Joint Ventures	3 Months Ended
Dec. 31, 2014
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 income 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 the level of equity investment at risk was not sufficient for BioCision to finance its activities without additional financial support and as a result, represented a variable interest entity. However, the Company does not have the power to direct the activities that most significantly impact BioCision’s economic performance, and therefore does not qualify as the primary beneficiary. For the three months ended December 31, 2014, the Company recorded a loss associated with BioCision of $0.2 million. At December 31, 2014, the carrying value of the investment in BioCision in the Company’s Consolidated Balance Sheet was $3.5 million. On December 22, 2014 the Company purchased BioCision five-year convertible debt securities with a warrant agreement to purchase preferred units of BioCision for a total of $2.5 million. The convertible debt securities were accounted for under the fair value method, and were recorded at fair value. The warrant was accounted for as a derivative and was recorded at fair value. The Company will subsequently measure the fair value of the BioCision convertible debt securities and warrant each reporting period, and the respective gain or loss will be recognized in earnings. Interest accrues on the convertible debt securities at a rate of 9% per annum, and is due with the principal upon maturity. Under this agreement with BioCision, the Company may provide additional financing up to $2.5 million subject to its satisfaction that certain financial criteria are met. As a result of the funding, the Company reconsidered whether BioCision represents a variable interest entity. The Company concluded that the level of equity investment at risk is still insufficient for BioCision to finance its activities without additional support, thus will remain a variable interest entity. However, the Company still does not have the power to direct the activities that most significantly impact BioCision’s economic performance, and therefore still does not qualify as the primary beneficiary. As such, the Company concluded that BioCision will not be consolidated in its financial statements. For further information regarding the convertible debt securities and warrant, see Note 17, “Fair Value Measurements”. 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 December 31, 2014 and 2013, the Company recorded income associated with UCI of $0.3 million and $0.8 million, respectively. At December 31, 2014, the carrying value of UCI in the Company’s Consolidated Balance Sheet was $21.9 million. For each of the three months ended December 31, 2014 and 2013, management fee payments received by the Company from UCI were $0.2 million. For each of the three months ended December 31, 2014 and 2013, the Company incurred charges from UCI for products or services of $0.1 million. At December 31, 2014 and September 30, 2014, the Company owed UCI $61,000 and $79,000, respectively, in connection with accounts payable for unpaid products and services. Yaskawa Brooks Automation, Inc. The Company participates in a 50% joint venture with Yaskawa Electric Corporation (“Yaskawa”) called Yaskawa Brooks Automation, Inc. (“YBA”) to exclusively market and sell 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. Related to this planned dissolution, YBA assessed the recoverability of assets held in the event of dissolution and communicated an impairment in the carrying value of its assets to the equity partners. The Company recognized the fair value adjustment through the YBA earnings in the amount of $0.7 million. Including these impairment charges, the Company recorded $0.7 million of losses associated with YBA for the three months ended December 31, 2014, compared to losses of $18,000, for the three months ended December 31, 2013. At December 31, 2014, the carrying value of YBA in the Company’s Consolidated Balance Sheet was $1.7 million. For the three months ended December 31, 2014 and 2013, revenue earned by the Company from YBA was $1.1 million and $0.7 million, respectively. For the three months ended December 31, 2014 and 2013, the Company incurred charges from YBA for products or services of $0.4 million and $0.1 million, respectively. The amount due from YBA included in accounts receivable at December 31, 2014 and September 30, 2014 was $1.5 million and $2.1 million, respectively. At each of December 31, 2014 and September 30, 2014, the Company owed YBA $0.1 million in connection with accounts payable for unpaid products and services. The Company expects the YBA dissolution to be completed within the second quarter of fiscal year 2015.

Equity Method Investments

The Company accounts for certain of its investments using the equity method. Under this method of accounting, the Company records in income 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 the level of equity investment at risk was not sufficient for BioCision to finance its activities without additional financial support and as a result, represented a variable interest entity. However, the Company does not have the power to direct the activities that most significantly impact BioCision’s economic performance, and therefore does not qualify as the primary beneficiary.

For the three months ended December 31, 2014, the Company recorded a loss associated with BioCision of $0.2 million. At December 31, 2014, the carrying value of the investment in BioCision in the Company’s Consolidated Balance Sheet was $3.5 million.

On December 22, 2014 the Company purchased BioCision five-year convertible debt securities with a warrant agreement to purchase preferred units of BioCision for a total of $2.5 million. The convertible debt securities were accounted for under the fair value method, and were recorded at fair value. The warrant was accounted for as a derivative and was recorded at fair value. The Company will subsequently measure the fair value of the BioCision convertible debt securities and warrant each reporting period, and the respective gain or loss will be recognized in earnings. Interest accrues on the convertible debt securities at a rate of 9% per annum, and is due with the principal upon maturity. Under this agreement with BioCision, the Company may provide additional financing up to $2.5 million subject to its satisfaction that certain financial criteria are met. As a result of the funding, the Company reconsidered whether BioCision represents a variable interest entity. The Company concluded that the level of equity investment at risk is still insufficient for BioCision to finance its activities without additional support, thus will remain a variable interest entity. However, the Company still does not have the power to direct the activities that most significantly impact BioCision’s economic performance, and therefore still does not qualify as the primary beneficiary. As such, the Company concluded that BioCision will not be consolidated in its financial statements. For further information regarding the convertible debt securities and warrant, see Note 17, “Fair Value Measurements”.

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 December 31, 2014 and 2013, the Company recorded income associated with UCI of $0.3 million and $0.8 million, respectively. At December 31, 2014, the carrying value of UCI in the Company’s Consolidated Balance Sheet was $21.9 million. For each of the three months ended December 31, 2014 and 2013, management fee payments received by the Company from UCI were $0.2 million. For each of the three months ended December 31, 2014 and 2013, the Company incurred charges from UCI for products or services of $0.1 million. At December 31, 2014 and September 30, 2014, the Company owed UCI $61,000 and $79,000, respectively, in connection with accounts payable for unpaid products and services.

Yaskawa Brooks Automation, Inc.

The Company participates in a 50% joint venture with Yaskawa Electric Corporation (“Yaskawa”) called Yaskawa Brooks Automation, Inc. (“YBA”) to exclusively market and sell 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. Related to this planned dissolution, YBA assessed the recoverability of assets held in the event of dissolution and communicated an impairment in the carrying value of its assets to the equity partners. The Company recognized the fair value adjustment through the YBA earnings in the amount of $0.7 million. Including these impairment charges, the Company recorded $0.7 million of losses associated with YBA for the three months ended December 31, 2014, compared to losses of $18,000, for the three months ended December 31, 2013. At December 31, 2014, the carrying value of YBA in the Company’s Consolidated Balance Sheet was $1.7 million. For the three months ended December 31, 2014 and 2013, revenue earned by the Company from YBA was $1.1 million and $0.7 million, respectively. For the three months ended December 31, 2014 and 2013, the Company incurred charges from YBA for products or services of $0.4 million and $0.1 million, respectively.

The amount due from YBA included in accounts receivable at December 31, 2014 and September 30, 2014 was $1.5 million and $2.1 million, respectively. At each of December 31, 2014 and September 30, 2014, the Company owed YBA $0.1 million in connection with accounts payable for unpaid products and services. The Company expects the YBA dissolution to be completed within the second quarter of fiscal year 2015.