Equity Method Investments	9 Months Ended
Jun. 30, 2015
Equity Method Investments and Joint Ventures [Abstract]
Equity Method Investments	Equity Method Investments The Company accounts for certain of its investments using the equity method. Under this method of accounting, the Company records in its unaudited Consolidated Statements of Operations its proportionate share of the earnings (losses) of the investee with a corresponding increase (decrease) in the carrying value of the investment. BioCision, LLC In March 2014, the Company acquired a 22% equity interest in BioCision, LLC (“BioCision”), a privately-held company based in Larkspur, California, for $4.0 million. BioCision develops, manufactures and markets cell cryopreservation products used to improve and standardize the tools and methods for biomaterial sample handling. The Company determined that BioCision represented a variable interest entity since the level of equity investment at risk was not sufficient to finance its activities without additional financial support. However, the Company does not qualify as a primary beneficiary since it does not have the power to direct BioCision's product research, development, selling and marketing activities that have the most significant impact on its economic performance. As such, the Company concluded that BioCision will not be consolidated in the Company's financial statements. During the three months ended June 30, 2015, the Company's equity investment was diluted from 22% to 20% as a result of stock options granted to new employees. For the three and nine months ended June 30, 2015, the Company recorded a loss associated with BioCision of $0.2 million and $0.7 million, respectively. For each of the three and nine months ended June 30, 2014, the Company recorded a loss associated with BioCision of $0.1 million. At June 30, 2015 and September 30, 2014, the carrying value of the investment in BioCision in the Company’s unaudited Consolidated Balance Sheets was $3.0 million and $3.7 million, respectively. The Company purchased BioCision five-year convertible debt securities with a warrant agreement to purchase preferred units of BioCision for $2.5 million on December 22, 2014 and February 2, 2015, resulting in a total purchase price of $5.0 million. The convertible debt securities were accounted for under the fair value method, and were recorded at fair value. The warrants were accounted for as a derivative and were recorded at fair value. As of June 30, 2015, the fair value of the convertible debt securities and warrants was $5.4 million and $0.1 million, respectively. For further information regarding the convertible debt securities and warrants, refer to Note 17, “Fair Value Measurements”. The Company re-measures the fair value of the BioCision convertible debt securities and warrants each reporting period and recognizes the respective gain or loss in earnings. For the three and nine months ended June 30, 2015, the Company recognized $0.2 million and $0.5 million, respectively, of such remeasurement gains. Interest accrues on the convertible debt securities at a rate of 9% per annum, and is due with the principal upon maturity. As a result of the funding, the Company reconsidered whether BioCision represents a variable interest entity subject to consolidation. The Company concluded that BioCision remains a variable interest entity since the level of equity investment at risk is not sufficient to finance its activities without additional financial support. However, the Company does not qualify as a primary beneficiary since it does not have the power to direct BioCision's product research, development, selling and marketing activities that have the most significant impact on its economic performance. As such, the Company concluded that BioCision will not be consolidated in the Company's financial statements. ULVAC Cryogenics, Inc. The Company participates in a 50% joint venture, ULVAC Cryogenics, Inc. (“UCI”), with ULVAC Corporation of Chigasaki, Japan. UCI manufactures and sells cryogenic vacuum pumps, principally to ULVAC Corporation. For the three months ended June 30, 2015 and 2014, the Company recorded income associated with UCI of $0.6 million and $0.2 million, respectively. For the nine months ended June 30, 2015 and 2014, the Company recorded income associated with UCI of $0.9 million and $1.4 million, respectively. At June 30, 2015 and September 30, 2014, the carrying value of UCI in the Company’s Consolidated Balance Sheets was $22.0 million and $22.6 million, respectively. For each of the three months ended June 30, 2015 and 2014, management fee payments received by the Company from UCI were $0.2 million. For the nine months ended June 30, 2015 and 2014, management fee payments received by the Company from UCI were $0.4 million and $0.5 million, respectively. For the three months ended June 30, 2015 and 2014, the Company incurred charges for UCI's products or services of $0.1 million and $0.2 million, respectively. For the nine months ended June 30, 2015 and 2014, the Company incurred charges for UCI's products or services of $0.2 million and $0.3 million, respectively. At both June 30, 2015 and September 30, 2014, the Company owed UCI $0.1 million in connection with accounts payable for unpaid products and services. Yaskawa Brooks Automation, Inc. The Company participated in a 50% joint venture with Yaskawa Electric Corporation (“Yaskawa”) called Yaskawa Brooks Automation, Inc. (“YBA”) which has come to closure in March 2015 and will be liquidated by the end of fiscal 2015. YBA exclusively marketed and sold Yaskawa’s semiconductor robotics products and Brooks’ automation hardware products to semiconductor customers in Japan. During the first quarter of fiscal year 2015, the Company and Yaskawa agreed in principle to dissolve the joint venture. On January 22, 2015, the Company entered into an agreement with YBA to facilitate the acquisition of certain assets and certain liabilities by the Company’s subsidiary in Japan. In accordance with the agreement, on March 20, 2015, the Company’s subsidiary in Japan received the net assets of YBA for cash consideration of approximately $1.8 million. The Company recorded the assets received and liabilities assumed from YBA at their fair value as of the acquisition date. As a result of the transaction, the Company recorded $0.2 million of goodwill, representing the excess of the consideration transferred over the fair value of the net assets acquired. The cash received by YBA will be used to pay off remaining liabilities and the liquidation costs of YBA. Any remaining cash after making these payments will be distributed to the equity partners in the form of a dividend, which is expected to occur by the end of fiscal year 2015. The Company recorded a loss of $69,000 associated with YBA for the three months ended June 30, 2015, compared to a loss of $70,000 for the corresponding period of the prior fiscal year. For the nine months ended June 30, 2015 and 2014, the Company recorded a loss associated with YBA of $0.5 million and $0.1 million, respectively. At June 30, 2015 and September 30, 2014, the carrying value of YBA in the Company’s Consolidated Balance Sheets was $1.7 million and $2.6 million, respectively. For the three months ended June 30, 2015 and 2014, revenue earned by the Company from YBA was $0.0 million and $2.7 million, respectively. For the nine months ended June 30, 2015 and 2014, revenue earned by the Company from YBA was $2.1 million and $5.6 million, respectively. For the three months ended June 30, 2015 and 2014, the Company incurred charges from YBA for products or services of $47,000 and $0.1 million, respectively. For the nine months ended June 30, 2015 and 2014, the Company incurred charges from YBA for products or services of $1.0 million and $0.4 million, respectively. The amount due from YBA included in accounts receivable at June 30, 2015 and September 30, 2014 was $0.0 million and $2.1 million, respectively. At June 30, 2015 and September 30, 2014, the Company owed YBA $0.0 million and $0.1 million, respectively, in connection with accounts payable for unpaid products and services.

Equity Method Investments

The Company accounts for certain of its investments using the equity method. Under this method of accounting, the Company records in its unaudited Consolidated Statements of Operations its proportionate share of the earnings (losses) of the investee with a corresponding increase (decrease) in the carrying value of the investment.

BioCision, LLC

In March 2014, the Company acquired a 22% equity interest in BioCision, LLC (“BioCision”), a privately-held company based in Larkspur, California, for $4.0 million. BioCision develops, manufactures and markets cell cryopreservation products used to improve and standardize the tools and methods for biomaterial sample handling. The Company determined that BioCision represented a variable interest entity since the level of equity investment at risk was not sufficient to finance its activities without additional financial support. However, the Company does not qualify as a primary beneficiary since it does not have the power to direct BioCision's product research, development, selling and marketing activities that have the most significant impact on its economic performance. As such, the Company concluded that BioCision will not be consolidated in the Company's financial statements. During the three months ended June 30, 2015, the Company's equity investment was diluted from 22% to 20% as a result of stock options granted to new employees.

For the three and nine months ended June 30, 2015, the Company recorded a loss associated with BioCision of $0.2 million and $0.7 million, respectively. For each of the three and nine months ended June 30, 2014, the Company recorded a loss associated with BioCision of $0.1 million. At June 30, 2015 and September 30, 2014, the carrying value of the investment in BioCision in the Company’s unaudited Consolidated Balance Sheets was $3.0 million and $3.7 million, respectively.

The Company purchased BioCision five-year convertible debt securities with a warrant agreement to purchase preferred units of BioCision for $2.5 million on December 22, 2014 and February 2, 2015, resulting in a total purchase price of $5.0 million. The convertible debt securities were accounted for under the fair value method, and were recorded at fair value. The warrants were accounted for as a derivative and were recorded at fair value. As of June 30, 2015, the fair value of the convertible debt securities and warrants was $5.4 million and $0.1 million, respectively. For further information regarding the convertible debt securities and warrants, refer to Note 17, “Fair Value Measurements”. The Company re-measures the fair value of the BioCision convertible debt securities and warrants each reporting period and recognizes the respective gain or loss in earnings. For the three and nine months ended June 30, 2015, the Company recognized $0.2 million and $0.5 million, respectively, of such remeasurement gains. Interest accrues on the convertible debt securities at a rate of 9% per annum, and is due with the principal upon maturity.

As a result of the funding, the Company reconsidered whether BioCision represents a variable interest entity subject to consolidation. The Company concluded that BioCision remains a variable interest entity since the level of equity investment at risk is not sufficient to finance its activities without additional financial support. However, the Company does not qualify as a primary beneficiary since it does not have the power to direct BioCision's product research, development, selling and marketing activities that have the most significant impact on its economic performance. As such, the Company concluded that BioCision will not be consolidated in the Company's financial statements.

ULVAC Cryogenics, Inc.

The Company participates in a 50% joint venture, ULVAC Cryogenics, Inc. (“UCI”), with ULVAC Corporation of Chigasaki, Japan. UCI manufactures and sells cryogenic vacuum pumps, principally to ULVAC Corporation.

For the three months ended June 30, 2015 and 2014, the Company recorded income associated with UCI of $0.6 million and $0.2 million, respectively. For the nine months ended June 30, 2015 and 2014, the Company recorded income associated with UCI of $0.9 million and $1.4 million, respectively. At June 30, 2015 and September 30, 2014, the carrying value of UCI in the Company’s Consolidated Balance Sheets was $22.0 million and $22.6 million, respectively. For each of the three months ended June 30, 2015 and 2014, management fee payments received by the Company from UCI were $0.2 million. For the nine months ended June 30, 2015 and 2014, management fee payments received by the Company from UCI were $0.4 million and $0.5 million, respectively. For the three months ended June 30, 2015 and 2014, the Company incurred charges for UCI's products or services of $0.1 million and $0.2 million, respectively. For the nine months ended June 30, 2015 and 2014, the Company incurred charges for UCI's products or services of $0.2 million and $0.3 million, respectively. At both June 30, 2015 and September 30, 2014, the Company owed UCI $0.1 million in connection with accounts payable for unpaid products and services.

Yaskawa Brooks Automation, Inc.

The Company participated in a 50% joint venture with Yaskawa Electric Corporation (“Yaskawa”) called Yaskawa Brooks Automation, Inc. (“YBA”) which has come to closure in March 2015 and will be liquidated by the end of fiscal 2015. YBA exclusively marketed and sold Yaskawa’s semiconductor robotics products and Brooks’ automation hardware products to semiconductor customers in Japan. During the first quarter of fiscal year 2015, the Company and Yaskawa agreed in principle to dissolve the joint venture. On January 22, 2015, the Company entered into an agreement with YBA to facilitate the acquisition of certain assets and certain liabilities by the Company’s subsidiary in Japan. In accordance with the agreement, on March 20, 2015, the Company’s subsidiary in Japan received the net assets of YBA for cash consideration of approximately $1.8 million. The Company recorded the assets received and liabilities assumed from YBA at their fair value as of the acquisition date. As a result of the transaction, the Company recorded $0.2 million of goodwill, representing the excess of the consideration transferred over the fair value of the net assets acquired. The cash received by YBA will be used to pay off remaining liabilities and the liquidation costs of YBA. Any remaining cash after making these payments will be distributed to the equity partners in the form of a dividend, which is expected to occur by the end of fiscal year 2015.

The Company recorded a loss of $69,000 associated with YBA for the three months ended June 30, 2015, compared to a loss of $70,000 for the corresponding period of the prior fiscal year. For the nine months ended June 30, 2015 and 2014, the Company recorded a loss associated with YBA of $0.5 million and $0.1 million, respectively. At June 30, 2015 and September 30, 2014, the carrying value of YBA in the Company’s Consolidated Balance Sheets was $1.7 million and $2.6 million, respectively. For the three months ended June 30, 2015 and 2014, revenue earned by the Company from YBA was $0.0 million and $2.7 million, respectively. For the nine months ended June 30, 2015 and 2014, revenue earned by the Company from YBA was $2.1 million and $5.6 million, respectively. For the three months ended June 30, 2015 and 2014, the Company incurred charges from YBA for products or services of $47,000 and $0.1 million, respectively. For the nine months ended June 30, 2015 and 2014, the Company incurred charges from YBA for products or services of $1.0 million and $0.4 million, respectively.

The amount due from YBA included in accounts receivable at June 30, 2015 and September 30, 2014 was $0.0 million and $2.1 million, respectively. At June 30, 2015 and September 30, 2014, the Company owed YBA $0.0 million and $0.1 million, respectively, in connection with accounts payable for unpaid products and services.