporting unit. ​ The Company transfers control of its performance obligations at a point in time or over time, depending on the nature of the product or service being provided. Revenue from contracts with customers is attributed to geographic areas based on locations in which the customer orders are placed. The Company reports financial results for two reportable segments which consist of Brooks Semiconductor Solutions Group segment and Brooks Life Sciences segment. The Company also consists of five reporting units, including three reporting units within the Brooks Semiconductor Solutions Group reportable segment and two reporting units within the Brooks Life Sciences reportable segment. The following is a reconciliation of revenue disaggregated in a manner discussed above to segment revenue for the three months ended December 31, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Brooks Semiconductor ​ Brooks Life ​ ​ ​ ​ ​ Solutions Group ​ Sciences ​ Total Three Months Ended December 31, 2019 ​ ​ ​ ​ ​ ​ ​ ​ ​ Point in time ​ $ 116,788 ​ $ 21,320 ​ $ 138,108 Over time ​ ​ 2,023 ​ ​ 70,369 ​ ​ 72,392 ​ ​ $ 118,811 ​ $ 91,689 ​ $ 210,500 Three Months Ended December 31, 2018 ​ ​ ​ ​ ​ ​ ​ ​ ​ Point in time ​ $ 111,916 ​ $ 23,167 ​ $ 135,083 Over time ​ ​ 791 ​ ​ 43,494 ​ ​ 44,285 ​ ​ $ 112,707 ​ $ 66,661 ​ $ 179,368 ​ The following is revenue by geographic location and reporting unit for the three months ended December 31, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, 2019 ​ Three Months Ended December 31, 2018 Geographic Location ​ ​ ​ ​ ​ ​ North America ​ $ 80,231 ​ $ 68,897 Asia/Pacific/Other ​ ​ 103,539 ​ ​ 79,460 United Kingdom ​ ​ 9,920 ​ ​ 12,078 Rest of Europe ​ ​ 16,810 ​ ​ 18,933 ​ ​ $ 210,500 ​ $ 179,368 ​ ​ ​ ​ ​ ​ ​ Reporting Unit ​ ​ ​ ​ ​ ​ Automation Solutions ​ $ 64,238 ​ $ 73,675 Contamination Control Solutions ​ ​ 44,340 ​ ​ 27,956 Global Semiconductor Services ​ ​ 10,233 ​ ​ 11,076 Brooks Semiconductor Solutions Group ​ ​ 118,811 ​ ​ 112,707 Sample Management ​ ​ 51,718 ​ ​ 50,303 GENEWIZ ​ ​ 39,971 ​ ​ 16,358 Brooks Life Sciences ​ ​ 91,689 ​ ​ 66,661 Total ​ $ 210,500 ​ $ 179,368 ​ Contract Balances Accounts Receivable, Net. Contract Assets. ​ Deferred Commissions. ​ Contract Liabilities. ​ Remaining Performance Obligations. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ As of December 31, 2019 ​ ​ Less than 1 Year ​ Greater than 1 Year ​ Total Remaining Performance Obligations ​ $ 25,013 ​ $ 10,398 ​ $ 35,411 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cost to Obtain and Fulfill a Contract The Company capitalizes sales commissions when incurred if they are (i) incremental costs of obtaining a contract, (ii) expected to be recovered and (iii) have an expected amortization period that is greater than one year. As part of the Company’s cumulative effect adjustment, incremental costs associated with obtaining a contract were capitalized and have been classified as deferred commissions within the Company’s Consolidated Balance Sheet. These amounts primarily relate to sales commissions within the Brooks Life Sciences segment and are being amortized over a 60 month period, which represents the average period of contract performance. The Company did not capitalize any sales commissions during the three months ended December 31, 2019 as the amount of sales commissions that qualified for capitalization during the reporting period was insignificant. Sales commissions incurred during the reporting period have been expensed as incurred. These costs are recorded within “Selling, general, and administration expenses”. The Company has concluded that none of its costs incurred in fulfillment of customer contracts meet the capitalization criteria. The Company will account for shipping and handling activities as fulfillment activities and recognize the associated expense when transfer of control of the product has transferred to the customer.

Segment Information

Segment Information	3 Months Ended
	Dec. 31, 2019
Segment Reporting [Abstract]
Segment Information	15. Segment Information The Company operates in two reportable segments: the Brooks Semiconductor Solutions Group segment and the Brooks Life Sciences segment. Brooks Life Sciences consists of two operating segments aggregated into one reportable segment. The Brooks Semiconductor Solutions Group segment provides a variety of products, services and solutions that enable improved throughput and yield in controlled operating environments, as well as an extensive range of support services. The solutions include atmospheric and vacuum robots, robotic modules, tool automation systems, contamination control of wafer carrier front opening unified pods and reticle storage. The support services include repair services, diagnostic support services, and installation services in support of the products, which enable customers to maximize process tool uptime and productivity. This segment also provides end-user customers with spare parts and productivity enhancement upgrades to maximize tool productivity. The Brooks Life Sciences segment provides comprehensive life cycle sample management solutions for life science and bioscience customers including complete end-to-end “cold chain of custody” solutions and sample-based laboratory services such as genomic sequencing and gene synthesis to advance scientific research and support drug development. The segment’s product offerings include automated cold sample management systems for compound and biological sample storage, equipment for sample preparation and handling, consumables, and informatics that help customers manage samples throughout their research discovery and development workflows. The segment’s service offerings include sample storage, genomic sequencing, gene synthesis, laboratory processing services, laboratory analysis, and other support services provided to a wide range of life science customers, including pharmaceutical companies, biotechnology companies, biorepositories and research institutes. The Company considers adjusted operating income, which excludes charges related to amortization of completed technology, the acquisition accounting impact on inventory contracts acquired and restructuring related charges as the primary performance metric when evaluating the business. Please refer to Note 21, "Segment and Geographic Information" to the Company’s consolidated financial statements included in the 2019 Annual Report on Form 10- K for further information on the operating segments’ description and accounting policies. In conjunction with the acquisition of GENEWIZ during the quarter ended December 31, 2018, the Company reassessed its segment reporting structure and determined that GENEWIZ represents a separate operating segment based on ASC 280, Segment Reporting (“ASC 280”). As permitted by ASC 280, the Company elected to aggregate the Sample Management operating segment and the GENEWIZ operating segment as a single reportable segment titled Brooks Life Sciences. The aggregation was based on similarities in long-term forecasted economic characteristics, particularly adjusted operating income, similarity in services they offer, the customers they serve, the nature of their service delivery models, and their regulatory environments. The Company believes that the aggregated presentation is more useful to investors and other financial users. Management formally assesses the long-term financial outlook of its operating segments on an annual basis as part of its strategic planning process and more frequently on an informal basis. The customer bases of the operating segments overlap, serving life science and bioscience customers in the pharmaceutical and bio-technology companies as well as academic and government institutions. Both of these operating segments provide services relating to the biological samples needed to advance non-clinical and clinical research, serving scientific and business operations functions. In a typical customer workflow, a biological sample is collected, processed and analyzed with results interpreted and used to make scientific judgements. Critical or valuable samples are then annotated and stored for many years in environments where they can be easily retrieved for additional study. These operating segments provide services across this workflow. Both of these operating segments offer services meeting the standards of Good Manufacturing Practices set forth by the U.S. Food and Drug Administration. The following is the summary of the financial information for the Company’s reportable segments for the three months ended December 31, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, 2019 ​ ​ ​ ​ ​ ​ ​ 2019 ​ ​ 2018 ​ Revenue: ​ ​ ​ ​ ​ ​ ​ Brooks Semiconductor Solutions Group ​ ​ ​ $ 118,811 ​ $ 112,707 ​ Brooks Life Sciences ​ ​ ​ ​ 91,689 ​ 66,661 ​ Total revenue ​ ​ ​ ​ $ 210,500 ​ $ 179,368 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating income: ​ ​ ​ ​ ​ ​ ​ ​ Brooks Semiconductor Solutions Group ​ ​ ​ ​ $ 15,000 ​ $ 17,263 ​ Brooks Life Sciences ​ ​ ​ ​ 5,974 ​ 2,660 ​ Reportable segment adjusted operating income ​ ​ ​ ​ ​ 20,974 ​ ​ 19,923 ​ Amortization of completed technology ​ ​ ​ ​ ​ 2,674 ​ ​ 2,007 ​ Acquisition accounting impact on inventory contracts acquired ​ ​ ​ ​ ​ — ​ ​ 184 ​ Amortization of acquired intangible assets ​ ​ ​ ​ ​ 7,910 ​ ​ 5,769 ​ Restructuring charges ​ ​ ​ ​ ​ 576 ​ ​ 59 ​ Other unallocated corporate (income) expenses ​ ​ ​ ​ ​ (852) ​ ​ 6,571 ​ Total operating income ​ ​ ​ ​ ​ 10,666 ​ ​ 5,333 ​ Interest income ​ ​ ​ ​ ​ 699 ​ ​ 423 ​ Interest expense ​ ​ ​ ​ ​ (737) ​ ​ (5,290) ​ Other expenses, net ​ ​ ​ ​ ​ (417) ​ ​ (30) ​ Income before income taxes ​ ​ ​ ​ $ 10,211 ​ $ 436 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Brooks ​ ​ ​ ​ ​ ​ ​ ​ ​ Semiconductor ​ ​ Brooks ​ ​ ​ ​ Assets: ​ ​ Solutions Group ​ ​ Life Sciences ​ ​ Total ​ December 31, 2019 ​ $ 267,221 ​ $ 932,613 ​ $ 1,199,834 ​ September 30, 2019 ​ 259,641 ​ ​ 909,154 ​ 1,168,795 ​ ​ The following is a reconciliation of the Company’s reportable segments’ segment assets to the corresponding amounts presented in the accompanying Consolidated Balance Sheets as of December 31, 2019 and September 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, September 30, ​ ​ 2019 ​ 2019 Segment assets $ 1,199,834 $ 1,168,795 Cash, cash equivalents, restricted cash, and marketable securities ​ 353,120 ​ 342,140 Deferred tax assets ​ 6,004 ​ 5,064 Total assets ​ $ 1,558,958 ​ $ 1,515,999 ​

Significant Customers

Significant Customers	3 Months Ended
	Dec. 31, 2019
Risks and Uncertainties [Abstract]
Significant Customers	16. Significant Customers The Company had one customer that accounted for 10% or more of its consolidated revenue, at 15%, during the three months ended December 31, 2019. The Company had no customer that accounted for 10% or more of its consolidated revenue during the three months ended December 31, 2018. As of December 31, 2019, the Company had one customer that accounted for more than 10% of its accounts receivable balance , at 11%. There were no customers that accounted for more than 10% of its accounts receivable balance 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 OEMs. 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.

Commitments and Contingencies

Commitments and Contingencies	3 Months Ended
	Dec. 31, 2019
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	17. Commitments and Contingencies Letters of Credit As of December 31, 2019, the Company had approximately $1.2 million of letters of credit outstanding related primarily to customer advances and other performance obligations. These arrangements guarantee the refund of advance payments received from the Company’s 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 three months ended December 31, 2019, and the Company currently does not anticipate any of these obligations to be called in the near future. Purchase Commitments At December 31, 2019, the Company had non-cancellable commitments of $130.2 million, including purchase orders for inventory of $84.9 million, information technology related commitments of $25.0 million, China facility commitments of $18.6 million and other commitments of $1.7 million. Contingencies 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	3 Months Ended
	Dec. 31, 2019
Subsequent Events [Abstract]
Subsequent Events	18. Subsequent Events Dividend On January 24, 2020, the Company’s Board of Directors declared a cash dividend of $0.10 per share payable on March 27, 2020 to common stockholders of record as of March 6, 2020. 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 Accoun_2

Summary of Significant Accounting Policies (Policies)	3 Months Ended
	Dec. 31, 2019
Accounting Policies [Abstract]
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 recording accounts receivable, inventories, goodwill, intangible assets other than goodwill, long-lived assets, derivative financial instruments, deferred income taxes, warranty obligations, revenue recognized in accordance with the percentage of completion method, 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.
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 expenses, net” in the Company’s unaudited Consolidated Statements of Operations. Net foreign currency transaction and remeasurement losses totaled $0.7 million and $0.1 million, respectively, during the three months ended December 31, 2019 and 2018.
Derivative Financial Instruments	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. The Company enters into foreign exchange contracts to reduce its exposure to currency fluctuations. The forward contract arrangements that the Company enters into, typically mature in 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 expenses, net" in the accompanying unaudited Consolidated Statements of Operations and are as follows for the three months ended December 31, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ ​ ​ December 31, ​ ​ 2019 2018 Realized gains (losses) on derivatives not designated as hedging instruments ​ $ (3,668) ​ $ 2,977 ​ ​ The fair values of the forward contracts 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”. 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 described below due to a lack of an active market for these contracts.
Fair Value Measurements	Fair Value Measurements The Company measures at fair value certain financial assets and liabilities, including cash equivalents and available for sale securities. FASB ASC 820, Fair Value Measurement and Disclosures Level 1 Inputs: Level 2 Inputs: Level 3 Inputs: As of December 31, the Company had no assets or liabilities measured and recorded at fair value on a recurring basis using Level 3 inputs.
Leases	Leases The Company has operating leases for real estate and non-real estate and finance leases for non-real estate. The classification of a lease as operating or finance and the determination of the right-of-use asset (ROU asset) and lease liability are determined at lease inception. The ROU asset represents the Company’s right to use an underlying asset for the lease term and the lease liability represents the Company’s obligation to make lease payments arising from the lease. Operating lease ROU assets and liabilities are recognized at commencement date based on the present value of lease payments over the lease term. As most of the Company’s leases do not provide an implicit rate, an incremental borrowing rate is used based on the estimated rate of interest for collateralized borrowing over a similar term of the lease payments at commencement date. Lease terms may include options to extend or terminate the lease when it is reasonably certain that the option will be exercised. Lease expense is recognized on a straight-line basis over the lease term. The Company’s lease agreements may contain lease and non-lease components. Non-lease components primarily include payments for maintenance and utilities. Fixed payments for non-lease components are combined with lease payments and accounted for as a single lease component which increases the amount of the ROU asset and liability. The ROU asset for operating leases is included within Other assets and the ROU asset for finance leases is included within Property, plant, and equipment, net on the Consolidated Balance Sheets. The short-term lease liabilities for both operating leases and finance leases are included within Accrued expenses and other current liabilities. The long-term lease liabilities for operating leases and finance leases are included within Long-term operating lease liabilities, and Other long-term liabilities, respectively, on the Consolidated Balance Sheets.
Recently Issued Accounting Pronouncements	Recently Issued Accounting Pronouncements In December 2019, the FASB issued ASU 2019-12: Simplifying the Accounting for Income Taxes (Topic 740) is permitted. The Company is evaluating the impact of this ASU. ​ In August 2018, the FASB issued ASU 2018-15, Intangibles – Goodwill and Other – Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract In August 2018, the FASB issued ASU 2018-14, Disclosure Framework — Changes to the Disclosure Requirements for Defined Benefit Plans In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework - Changes to the Disclosure Requirements for Fair Value Measurement disclosure requirements related to fair value measurement. The amendments include new disclosure requirement for changes in unrealized gains or losses included in other comprehensive income for recurring Level 3 fair value measurements held at the end of the reporting period and the range and weighted average used to develop significant unobservable inputs for Level 3 fair value measurements. The amendments eliminated disclosure requirements for amount of and reasons for transfers between Level 1 and Level 2, valuation processes for Level 3 fair value measurements, and policy for timing of transfers between levels of the fair value hierarchy. In addition, the amendments modified certain disclosure requirement to provide clarification or to promote appropriate exercise of discretion by entities. ASU 2018-13 is effective for fiscal years beginning after December 15, 2019, including interim periods therein. Early adoption is permitted. The Company is currently evaluating the impact of this ASU. In June 2016, the FASB issued ASU 2016-13, Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments Codification Improvements to Topic 326, Financial Instruments - Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments Codification Improvements to Topic 326, Financial Instruments - Credit Losses Financial Instruments - Credit Losses (Topic 326): Targeted Transition Relief Financial Instruments - Overall Recently Adopted Accounting Pronouncements In July 2019, the FASB issued ASU 2019-07, Codification Updates to SEC Sections - Amendments to SEC Paragraphs Pursuant to SEC Final Rule Releases No. 33-10532, Disclosure Update and Simplification, and Nos. 33-10231 and 33-10442, Investment Company Reporting Modernization and Miscellaneous Updates (SEC Update) . ASU 2019-07 aligns the guidance in various SEC sections of the Codification with the requirements of certain SEC final rules. ASU 2019 -07 was effective immediately during the Company’s third quarter of fiscal 2020 and the adoption did not have any impact on our consolidated financial statements and related disclosures. ​ In March 2018, the FASB issued ASU 2018-02, Reclassification of Certain Tax Effects from Accumulated Other Comprehensive Income ​ In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842) modified retrospective million on its Consolidated Balance Sheets. There was no impact to the Company’s finance ROU asset and liability on October 1, 2019. The adoption of the standard does not impact the Consolidated Results of Operations or Consolidated Statement of Cash Flows. See Note 9, “Leases” for further information.
Other	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 2019 Annual Report on Form 10-K.

Summary of Significant Accoun_3

Summary of Significant Accounting Policies (Tables)	3 Months Ended
	Dec. 31, 2019
Accounting Policies [Abstract]
Realized gains (losses) on derivatives not designated as hedging instruments	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ ​ ​ December 31, ​ ​ 2019 2018 Realized gains (losses) on derivatives not designated as hedging instruments ​ $ (3,668) ​ $ 2,977 ​

Discontinued Operations (Tables

Discontinued Operations (Tables)	3 Months Ended
	Dec. 31, 2019
Discontinued Operations and Disposal Groups [Abstract]
Schedule of discontinued operations	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, ​ ​ ​ ​ 2019 2018 ​ Revenue ​ ​ ​ ​ ​ ​ ​ ​ Products ​ ​ ​ $ - ​ $ 28,786 ​ Services ​ ​ ​ ​ - ​ ​ 10,538 ​ Total revenue ​ ​ ​ ​ - ​ ​ 39,324 ​ Cost of revenue ​ ​ ​ ​ ​ ​ ​ ​ ​ Products ​ ​ ​ ​ - ​ ​ 16,516 ​ Services ​ ​ ​ ​ - ​ ​ 6,049 ​ Total cost of revenue ​ ​ ​ ​ - ​ ​ 22,565 ​ Gross profit ​ ​ ​ ​ - ​ ​ 16,759 ​ Operating expenses ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development ​ ​ ​ ​ - ​ ​ 2,158 ​ Selling, general and administrative ​ ​ ​ ​ (257) ​ ​ 7,203 ​ Total operating expenses ​ ​ ​ ​ (257) ​ ​ 9,361 ​ Operating income ​ ​ ​ ​ 257 ​ ​ 7,398 ​ Other (loss) income, net ​ ​ ​ ​ (410) ​ ​ 289 ​ (Loss) income before income taxes and earnings of equity method investment ​ ​ ​ ​ (153) ​ ​ 7,687 ​ Income tax provision ​ ​ ​ ​ (36) ​ ​ 1,310 ​ (Loss) income before equity in earnings of equity method investment ​ ​ ​ ​ (117) ​ ​ 6,377 ​ Equity in earnings of equity method investment ​ ​ ​ ​ - ​ ​ 1,772 ​ Net (loss) income ​ ​ ​ $ (117) ​ $ 8,149 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, ​ ​ ​ ​ ​ ​ ​ 2018 ​ Depreciation and amortization ​ ​ ​ ​ ​ ​ $ 2 ​ Capital expenditures ​ ​ ​ ​ ​ ​ ​ 308 ​ Stock-based compensation ​ ​ ​ ​ ​ ​ ​ 291 ​ Earnings of equity method investment ​ ​ ​ ​ ​ ​ ​ (1,772) ​
Schedule of unconsolidated subsidiaries accounted for based on the equity method	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, ​ ​ ​ ​ ​ 2018 ​ Statements of Operations: ​ ​ ​ ​ ​ ​ ​ ​ Total revenue ​ ​ ​ ​ ​ ​ $ 22,299 ​ Gross profit ​ ​ ​ ​ ​ ​ ​ 8,928 ​ Operating Income ​ ​ ​ ​ ​ ​ ​ 5,124 ​ Net income ​ ​ ​ ​ ​ ​ ​ 3,496 ​

Marketable Securities (Tables)

Marketable Securities (Tables)	3 Months Ended
	Dec. 31, 2019
Investments, Debt and Equity Securities [Abstract]
Summary of Amortized Cost and Fair Value, Including Accrued Interest Receivable and Unrealized Holding Gains (Losses) on Short-term and Long-term Marketable Securities	The following is a summary of the amortized cost and the fair value, including accrued interest receivable and unrealized holding gains (losses) on the short-term and long-term marketable securities as of December 31, 2019 and September 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Gross Gross ​ ​ ​ Amortized ​ Unrealized ​ Unrealized ​ ​ ​ ​ Cost ​ Losses ​ Gains ​ Fair Value December 31, 2019: ​ ​ ​ ​ U.S. Treasury securities and obligations of U.S. government agencies $ 6,696 ​ $ — ​ $ 1 $ 6,697 Bank certificates of deposits ​ ​ 500 ​ ​ — ​ ​ — ​ ​ 500 Corporate securities ​ ​ 4,519 ​ ​ — ​ ​ — ​ ​ 4,519 Municipal securities ​ 2,515 ​ ​ — ​ ​ — ​ 2,515 Other debt securities ​ 41 ​ ​ — ​ ​ — ​ 41 ​ ​ $ 14,271 ​ $ — ​ $ 1 ​ $ 14,272 September 30, 2019: ​ ​ ​ ​ U.S. Treasury securities and obligations of U.S. government agencies ​ $ 31,863 $ (2) $ 5 $ 31,866 Bank certificates of deposits ​ ​ 750 ​ ​ — ​ ​ — ​ ​ 750 Corporate securities ​ ​ 4,317 ​ ​ — ​ ​ 1 ​ ​ 4,318 Other debt securities ​ 35 ​ — ​ — ​ 35 ​ ​ $ 36,965 ​ $ (2) ​ $ 6 ​ $ 36,969
Fair Value of Marketable Securities by Contractual Maturity	The fair values of the marketable securities by contractual maturities at December 31, 2019 are presented below (in thousands): ​ ​ ​ ​ ​ Fair Value Due in one year or less ​ $ 11,233 Due after one year through five years ​ — Due after five years through ten years ​ ​ — Due after ten years ​ 3,039 Total marketable securities ​ $ 14,272

Acquisitions (Tables)

Acquisitions (Tables)	3 Months Ended
	Dec. 31, 2019
Business Combinations [Abstract]
Amounts of Assets and Liabilities at Fair Value as of Acquisition Date	​ ​ ​ ​ ​ ​ Fair Value of ​ ​ Assets and ​ ​ Liabilities Accounts receivable (approximates contractual value) ​ $ 28,566 Inventories ​ 4,370 Prepaid expenses and other current assets ​ ​ 11,635 Property, plant and equipment ​ 36,379 Goodwill ​ 235,160 Intangible assets ​ 189,129 Other assets ​ ​ 15,998 Current portion of long-term debt ​ (3,170) Accounts payable ​ (6,522) Deferred revenue ​ (67) Accrued compensation and benefits ​ ​ (5,145) Other current liabilities ​ (10,073) Long-term debt ​ ​ (2,482) Long-term tax reserves ​ ​ (13,400) Long-term deferred tax liabilities ​ ​ (34,993) Other long-term liabilities ​ ​ (2,681) Total purchase price, net of cash acquired ​ $ 442,704
Pro Forma Information	​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, 2018 ​ ​ (pro forma) ​ ​ ​ ​ ​ Revenue $ 196,021 ​ Net income from continuing operations ​ 6,795 ​

Goodwill and Intangible Assets

Goodwill and Intangible Assets (Tables)	3 Months Ended
	Dec. 31, 2019
Goodwill and Intangible Assets Disclosure [Abstract]
Components of Goodwill by Business Segment	The changes in the Company’s goodwill by reportable segment since September 30, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Brooks ​ ​ ​ ​ ​ ​ ​ ​ Semiconductor ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Solutions ​ Brooks ​ ​ ​ ​ ​ ​ ​ ​ Group ​ Life Sciences ​ Other ​ Total Gross goodwill, at September 30, 2019 ​ $ 636,791 ​ $ 440,755 ​ $ 26,014 ​ $ 1,103,560 Accumulated goodwill impairments ​ (588,944) ​ — ​ (26,014) ​ (614,958) Goodwill, net of accumulated impairments, at September 30, 2019 ​ 47,847 ​ 440,755 ​ — ​ 488,602 Acquisitions and adjustments ​ 35 ​ 1,733 ​ — ​ 1,768 Gross goodwill, at December 31, 2019 ​ ​ 636,826 ​ ​ 442,488 ​ ​ 26,014 ​ ​ 1,105,328 Accumulated goodwill impairments ​ (588,944) ​ — ​ (26,014) ​ (614,958) Goodwill, net of accumulated impairments, at December 31, 2019 ​ $ 47,882 ​ $ 442,488 ​ $ — ​ $ 490,370 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​
Components of Identifiable Intangible Assets	The components of the Company’s identifiable intangible assets as of December 31, 2019 and September 30, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ September 30, 2019 ​ ​ ​ ​ Accumulated ​ Net Book ​ ​ ​ Accumulated ​ Net Book ​ Cost Amortization Value Cost Amortization Value Patents ​ $ 5,302 ​ $ 4,702 ​ $ 600 ​ $ 5,302 ​ $ 4,628 ​ $ 674 Completed technology ​ 88,819 ​ 41,548 ​ 47,271 ​ 88,288 ​ 38,778 ​ 49,510 Trademarks and trade names ​ 25,424 ​ 6,689 ​ 18,735 ​ 25,340 ​ 5,807 ​ 19,533 Customer relationships ​ 267,087 ​ 91,474 ​ 175,613 ​ 265,450 ​ 84,047 ​ 181,403 Other intangibles ​ ​ 233 ​ ​ 204 ​ ​ 29 ​ ​ 231 ​ ​ 183 ​ ​ 48 ​ ​ $ 386,865 ​ $ 144,617 ​ $ 242,248 ​ $ 384,611 ​ $ 133,443 ​ $ 251,168
Schedule of Future Amortization Expense	Estimated future amortization expense for the intangible assets for the remainder of fiscal year 2020, the subsequent four fiscal years and thereafter is as follows (in thousands): ​ ​ ​ ​ Fiscal year ended September 30, ​ 2020 ​ $ 30,729 2021 ​ 37,494 2022 ​ 34,390 2023 ​ 31,267 2024 ​ 26,500 Thereafter ​ 81,868 ​ ​ $ 242,248

Debt (Tables)

Debt (Tables)	3 Months Ended
	Dec. 31, 2019
Debt Disclosure [Abstract]
Schedule of Future Minimum Principal Payment Obligations	The following are the future minimum principal payment obligations under all of the Company’s outstanding debt as of December 31, 2019 (in thousands): ​ ​ ​ ​ ​ ​ Amount Fiscal year ended September 30, ​ ​ ​ 2020 ​ $ 827 2021 ​ ​ 414 2022 ​ ​ — 2023 ​ ​ — 2024 ​ ​ — Thereafter ​ ​ 50,000 Total outstanding principal balance ​ ​ 51,241 Unamortized deferred financing costs ​ ​ (496) ​ ​ ​ 50,745 Current portion of long-term debt ​ ​ 827 Non-current portion of long-term debt ​ $ 49,918

Leases (Tables)

Leases (Tables)	3 Months Ended
	Dec. 31, 2019
Leases [Abstract]
Schedule of leases	​ ​ ​ ​ ​ Three Months Ended December 31, 2019 ​ ​ ​ Operating lease costs $ 2,122 Finance lease costs: ​ ​ Amortization of assets ​ 311 Interest on lease liabilities ​ 29 Total finance lease costs ​ 340 Variable lease costs ​ 406 Short-term lease costs ​ 164 Total lease costs $ 3,032 ​ ​ ​ ​ ​ ​ As of December 31, 2019 ​ Operating Leases: ​ ​ ​ Operating lease right-of-use assets $ 27,439 ​ ​ ​ ​ ​ Accrued expenses and other current liabilities $ 6,177 ​ Long-term operating lease liabilities ​ 20,526 ​ Total operating lease liabilities $ 26,703 ​ ​ ​ ​ ​ Finance Leases: ​ ​ ​ Property, plant and equipment, at cost $ 2,540 ​ Accumulated amortization ​ (311) ​ Property, plant and equipment, net $ 2,229 ​ ​ ​ ​ ​ Accrued expenses and other current liabilities $ 1,195 ​ Other long-term liabilities ​ 1,175 ​ Total finance lease liabilities $ 2,370 ​ ​ ​ ​ ​ Weighted average remaining lease term (in years): ​ ​ ​ Operating leases ​ 2.02 ​ Finance leases ​ 7.98 ​ ​ ​ ​ ​ Weighted average discount rate: ​ ​ ​ Operating leases ​ 4.7 % Finance leases ​ 4.1 % ​ ​ ​ ​ ​ Three Months Ended December 31, 2019 Cash paid for amounts included in measurement of liabilities: ​ ​ Operating cash flows from operating leases $ 1,807 Operating cash flows from finance leases ​ 29 Financing cash flows from finance leases ​ 290
Schedule of future lease payments of operating leases - ASC 840	​ ​ ​ ​ ​ ​ ​ ​ Operating Leases ​ Capital Leases Fiscal year ended September 30, ​ ​ ​ ​ ​ 2020 $ 6,794 ​ $ 1,276 2021 ​ 5,520 ​ ​ 1,171 2022 ​ 3,904 ​ ​ 363 2023 ​ 3,110 ​ ​ - 2024 ​ 2,934 ​ ​ - Thereafter ​ 10,499 ​ ​ - Total future lease payments ​ 32,761 ​ ​ 2,810 Less imputed interest ​ (5,685) ​ ​ (150) Total lease liability balance $ 27,076 ​ $ 2,660 ​ ​
Schedule of future lease payments of capital leases - ASC 840	​ ​ ​ ​ ​ ​ ​ ​ Operating Leases ​ Capital Leases Fiscal year ended September 30, ​ ​ ​ ​ ​ 2020 $ 6,794 ​ $ 1,276 2021 ​ 5,520 ​ ​ 1,171 2022 ​ 3,904 ​ ​ 363 2023 ​ 3,110 ​ ​ - 2024 ​ 2,934 ​ ​ - Thereafter ​ 10,499 ​ ​ - Total future lease payments ​ 32,761 ​ ​ 2,810 Less imputed interest ​ (5,685) ​ ​ (150) Total lease liability balance $ 27,076 ​ $ 2,660 ​
Schedule of future lease payments of operating leases - ASC 842	​ ​ ​ ​ ​ ​ ​ ​ Operating Leases ​ Finance Leases Fiscal year ended September 30, ​ ​ ​ ​ ​ 2020 $ 5,539 ​ $ 957 2021 ​ 5,827 ​ ​ 1,171 2022 ​ 4,182 ​ ​ 363 2023 ​ 3,151 ​ ​ - 2024 ​ 2,941 ​ ​ - Thereafter ​ 10,506 ​ ​ - Total future lease payments ​ 32,146 ​ ​ 2,491 Less imputed interest ​ (5,443) ​ ​ (121) Total lease liability balance $ 26,703 ​ $ 2,370 ​ ​
Schedule of future lease payments of finance leases - ASC 842	​ ​ ​ ​ ​ ​ ​ ​ Operating Leases ​ Finance Leases Fiscal year ended September 30, ​ ​ ​ ​ ​ 2020 $ 5,539 ​ $ 957 2021 ​ 5,827 ​ ​ 1,171 2022 ​ 4,182 ​ ​ 363 2023 ​ 3,151 ​ ​ - 2024 ​ 2,941 ​ ​ - Thereafter ​ 10,506 ​ ​ - Total future lease payments ​ 32,146 ​ ​ 2,491 Less imputed interest ​ (5,443) ​ ​ (121) Total lease liability balance $ 26,703 ​ $ 2,370 ​

Other Balance Sheet Informati_2

Other Balance Sheet Information (Tables)	3 Months Ended
	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Summary of Accounts Receivable	The following is a summary of accounts receivable at December 31, 2019 and September 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ September 30, ​ ​ 2019 2019 Accounts receivable ​ $ 168,851 ​ $ 169,317 ​ Less allowance for doubtful accounts ​ (3,592) ​ (3,644) ​ Less allowance for sales returns ​ (83) ​ (71) ​ Accounts receivable, net ​ $ 165,176 ​ $ 165,602 ​
Summary of Inventories	The following is a summary of inventories at December 31, 2019 and September 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ September 30, ​ ​ 2019 2019 Inventories ​ ​ Raw materials and purchased parts ​ $ 70,694 ​ $ 67,176 ​ Work-in-process ​ 13,625 ​ 13,684 ​ Finished goods ​ 20,862 ​ 18,585 ​ Total inventories ​ $ 105,181 ​ $ 99,445 ​
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 months ended December 31, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Activity -Three Months Ended December 31, 2019 Balance ​ ​ ​ ​ Balance September 30, ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Accruals ​ Costs Incurred ​ 2019 $ 7,175 ​ $ 2,479 ​ $ (2,161) ​ $ 7,493 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Activity -Three Months Ended December 31, 2018 Balance ​ ​ ​ ​ Balance September 30, ​ ​ ​ ​ ​ ​ ​ December 31, 2018 ​ Accruals ​ Costs Incurred ​ 2018 $ 6,340 ​ $ 2,355 ​ $ (1,844) ​ $ 6,851 ​

Stock-Based Compensation (Table

Stock-Based Compensation (Tables)	3 Months Ended
	Dec. 31, 2019
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Summary of stock-based compensation expense	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, ​ ​ 2019 2018 Restricted stock units ​ $ 4,092 ​ $ 3,960 ​ Employee stock purchase plan ​ 318 ​ 216 ​ Total stock-based compensation expense ​ $ 4,410 ​ $ 4,176 ​ ​
Restricted Stock Unit Activity	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Time-Based Stock Performance- ​ ​ Total Units ​ Units ​ Grants ​ Based Units Three months ended December 31, 2019 377,212 155,461 181 221,570 Three months ended December 31, 2018 745,776 321,835 552 423,389 ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted ​ ​ ​ ​ Average ​ ​ ​ ​ Grant-Date ​ ​ Shares ​ Fair Value Outstanding at September 30, 2019 1,782,726 ​ $ 24.63 Granted 377,212 ​ ​ 47.01 Vested (820,058) ​ ​ 26.35 Forfeited (26,264) ​ ​ 35.60 Outstanding at December 31, 2019 1,313,616 ​ ​ 35.07

Earnings per Share (Tables)

Earnings per Share (Tables)	3 Months Ended
	Dec. 31, 2019
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 per share and basic and diluted weighted average shares outstanding are as follows for the three months ended December 31, 2019 and 2018 (in thousands, except per share data): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ ​ ​ December 31, ​ ​ 2019 2018 Income from continuing operations ​ $ 13,174 ​ $ 6,266 ​ (Loss) income from discontinued operations, net of tax ​ (117) ​ 8,149 ​ Net income ​ $ 13,057 ​ $ 14,415 ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average common shares outstanding used in computing basic earnings per share ​ 72,972 ​ 71,450 ​ Dilutive restricted stock units ​ 673 ​ 715 ​ Weighted average common shares outstanding used in computing diluted earnings per share ​ 73,645 ​ 72,165 ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic net income per share: ​ ​ ​ Income from continuing operations ​ $ 0.18 ​ $ 0.09 ​ (Loss) income from discontinued operations, net of tax ​ (0.00) ​ 0.11 ​ Basic net income per share ​ $ 0.18 ​ $ 0.20 ​ ​ ​ ​ ​ ​ ​ ​ ​ Diluted net income per share: ​ ​ ​ Income from continuing operations ​ $ 0.18 ​ $ 0.09 ​ (Loss) income from discontinued operations, net of tax ​ (0.00) ​ 0.11 ​ Diluted net income per share ​ $ 0.18 ​ $ 0.20 ​ Dividend declared per share ​ $ 0.10 ​ $ 0.10 ​

Revenue from Contracts with C_2

Revenue from Contracts with Customers (Tables)	3 Months Ended
	Dec. 31, 2019
Revenue from Contract with Customer [Abstract]
Disaggregated Revenue	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Brooks Semiconductor ​ Brooks Life ​ ​ ​ ​ ​ Solutions Group ​ Sciences ​ Total Three Months Ended December 31, 2019 ​ ​ ​ ​ ​ ​ ​ ​ ​ Point in time ​ $ 116,788 ​ $ 21,320 ​ $ 138,108 Over time ​ ​ 2,023 ​ ​ 70,369 ​ ​ 72,392 ​ ​ $ 118,811 ​ $ 91,689 ​ $ 210,500 Three Months Ended December 31, 2018 ​ ​ ​ ​ ​ ​ ​ ​ ​ Point in time ​ $ 111,916 ​ $ 23,167 ​ $ 135,083 Over time ​ ​ 791 ​ ​ 43,494 ​ ​ 44,285 ​ ​ $ 112,707 ​ $ 66,661 ​ $ 179,368 ​
Geographic Location and Reporting Unit	The following is revenue by geographic location and reporting unit for the three months ended December 31, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, 2019 ​ Three Months Ended December 31, 2018 Geographic Location ​ ​ ​ ​ ​ ​ North America ​ $ 80,231 ​ $ 68,897 Asia/Pacific/Other ​ ​ 103,539 ​ ​ 79,460 United Kingdom ​ ​ 9,920 ​ ​ 12,078 Rest of Europe ​ ​ 16,810 ​ ​ 18,933 ​ ​ $ 210,500 ​ $ 179,368 ​ ​ ​ ​ ​ ​ ​ Reporting Unit ​ ​ ​ ​ ​ ​ Automation Solutions ​ $ 64,238 ​ $ 73,675 Contamination Control Solutions ​ ​ 44,340 ​ ​ 27,956 Global Semiconductor Services ​ ​ 10,233 ​ ​ 11,076 Brooks Semiconductor Solutions Group ​ ​ 118,811 ​ ​ 112,707 Sample Management ​ ​ 51,718 ​ ​ 50,303 GENEWIZ ​ ​ 39,971 ​ ​ 16,358 Brooks Life Sciences ​ ​ 91,689 ​ ​ 66,661 Total ​ $ 210,500 ​ $ 179,368
Remaining Performance Obligations	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ As of December 31, 2019 ​ ​ Less than 1 Year ​ Greater than 1 Year ​ Total Remaining Performance Obligations ​ $ 25,013 ​ $ 10,398 ​ $ 35,411 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​

Segment Information (Tables)

Segment Information (Tables)	3 Months Ended
	Dec. 31, 2019
Segment Reporting [Abstract]
Financial Information for Business Segments	The following is the summary of the financial information for the Company’s reportable segments for the three months ended December 31, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended December 31, 2019 ​ ​ ​ ​ ​ ​ ​ 2019 ​ ​ 2018 ​ Revenue: ​ ​ ​ ​ ​ ​ ​ Brooks Semiconductor Solutions Group ​ ​ ​ $ 118,811 ​ $ 112,707 ​ Brooks Life Sciences ​ ​ ​ ​ 91,689 ​ 66,661 ​ Total revenue ​ ​ ​ ​ $ 210,500 ​ $ 179,368 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating income: ​ ​ ​ ​ ​ ​ ​ ​ Brooks Semiconductor Solutions Group ​ ​ ​ ​ $ 15,000 ​ $ 17,263 ​ Brooks Life Sciences ​ ​ ​ ​ 5,974 ​ 2,660 ​ Reportable segment adjusted operating income ​ ​ ​ ​ ​ 20,974 ​ ​ 19,923 ​ Amortization of completed technology ​ ​ ​ ​ ​ 2,674 ​ ​ 2,007 ​ Acquisition accounting impact on inventory contracts acquired ​ ​ ​ ​ ​ — ​ ​ 184 ​ Amortization of acquired intangible assets ​ ​ ​ ​ ​ 7,910 ​ ​ 5,769 ​ Restructuring charges ​ ​ ​ ​ ​ 576 ​ ​ 59 ​ Other unallocated corporate (income) expenses ​ ​ ​ ​ ​ (852) ​ ​ 6,571 ​ Total operating income ​ ​ ​ ​ ​ 10,666 ​ ​ 5,333 ​ Interest income ​ ​ ​ ​ ​ 699 ​ ​ 423 ​ Interest expense ​ ​ ​ ​ ​ (737) ​ ​ (5,290) ​ Other expenses, net ​ ​ ​ ​ ​ (417) ​ ​ (30) ​ Income before income taxes ​ ​ ​ ​ $ 10,211 ​ $ 436 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Brooks ​ ​ ​ ​ ​ ​ ​ ​ ​ Semiconductor ​ ​ Brooks ​ ​ ​ ​ Assets: ​ ​ Solutions Group ​ ​ Life Sciences ​ ​ Total ​ December 31, 2019 ​ $ 267,221 ​ $ 932,613 ​ $ 1,199,834 ​ September 30, 2019 ​ 259,641 ​ ​ 909,154 ​ 1,168,795 ​ ​
Reconciliation of Reportable Segment Assets to Corresponding Consolidated Amounts	​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, September 30, ​ ​ 2019 ​ 2019 Segment assets $ 1,199,834 $ 1,168,795 Cash, cash equivalents, restricted cash, and marketable securities ​ 353,120 ​ 342,140 Deferred tax assets ​ 6,004 ​ 5,064 Total assets ​ $ 1,558,958 ​ $ 1,515,999

Basis of Presentation (Details)

Basis of Presentation (Details) - Discontinued Operations, Disposed of by Sale - Semiconductor Cryogenics Business $ in Millions	Jul. 01, 2019USD ($)
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Consideration	$ 661.1
Net working capital adjustments	6.3
Net proceeds from the sale	$ 553.1

Summary of Significant Accoun_4

Summary of Significant Accounting Policies - Foreign Currency Translation (Details) - USD ($) $ in Millions	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Foreign Currency Transaction Gain (Loss), before Tax [Abstract]
Foreign currency transaction and remeasurement losses	$ (0.7)	$ (0.1)

Summary of Significant Accoun_5

Summary of Significant Accounting Policies - Derivative Instruments (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Derivative Instruments Not Designated as Hedging Instruments, Gain (Loss), Net [Abstract]
Realized gains (losses) on derivatives not designated as hedging instruments	$ (3,668)	$ 2,977

Summary of Significant Accoun_6

Summary of Significant Accounting Policies - Fair Value Measurements (Details) - Fair Value, Measurements, Recurring - Significant Unobservable Inputs (Level 3) $ in Millions	Dec. 31, 2019USD ($)
Assets
Assets measured at fair value	$ 0
Liabilities
Liabilities measured at fair value	$ 0

Summary of Significant Accoun_7

Summary of Significant Accounting Policies - Recently Issued and Adopted Accounting Pronouncements (Details)	Dec. 31, 2019
Accounting Standards Update 2019-12
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-15
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-14
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-13
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2016-13
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-02
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2016-02
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Oct. 1, 2019
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Change in Accounting Principle, Accounting Standards Update, Transition Option Elected	Modified Retrospective

Summary of Significant Accoun_8

Summary of Significant Accounting Policies - ASC 842 (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Oct. 01, 2019
Assets and Liabilities, Lessee [Abstract]
Operating lease right-of-use assets	$ 27,439	$ 28,100
Operating lease liability	$ 26,703	$ 27,100

Discontinued Operations - Gener

Discontinued Operations - General Information (Details) - USD ($) $ in Millions	Jul. 01, 2019	Aug. 27, 2018
Edwards Vacuum LLC
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Transition service agreement, term, high end of range		9 months
Aggregate amount to purchase goods		$ 1
Supply agreement term		1 year
Lease term		3 years
Option to renew		true
ULVAC Cryogenics, Inc.
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Ownership interest (as a percent)		50.00%
Discontinued Operations, Held-for-sale | Semiconductor Cryogenics Business
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Consideration		$ 675
Discontinued operation, name of segment		brks:BrooksSemiconductorSolutionsGroupMember
Discontinued Operations, Disposed of by Sale | Semiconductor Cryogenics Business
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Consideration	$ 661.1
Net working capital adjustments	6.3
Net proceeds from the sale	$ 553.1

Discontinued Operations - Finan

Discontinued Operations - Financial Results (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Disposal Group, Including Discontinued Operation, Income Statement Disclosures [Abstract]
Net (loss) income	$ (117)	$ 8,149
Discontinued Operations, Held-for-sale | Semiconductor Cryogenics Business
Disposal Group, Including Discontinued Operation, Income Statement Disclosures [Abstract]
Total revenue		39,324
Total cost of revenue		22,565
Gross profit		16,759
Research and development		2,158
Selling, general and administrative	(257)	7,203
Total operating expenses	(257)	9,361
Operating income	257	7,398
Other (loss) income, net	(410)	289
(Loss) income before income taxes and earnings of equity method investment	(153)	7,687
Income tax provision	(36)	1,310
(Loss) income before equity in earnings of equity method investment	(117)	6,377
Equity in earnings of equity method investment		1,772
Net (loss) income	$ (117)	8,149
Discontinued Operations, Held-for-sale | Semiconductor Cryogenics Business | Products
Disposal Group, Including Discontinued Operation, Income Statement Disclosures [Abstract]
Total revenue		28,786
Total cost of revenue		16,516
Discontinued Operations, Held-for-sale | Semiconductor Cryogenics Business | Services
Disposal Group, Including Discontinued Operation, Income Statement Disclosures [Abstract]
Total revenue		10,538
Total cost of revenue		$ 6,049

Discontinued Operations - Uncon

Discontinued Operations - Unconsolidated Subsidiaries - Statements of Operations (Details) - ULVAC Cryogenics, Inc. $ in Thousands	3 Months Ended
	Dec. 31, 2018USD ($)
Equity Method Investment, Summarized Financial Information, Income Statement [Abstract]
Total revenue	$ 22,299
Gross profit	8,928
Operating Income	5,124
Net income	$ 3,496

Discontinued Operations - Non-c

Discontinued Operations - Non-cash Items and Capital Expenditures (Details) - Discontinued Operations, Held-for-sale - Semiconductor Cryogenics Business $ in Thousands	3 Months Ended
	Dec. 31, 2018USD ($)
Discontinued Operation, Alternative Cash Flow Information [Abstract]
Depreciation and amortization	$ 2
Capital expenditures	308
Stock-based compensation	291
Earnings of equity method investment	$ (1,772)

Marketable Securities - General

Marketable Securities - General Information (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Investments, Debt and Equity Securities [Abstract]
Marketable securities sold during period, fair value	$ 0	$ 49,400
Marketable securities sold during period, amortized cost basis		49,500
Net realized losses		100
Sales of marketable securities		48,904
Reclassification unrealized net holding losses		$ 100

Marketable Securities - Summary

Marketable Securities - Summary of Amortized Cost and Fair Value (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	$ 14,271	$ 36,965
Gross Unrealized Losses		(2)
Gross Unrealized Gains	1	6
Fair Value	14,272	36,969
U.S. Treasury securities and obligations of U.S. government agencies
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	6,696	31,863
Gross Unrealized Losses		(2)
Gross Unrealized Gains	1	5
Fair Value	6,697	31,866
Bank certificates of deposits
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	500	750
Fair Value	500	750
Corporate securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	4,519	4,317
Gross Unrealized Gains		1
Fair Value	4,519	4,318
Municipal securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	2,515
Fair Value	2,515
Other debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	41	35
Fair Value	$ 41	$ 35

Marketable Securities - Fair Va

Marketable Securities - Fair Value of Marketable Securities by Contractual Maturity (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Investments, Debt and Equity Securities [Abstract]
Due in one year or less	$ 11,233
Due after ten years	3,039
Fair Value	$ 14,272	$ 36,969

Marketable Securities - Unreali

Marketable Securities - Unrealized Loss Position (Details) - USD ($) $ in Millions	12 Months Ended
	Sep. 30, 2019	Dec. 31, 2019
Debt Securities, Available-for-sale, Unrealized Loss Position [Abstract]
Fair value of marketable securities in unrealized loss position	$ 12	$ 0
Other-than-temporary Impairment Loss, Debt Securities, Available-for-sale [Abstract]
Impairment losses	$ 0

Marketable Securities - Cash Eq

Marketable Securities - Cash Equivalents (Details) - Fair Value, Measurements, Recurring - USD ($) $ in Millions	Dec. 31, 2019	Sep. 30, 2019
Quoted Prices in Active Markets for Identical Assets (Level 1) | Money market funds
Assets:
Cash equivalents		$ 6.2
Significant Other Observable Inputs (Level 2)
Assets:
Cash equivalents	$ 37.2	$ 10

Acquisitions - Purchase Conside

Acquisitions - Purchase Consideration (Details) $ in Thousands	Nov. 15, 2018USD ($)customer	Dec. 31, 2018USD ($)	Sep. 30, 2019USD ($)
Business Acquisition [Line Items]
Net cash outflow		$ 445,210
GENEWIZ
Business Acquisition [Line Items]
Total purchase price	$ 442,700
Change in purchase price			$ (4,000)
Working capital adjustment	$ 400
GENEWIZ | Minimum
Business Acquisition [Line Items]
Number of institutional customers | customer	4,000

Acquisitions - Escrow (Details)

Acquisitions - Escrow (Details) - GENEWIZ - USD ($) $ in Millions	Nov. 15, 2018	Sep. 30, 2019
Business Acquisition [Line Items]
Escrow deposit	$ 32.3
Escrow deposit for acquiree's employees retention obligations	1.5
Reversal of liability associated with adjustment holdback		$ 1.5
Seller's cash	$ 0.7
Escrow collected		$ 1.8

Acquisitions - Amounts of Asset

Acquisitions - Amounts of Assets and Liabilities at Fair Value as of Acquisition Date (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019	Nov. 15, 2018
Business Combination, Recognized Identifiable Assets Acquired, Goodwill, and Liabilities Assumed, Net [Abstract]
Goodwill	$ 490,370	$ 488,602
GENEWIZ
Business Combination, Recognized Identifiable Assets Acquired, Goodwill, and Liabilities Assumed, Net [Abstract]
Accounts receivable			$ 28,566
Inventories			4,370
Prepaid expenses and other current assets			11,635
Property, plant and equipment			36,379
Goodwill			235,160
Intangible assets, net			189,129
Other assets			15,998
Current portion of long-term debt			(3,170)
Accounts payable			(6,522)
Deferred revenue			(67)
Accrued compensation and benefits			(5,145)
Other current liabilities			(10,073)
Long-term debt			(2,482)
Long term tax reserves			(13,400)
Long-term deferred tax liabilities			(34,993)
Other long-term liabilities			(2,681)
Total purchase price			$ 442,704

Acquisitions - Intangible Asset

Acquisitions - Intangible Assets Acquired (Details) - GENEWIZ $ in Millions	Nov. 15, 2018USD ($)
Acquired Finite-Lived Intangible Assets [Line Items]
Weighted average useful life of intangible assets	13 years 3 months 18 days
Customer Relationships
Acquired Finite-Lived Intangible Assets [Line Items]
Finite-lived intangible assets acquired	$ 125.5
Useful life	14 years
Completed Technology
Acquired Finite-Lived Intangible Assets [Line Items]
Finite-lived intangible assets acquired	$ 44.5
Completed Technology | Minimum
Acquired Finite-Lived Intangible Assets [Line Items]
Useful life	10 years
Completed Technology | Maximum
Acquired Finite-Lived Intangible Assets [Line Items]
Useful life	15 years
Trademarks
Acquired Finite-Lived Intangible Assets [Line Items]
Finite-lived intangible assets acquired	$ 19.1
Useful life	13 years

Acquisitions - Goodwill (Detail

Acquisitions - Goodwill (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019	Nov. 15, 2018
Goodwill
Goodwill	$ 490,370	$ 488,602
Brooks Semiconductor Solutions Group
Goodwill
Goodwill	47,882	47,847
Brooks Life Sciences
Goodwill
Goodwill	$ 442,488	$ 440,755
GENEWIZ
Goodwill
Goodwill			$ 235,160
GENEWIZ | Brooks Life Sciences
Goodwill
Goodwill			235,200
Goodwill deductible for tax purposes			$ 0

Acquisitions - Pro Forma Inform

Acquisitions - Pro Forma Information - Tabular Disclosure - Pro Forma (Details) $ in Thousands	3 Months Ended
	Dec. 31, 2018USD ($)
Business Acquisition, Pro Forma Information [Abstract]
Revenue	$ 196,021
Net income from continuing operations	$ 6,795

Acquisitions - Results of Opera

Acquisitions - Results of Operations (Details) - USD ($) $ in Millions	2 Months Ended	3 Months Ended
	Dec. 31, 2018	Dec. 31, 2019	Dec. 31, 2018
Business Acquisition, Pro Forma Information [Abstract]
Amortization of intangible assets		$ 10.6	$ 7.8
GENEWIZ
Business Acquisition, Pro Forma Information [Abstract]
Actual revenues	$ 16.4	40
Actual net income (loss)	0.9	0.8
Amortization of intangible assets	$ 1.6	$ 5.1

Acquisitions - Pro Forma Info_2

Acquisitions - Pro Forma Information - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Business Acquisition, Pro Forma Information [Abstract]
Revenue		$ 196,021
Net income (loss)		6,795
GENEWIZ
Business Acquisition, Pro Forma Information [Abstract]
Property, plant, and equipment, leases, and intangible asset step-up depreciation and amortization expense		1,600
Interest expense related to financing activities		2,000
One-time nonrecurring compensation and transaction costs		42,100
Selling, General and Administrative Expenses | GENEWIZ
Business Acquisition, Pro Forma Information [Abstract]
Acquisition related costs		$ 6,300
Maximum | Selling, General and Administrative Expenses | GENEWIZ
Business Acquisition, Pro Forma Information [Abstract]
Acquisition related costs	$ 100

Goodwill and Intangible Asset_2

Goodwill and Intangible Assets - Components of Goodwill by Operating Segment (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Goodwill [Line Items]
Gross goodwill	$ 1,105,328	$ 1,103,560
Accumulated goodwill impairments	(614,958)	(614,958)
Goodwill	490,370	488,602
Brooks Semiconductor Solutions Group
Goodwill [Line Items]
Gross goodwill	636,826	636,791
Accumulated goodwill impairments	(588,944)	(588,944)
Goodwill	47,882	47,847
Brooks Life Sciences
Goodwill [Line Items]
Gross goodwill	442,488	440,755
Goodwill	442,488	440,755
Other
Goodwill [Line Items]
Gross goodwill	26,014	26,014
Accumulated goodwill impairments	$ (26,014)	$ (26,014)

Goodwill and Intangible Asset_3

Goodwill and Intangible Assets - Goodwill Roll Forward (Details) $ in Thousands	3 Months Ended
	Dec. 31, 2019USD ($)
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	$ 488,602
Acquisitions and adjustments	1,768
Goodwill, net of accumulated impairments, ending balance	490,370
Brooks Semiconductor Solutions Group
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	47,847
Acquisitions and adjustments	35
Goodwill, net of accumulated impairments, ending balance	47,882
Brooks Life Sciences
Goodwill [Roll Forward]
Goodwill, net of accumulated impairments, beginning balance	440,755
Acquisitions and adjustments	1,733
Goodwill, net of accumulated impairments, ending balance	$ 442,488

Goodwill and Intangible Asset_4

Goodwill and Intangible Assets - Goodwill Acquired (Details) $ in Millions	3 Months Ended
	Dec. 31, 2019USD ($)
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill acquired during period	$ 1.8

Goodwill and Intangible Asset_5

Goodwill and Intangible Assets - Components of Identifiable Intangible Assets (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Finite-Lived Intangible Assets [Line Items]
Cost	$ 386,865	$ 384,611
Accumulated Amortization	144,617	133,443
Net Book Value	242,248	251,168
Patents
Finite-Lived Intangible Assets [Line Items]
Cost	5,302	5,302
Accumulated Amortization	4,702	4,628
Net Book Value	600	674
Completed Technology
Finite-Lived Intangible Assets [Line Items]
Cost	88,819	88,288
Accumulated Amortization	41,548	38,778
Net Book Value	47,271	49,510
Trademarks and Trade Names
Finite-Lived Intangible Assets [Line Items]
Cost	25,424	25,340
Accumulated Amortization	6,689	5,807
Net Book Value	18,735	19,533
Customer Relationships
Finite-Lived Intangible Assets [Line Items]
Cost	267,087	265,450
Accumulated Amortization	91,474	84,047
Net Book Value	175,613	181,403
Other Intangible Assets
Finite-Lived Intangible Assets [Line Items]
Cost	233	231
Accumulated Amortization	204	183
Net Book Value	$ 29	$ 48

Goodwill and Intangible Asset_6

Goodwill and Intangible Assets - Amortization Expense (Details) - USD ($) $ in Millions	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Goodwill and Intangible Assets Disclosure [Abstract]
Amortization of intangible assets	$ 10.6	$ 7.8

Goodwill and Intangible Asset_7

Goodwill and Intangible Assets - Estimated Future Amortization Expense of Intangible Assets (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Finite-Lived Intangible Assets, Net, Amortization Expense, Fiscal Year Maturity [Abstract]
2020	$ 30,729
2021	37,494
2022	34,390
2023	31,267
2024	26,500
Thereafter	81,868
Net Book Value	$ 242,248	$ 251,168

Line of Credit (Details)

Line of Credit (Details) - USD ($) $ in Millions	3 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Oct. 04, 2017
Letter of Credit
Line of Credit Facility [Line Items]
Line of credit, expiration date	Oct. 4, 2022
Letter of Credit | Minimum
Line of Credit Facility [Line Items]
Line of credit, expiration period	90 days
Line of Credit | Credit Agreement | Revolving Credit Facility
Line of Credit Facility [Line Items]
Line of credit, maximum borrowing capacity	$ 75		$ 75
Outstanding line of credit	0	$ 0
Deferred finance costs	0.3	$ 0.4
Line of credit, remaining borrowing capacity	$ 43.6
Line of Credit | Credit Agreement | Letter of Credit
Line of Credit Facility [Line Items]
Line of credit, maximum borrowing capacity			7.5
Secured Debt | Senior Secured Term Loan Facility
Line of Credit Facility [Line Items]
Face amount			$ 200

Debt - General Information (Det

Debt - General Information (Details) $ in Millions	Jul. 01, 2019USD ($)loan	Feb. 15, 2019USD ($)	Nov. 15, 2018USD ($)	Oct. 04, 2017USD ($)
Debt Instrument [Line Items]
Issue amount		$ 345.2
Aggregate increase amount				$ 75
Maximum secured leverage ratio				3
Secured Debt
Debt Instrument [Line Items]
Loss on extinguishment of debt	$ 5.2
Number of term loans | loan	2
Senior Secured Term Loan Facility | Secured Debt
Debt Instrument [Line Items]
Debt extinguished	$ 147
Face amount				$ 200
Issue amount				$ 197.6
Percentage of par (as a percent)				98.80%
Discount				$ 2.4
Discount percentage (as a percent)				1.20%
Senior Secured Incremental Term Loan Facility | Secured Debt
Debt Instrument [Line Items]
Debt extinguished	$ 348.3	340.1
Loss on extinguishment of debt		9.1
Face amount		$ 349.1	$ 350
Issue amount			$ 340.5
Percentage of par (as a percent)		98.90%	97.30%
Discount		$ 4	$ 9.5
Discount percentage (as a percent)			2.70%

Debt - Term Loans (Details)

Debt - Term Loans (Details) $ in Thousands	3 Months Ended
	Dec. 31, 2019USD ($)loaninstallment	Jul. 01, 2019loan
Debt Instrument [Line Items]
Deferred financing costs	$ 496
Outstanding principal balance	$ 51,241
Secured Debt
Debt Instrument [Line Items]
Number of term loans | loan		2
Secured Debt | Five-year Term Loans Maturing 2021
Debt Instrument [Line Items]
Number of term loans | loan	3
Debt instrument, term	5 years
Face amount	$ 3,300
Number of installments | installment	8
Installment payment, percentage of initial principal amount (as a percent)	12.50%
Deferred financing costs	$ 0
Outstanding principal balance	$ 1,200
Secured Debt | Five-year Term Loans Maturing 2021 | London Interbank Offered Rate (LIBOR)
Debt Instrument [Line Items]
Debt instrument, basis spread on variable rate (as a percent)	3.10%
Secured Debt | One-year Term Loans Maturing 2019
Debt Instrument [Line Items]
Number of term loans | loan	2
Debt instrument, term	1 year
Face amount	$ 3,200
Secured Debt | One-year Term Loans Maturing 2019, Loan One
Debt Instrument [Line Items]
Debt instrument, interest rate, stated percentage (as a percentage)	4.56%
Secured Debt | One-year Term Loans Maturing 2019, Loan Two
Debt Instrument [Line Items]
Debt instrument, interest rate, stated percentage (as a percentage)	4.35%

Debt - Additional Information (

Debt - Additional Information (Details) - USD ($) $ in Thousands	Jul. 01, 2019	Feb. 15, 2019	Dec. 31, 2019	Oct. 04, 2017
Debt Instrument [Line Items]
Deferred financing costs			$ 496
Senior Secured Term Loan Facility | Secured Debt
Debt Instrument [Line Items]
Prepayments as a percentage of the preceding year excess cash flow (as a percent)			50.00%
Deferred financing costs			$ 500
Weighted average interest rate (as a percent)			4.50%
Interest expense			$ 600
Deferred financing costs amortization			$ 100
Interest rate above applicable rate (as a percent)				2.00%
Debt extinguished	$ 147,000
Senior Secured Incremental Term Loan Facility | Secured Debt
Debt Instrument [Line Items]
Debt extinguished	$ 348,300	$ 340,100

Debt - Long-term Debt - Future

Debt - Long-term Debt - Future Minimum Principal Payment Obligations (Details) $ in Thousands	Dec. 31, 2019USD ($)
Long-term Debt, Fiscal Year Maturity [Abstract]
2020	$ 827
2021	414
Thereafter	50,000
Total outstanding principal balance	51,241
Unamortized deferred financing costs	(496)
Long-term debt	$ 50,745

Debt - Long-term Debt - Current

Debt - Long-term Debt - Current and Non-current (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Long-term Debt, by Current and Noncurrent [Abstract]
Long-term debt	$ 50,745
Current portion of long-term debt	827	$ 829
Non-current portion of long-term debt	$ 49,918	$ 50,315

Leases - Operating Lease Expens

Leases - Operating Lease Expense (Details) $ in Thousands	3 Months Ended
	Dec. 31, 2019USD ($)
Lease, Cost [Abstract]
Operating lease costs	$ 2,122
Amortization of assets	311
Interest on lease liabilities	29
Total finance lease costs	340
Variable lease cost	406
Short-term lease costs	164
Total lease costs	$ 3,032

Leases - Assets and Liabilities

Leases - Assets and Liabilities - Operating Leases (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Oct. 01, 2019
Assets and Liabilities, Lessee [Abstract]
Operating lease right-of-use assets	$ 27,439	$ 28,100
Accrued expenses and other current liabilities	$ 6,177
Operating Lease Liability Current, Statement of Financial Position	brks:AccruedExpensesAndOtherCurrentLiabilities
Long-term operating lease liabilities	$ 20,526
Total lease liability balance	$ 26,703	$ 27,100

Leases - Assets and Liabiliti_2

Leases - Assets and Liabilities - Finance Leases (Details) $ in Thousands	Dec. 31, 2019USD ($)
Finance Lease, Right-of-Use Asset, after Accumulated Amortization [Abstract]
Property, plant and equipment, at cost	$ 2,540
Accumulated amortization	(311)
Property, plant and equipment, net	2,229
Finance Lease Liability [Abstract]
Accrued expenses and other current liabilities	$ 1,195
Finance Lease Liability Current, Statement of Financial Position	brks:AccruedExpensesAndOtherCurrentLiabilities
Other long-term liabilities	$ 1,175
Finance Lease Liability Non Current, Statement of Financial Position	us-gaap:OtherLiabilitiesNoncurrent
Total finance lease liabilities	$ 2,370

Leases - Additional Information

Leases - Additional Information (Details)	Dec. 31, 2019
Leases [Abstract]
Weighted average remaining lease term, operating leases	2 years 7 days
Weighted average remaining lease term, finance leases	7 years 11 months 23 days
Weighted average discount rate, operating leases (as a percent)	4.70%
Weighted average discount rate, finance leases (as a percent)	4.10%

Leases - Supplemental Cash Flow

Leases - Supplemental Cash Flow Information (Details) $ in Thousands	3 Months Ended
	Dec. 31, 2019USD ($)
Cash Flow, Operating Activities, Lessee [Abstract]
Operating cash flows from operating leases	$ 1,807
Operating cash flows from finance leases	29
Financing cash flows from finance leases	$ 290

Leases - Future Lease Payments

Leases - Future Lease Payments - Operating Leases - ASC 840 (Details) $ in Thousands	Sep. 30, 2019USD ($)
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2020	$ 6,794
2021	5,520
2022	3,904
2023	3,110
2024	2,934
Thereafter	10,499
Total future lease payments	32,761
Less imputed interest	(5,685)
Total lease liability balance	$ 27,076

Leases - Future Lease Payment_2

Leases - Future Lease Payments - Capital Leases - ASC 840 (Details) $ in Thousands	Sep. 30, 2019USD ($)
Capital Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2020	$ 1,276
2021	1,171
2022	363
Total future lease payments	2,810
Less imputed interest	(150)
Total lease liability balance	$ 2,660

Leases - Future Lease Payment_3

Leases - Future Lease Payments - Operating Leases - ASC 842 (Details) $ in Thousands	Dec. 31, 2019USD ($)
Lessee, Operating Lease, Liability, Payment, Due [Abstract]
Remainder of 2020	$ 5,539
2021	5,827
2022	4,182
2023	3,151
2024	2,941
Thereafter	10,506
Total future lease payments	$ 32,146

Leases - Gross Difference - Ope

Leases - Gross Difference - Operating Leases - ASC 842 (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Oct. 01, 2019
Operating Lease Liabilities, Gross Difference, Amount [Abstract]
Total future lease payments	$ 32,146
Less imputed interest	(5,443)
Total lease liability balance	$ 26,703	$ 27,100

Leases - Future Lease Payment_4

Leases - Future Lease Payments - Finance Leases - ASC 842 (Details) $ in Thousands	Dec. 31, 2019USD ($)
Finance Lease, Liability, Payment, Due [Abstract]
Remainder of 2020	$ 957
2021	1,171
2022	363
Total future lease payments	$ 2,491

Leases - Gross Difference - Fin

Leases - Gross Difference - Finance Leases - ASC 842 (Details) $ in Thousands	Dec. 31, 2019USD ($)
Finance Lease Liabilities, Gross Difference, Amount [Abstract]
Total future lease payments	$ 2,491
Less imputed interest	(121)
Total finance lease liabilities	$ 2,370

Leases - Future Lease Payment_5

Leases - Future Lease Payments Not Commenced (Details) $ in Millions	Dec. 31, 2019USD ($)
Leases [Abstract]
Leases that have not commenced with future lease payments	$ 8.2

Income Taxes - Provision (Benef

Income Taxes - Provision (Benefit) (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Income Tax Expense (Benefit), Continuing Operations [Abstract]
Income tax (benefit) provision	$ 2,963	$ 5,830
Reduction in deferred tax liabilities related to extension of tax rate in china	(500)
Benefit related to stock compensation windfalls	$ 5,800	3,700
Benefit related to remeasurement of net U.S. deferred tax assets		1,400
Transition tax reduction		$ 1,100

Income Taxes - Additional Infor

Income Taxes - Additional Information (Details) $ in Millions	3 Months Ended
	Dec. 31, 2018USD ($)
Income Tax Disclosure [Abstract]
Toll charge, reduction in provisional accrual	$ 1.1

Income Taxes - Unrecognized Tax

Income Taxes - Unrecognized Tax Benefits - General Information (Details) $ in Millions	3 Months Ended
	Dec. 31, 2019USD ($)
Unrecognized Tax Benefits, Income Tax Penalties and Interest Expense [Abstract]
Interest related to unrecognized benefits	$ 0.3
Anticipated unrecognized tax benefit reduction during next twelve months	$ 0.2

Other Balance Sheet Informati_3

Other Balance Sheet Information - Summary of Account Receivable (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Valuation and Qualifying Accounts Disclosure [Line Items]
Accounts receivable	$ 168,851	$ 169,317
Less allowance for doubtful accounts	(3,592)	(3,644)
Accounts receivable, net	165,176	165,602
Allowance for Sales Returns
Valuation and Qualifying Accounts Disclosure [Line Items]
Less allowance for sales returns	$ (83)	$ (71)

Other Balance Sheet Informati_4

Other Balance Sheet Information - Summary of Inventories (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Raw materials and purchased parts	$ 70,694	$ 67,176
Work-in-process	13,625	13,684
Finished goods	20,862	18,585
Inventory, net	105,181	99,445
Reserves for excess and obsolete inventory	$ 16,000	$ 16,300

Other Balance Sheet Informati_5

Other Balance Sheet Information - Capitalized Direct Costs (Details) - USD ($) $ in Millions	3 Months Ended
	Dec. 31, 2019	Sep. 30, 2019
Property, Plant and Equipment, Gross [Abstract]
Capitalized computer software, gross	$ 12.5	$ 11.6
Capitalized computer software costs	$ 0.9

Other Balance Sheet Informati_6

Other Balance Sheet Information - Product Warranty and Retrofit Activity on Gross Basis (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Movement in Standard and Extended Product Warranty Accrual, Increase (Decrease) [Roll Forward]
Beginning Balance	$ 7,175	$ 6,340
Accruals for warranties	2,479	2,355
Costs incurred	(2,161)	(1,844)
Ending Balance	$ 7,493	$ 6,851

Stock-Based Compensation - Stoc

Stock-Based Compensation - Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	$ 4,410	$ 4,176
Restricted Stock Units (RSUs)
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	4,092	3,960
Employee Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	$ 318	$ 216

Stock-Based Compensation - Rest

Stock-Based Compensation - Restricted Stock Units Granted - Tabular Disclosure (Details) - shares	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Restricted Stock Units (RSUs)
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted stocks granted (in shares)	377,212	745,776
Restricted Stock, Time Based Shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted stocks granted (in shares)	155,461	321,835
Board of Director Units
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted stocks granted (in shares)	181	552
Restricted Stock, Performance Based Shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted stocks granted (in shares)	221,570	423,389

Stock-Based Compensation - Time

Stock-Based Compensation - Time-Based Grants (Details) - Restricted Stock, Time Based Shares	3 Months Ended
	Dec. 31, 2019
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 - St_2

Stock-Based Compensation - Stock Grants (Details)	12 Months Ended
	Sep. 30, 2019
Restricted stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting period (in years)	1 year

Stock-Based Compensation - Perf

Stock-Based Compensation - Performance-Based Grants (Details)	3 Months Ended	12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Sep. 30, 2018
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Performance-based awards granted, percentage (as a percent)	100.00%	100.00%	100.00%
Performance-based awards granted, percentage, maximum threshold met (as a percent)	200.00%	200.00%	200.00%
Performance goal measurement period (in years)	3 years

Stock-Based Compensation - Re_2

Stock-Based Compensation - Restricted Stock Unit Activity - Tabular Disclosure (Details) - Restricted Stock Units (RSUs) - $ / shares	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Shares
Outstanding at beginning of period (in shares)	1,782,726
Restricted stocks granted (in shares)	377,212	745,776
Vested (in shares)	(820,058)
Forfeited (in shares)	(26,264)
Outstanding at end of period (in shares)	1,313,616
Weighted Average Grant-Date Fair Value
Outstanding at beginning of period (in dollars per share)	$ 24.63
Granted (in dollars per share)	47.01	$ 30.49
Vested (in dollars per share)	26.35
Forfeited (in dollars per share)	35.60
Outstanding at end of period (in dollars per share)	$ 35.07

Stock-Based Compensation - Re_3

Stock-Based Compensation - Restricted Stock Unit Activity - Additional Information (Details) - Restricted Stock Units (RSUs) - USD ($) $ / shares in Units, $ in Millions	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Granted (in dollars per share)	$ 47.01	$ 30.49
Fair value of restricted stock awards vested	$ 38.5	$ 27.1
Proceeds from employees to satisfy tax obligation	$ 24	$ 14.2

Stock-Based Compensation - Re_4

Stock-Based Compensation - Restricted Stock Unit Activity - Unrecognized Compensation Cost (Details) - Restricted Stock Units (RSUs) $ in Millions	3 Months Ended
	Dec. 31, 2019USD ($)
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized compensation cost	$ 33.3
Unrecognized compensation cost, estimated weighted average amortization period	2 years

Stock-Based Compensation - Empl

Stock-Based Compensation - Employee Stock Purchase Plan (Details) - shares	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares issued under employee stock purchase plan (in shares)	0	0
Employee Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Purchase price of common stock (as a percent)	85.00%

Earnings per Share - Tabular Di

Earnings per Share - Tabular Disclosure (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Earnings Per Share [Abstract]
Income from continuing operations	$ 13,174	$ 6,266
(Loss) income from discontinued operations, net of tax	(117)	8,149
Net income	$ 13,057	$ 14,415
Weighted average common shares outstanding used in computing basic earnings per share (in shares)	72,972	71,450
Dilutive restricted stock units	673	715
Weighted average common shares outstanding used in computing diluted earnings per share (in shares)	73,645	72,165
Basic net income per share attributable to Brooks Automation, Inc. common stockholders:
Income from continuing operations	$ 0.18	$ 0.09
(Loss) income from discontinued operations, net of tax	0	0.11
Basic net income per share attributable to Brooks Automation, Inc. (in dollars per share)	0.18	0.20
Diluted net income per share:
Income from continuing operations	0.18	0.09
(Loss) income from discontinued operations, net of tax	0	0.11
Diluted net income per share attributable to Brooks Automation, Inc. common stockholders (in dollars per share)	0.18	0.20
Dividend declared per share (in dollars per share)	$ 0.10	$ 0.10

Earnings per Share - Anti-dilut

Earnings per Share - Anti-dilutive Securities (Details) - shares	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
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 (in shares)	158,058	261,384

Revenue from Contracts with C_3

Revenue from Contracts with Customers - Segment Information (Details) - segment	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Segment Reporting Information [Line Items]
Number of reportable segments	2	2
Number of reporting units	5	5
Brooks Semiconductor Solutions Group
Segment Reporting Information [Line Items]
Number of reporting units	3	3
Brooks Life Sciences
Segment Reporting Information [Line Items]
Number of reporting units	2	2

Revenue from Contracts with C_4

Revenue from Contracts with Customers - Disaggregated By Timing (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Disaggregation of Revenue [Line Items]
Total revenue	$ 210,500	$ 179,368
Brooks Semiconductor Solutions Group
Disaggregation of Revenue [Line Items]
Total revenue	118,811	112,707
Brooks Life Sciences
Disaggregation of Revenue [Line Items]
Total revenue	91,689	66,661
Point in time
Disaggregation of Revenue [Line Items]
Total revenue	138,108	135,083
Point in time | Brooks Semiconductor Solutions Group
Disaggregation of Revenue [Line Items]
Total revenue	116,788	111,916
Point in time | Brooks Life Sciences
Disaggregation of Revenue [Line Items]
Total revenue	21,320	23,167
Over time
Disaggregation of Revenue [Line Items]
Total revenue	72,392	44,285
Over time | Brooks Semiconductor Solutions Group
Disaggregation of Revenue [Line Items]
Total revenue	2,023	791
Over time | Brooks Life Sciences
Disaggregation of Revenue [Line Items]
Total revenue	$ 70,369	$ 43,494

Revenue from Contracts with C_5

Revenue from Contracts with Customers - Disaggregated By Geographic Location (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Disaggregation of Revenue [Line Items]
Total revenue	$ 210,500	$ 179,368
North America
Disaggregation of Revenue [Line Items]
Total revenue	80,231	68,897
Asia/Pacific/Other
Disaggregation of Revenue [Line Items]
Total revenue	103,539	79,460
United Kingdom
Disaggregation of Revenue [Line Items]
Total revenue	9,920	12,078
Rest of Europe
Disaggregation of Revenue [Line Items]
Total revenue	$ 16,810	$ 18,933

Revenue from Contracts with C_6

Revenue from Contracts with Customers - Disaggregated By Reporting Unit (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Disaggregation of Revenue [Line Items]
Total revenue	$ 210,500	$ 179,368
Automation Solutions
Disaggregation of Revenue [Line Items]
Total revenue	$ 64,238	73,675
Reporting unit, name of segment	brks:BrooksSemiconductorSolutionsGroupMember
Contamination Control Solutions
Disaggregation of Revenue [Line Items]
Total revenue	$ 44,340	27,956
Reporting unit, name of segment	brks:BrooksSemiconductorSolutionsGroupMember
Global Semiconductor Services
Disaggregation of Revenue [Line Items]
Total revenue	$ 10,233	11,076
Reporting unit, name of segment	brks:BrooksSemiconductorSolutionsGroupMember
Sample Management
Disaggregation of Revenue [Line Items]
Total revenue	$ 51,718	50,303
Reporting unit, name of segment	brks:BrooksLifeSciencesMember
GENEWIZ
Disaggregation of Revenue [Line Items]
Total revenue	$ 39,971	16,358
Reporting unit, name of segment	brks:BrooksLifeSciencesMember
Brooks Semiconductor Solutions Group
Disaggregation of Revenue [Line Items]
Total revenue	$ 118,811	112,707
Brooks Life Sciences
Disaggregation of Revenue [Line Items]
Total revenue	$ 91,689	$ 66,661

Revenue from Contracts with C_7

Revenue from Contracts with Customers - Contract Balances (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Sep. 30, 2019
Accounts Receivable, after Allowance for Credit Loss, Current [Abstract]
Accounts receivable, net	$ 165,176		$ 165,602
Contract with Customer, Asset, Net, Current [Abstract]
Contract assets	$ 17,000		14,000
Capitalized Contract Cost [Abstract]
Sales commission amortization period	60 months
Deferred commissions	$ 700		800
Deferred commission amortization expense	100	$ 200
Contract with Customer, Liability [Abstract]
Current contract liabilities	29,042		29,435
Contract liabilities	29,000		$ 29,400
Revenue recognized	$ 19,100

Revenue from Contracts with C_8

Revenue from Contracts with Customers - Remaining Performance Obligations (Details) $ in Thousands	Dec. 31, 2019USD ($)
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Remaining performance obligations	$ 35,411
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Remaining performance obligations	$ 25,013
Unsatisfied performance obligation, period	12 months
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Remaining performance obligations	$ 10,398
Unsatisfied performance obligation, period

Revenue from Contracts with C_9

Revenue from Contracts with Customers - Costs to Obtain and Fulfill a Contract (Details)	Dec. 31, 2019
Capitalized Contract Cost [Abstract]
Sales commission amortization period	60 months

Segment Information - General I

Segment Information - General Information (Details) - segment	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Segment Reporting, Disclosure of Entity's Reportable Segments [Abstract]
Number of reportable segments	2	2
Brooks Life Sciences
Segment Reporting, Disclosure of Entity's Reportable Segments [Abstract]
Number of operating segments	2	2

Segment Information - Reconcili

Segment Information - Reconciliation of Reportable Segment Operating Income (Loss) to Corresponding Consolidated Amounts (Details) - USD ($) $ in Thousands	3 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Segment Reporting Information [Line Items]
Total revenue	$ 210,500	$ 179,368
Amortization of intangible assets	10,600	7,800
Acquisition accounting impact on inventory contracts acquired		184
Operating income	10,666	5,333
Restructuring charges	576	59
Interest income	699	423
Interest expense	(737)	(5,290)
Other expenses, net	(417)	(30)
Income before income taxes	10,211	436
Brooks Semiconductor Solutions Group
Segment Reporting Information [Line Items]
Total revenue	118,811	112,707
Operating income	15,000	17,263
Brooks Life Sciences
Segment Reporting Information [Line Items]
Total revenue	91,689	66,661
Operating income	5,974	2,660
Segment Reconciling Items
Segment Reporting Information [Line Items]
Operating income	20,974	19,923
Corporate, Non-Segment
Segment Reporting Information [Line Items]
Other unallocated corporate (income) expenses	(852)	6,571
Completed Technology
Segment Reporting Information [Line Items]
Amortization of intangible assets	2,674	2,007
Acquired Intangible Assets
Segment Reporting Information [Line Items]
Amortization of intangible assets	$ 7,910	$ 5,769

Segment Information - Financial

Segment Information - Financial Information for Business Segments - Assets (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Segment Reporting Information [Line Items]
Total assets	$ 1,558,958	$ 1,515,999
Reportable Segments
Segment Reporting Information [Line Items]
Total assets	1,199,834	1,168,795
Reportable Segments | Brooks Semiconductor Solutions Group
Segment Reporting Information [Line Items]
Total assets	267,221	259,641
Reportable Segments | Brooks Life Sciences
Segment Reporting Information [Line Items]
Total assets	$ 932,613	$ 909,154

Segment Information - Reconci_2

Segment Information - Reconciliation of Reportable Segment Assets to Corresponding Consolidated Amounts (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 30, 2019
Segment Reporting Information [Line Items]
Cash, cash equivalents and marketable securities	$ 353,120	$ 342,140
Deferred tax assets	6,004	5,064
Assets	1,558,958	1,515,999
Reportable Segments
Segment Reporting Information [Line Items]
Assets	$ 1,199,834	$ 1,168,795

Significant Customers (Details)

Significant Customers (Details) - Credit Concentration Risk	3 Months Ended
	Dec. 31, 2019
Sales Revenue, Net
Concentration Risk [Line Items]
Concentration risk, percentage (as a percent)	15.00%
Accounts Receivable
Concentration Risk [Line Items]
Concentration risk, percentage (as a percent)	11.00%

Commitments and Contingencies -

Commitments and Contingencies - Letters of Credit (Details) $ in Millions	Dec. 31, 2019USD ($)
Commitments and Contingencies Disclosure [Abstract]
Outstanding letters of credit	$ 1.2

Commitments and Contingencies_2

Commitments and Contingencies - Purchase Commitments (Details) $ in Millions	Dec. 31, 2019USD ($)
Non-cancelable commitments
Other Commitments [Line Items]
Other commitment	$ 130.2
Non-cancellable contracts and purchase orders for inventory
Other Commitments [Line Items]
Other commitment	84.9
Non-cancelable IT-related commitments
Other Commitments [Line Items]
Other commitment	25
Non-cancelable China facility commitments
Other Commitments [Line Items]
Other commitment	18.6
Non-cancelable commitments, other
Other Commitments [Line Items]
Other commitment	$ 1.7

Subsequent Events (Details)

Subsequent Events (Details) - $ / shares	3 Months Ended
	Mar. 31, 2020	Dec. 31, 2019	Dec. 31, 2018
Subsequent Event [Line Items]
Cash dividend declared (in dollars per share)		$ 0.10	$ 0.10
Subsequent Event
Subsequent Event [Line Items]
Cash dividend declared, date	Jan. 24, 2020
Cash dividend declared (in dollars per share)	$ 0.10
Cash dividend declared, payment date	Mar. 27, 2020
Cash dividend declared, record date	Mar. 6, 2020