Joint Ventures	6 Months Ended
Mar. 31, 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 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. As such, the Company concluded that BioCision will not be consolidated in the Company's financial statements. For the three and six months ended March 31, 2015, the Company recorded a loss associated with BioCision of $0.3 million and $0.5 million. At March 31, 2015, the carrying value of the investment in BioCision in the Company’s Consolidated Balance Sheet was $3.2 million. 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 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. The Company will re-measure the fair value of the BioCision convertible debt securities and warrants 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. As a result of the funding, the Company reconsidered whether BioCision represents a variable interest entity, which is subject to consolidation. 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 the Company's financial statements. As of March 31, 2015, the fair value of the convertible debt securities and warrants was $5.2 million and $70,000, respectively. For further information regarding the convertible debt securities and warrants, 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 March 31, 2015 and 2014, the Company recorded income associated with UCI of $16,000 and $0.5 million, respectively. For the six months ended March 31, 2015 and 2014, the Company recorded income associated with UCI of $0.4 million and $1.2 million, respectively. At March 31, 2015, the carrying value of UCI in the Company’s Consolidated Balance Sheet was $21.9 million. For each of the three months ended March 31, 2015 and 2014, management fee payments received by the Company from UCI were $0.2 million. For each of the six months ended March 31, 2015 and 2014, management fee payments received by the Company from UCI were $0.3 million. For the three months ended March 31, 2015 and 2014, the Company incurred charges from UCI for products or services of $46,000 and $37,000, respectively. For each of the six months ended March 31, 2015 and 2014, the Company incurred charges from UCI for products or services of $0.1 million. At March 31, 2015 and September 30, 2014, the Company owed UCI $46,000 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. 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 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 $0.2 million of income associated with YBA for the three months ended March 31, 2015, compared to $35,000, for the three months ended March 31, 2014. For the six months ended March 31, 2015 and 2014, the Company recorded income (expense) associated with YBA of $(0.5) million and $17,000, respectively. At March 31, 2015, the carrying value of YBA in the Company’s Consolidated Balance Sheet was $1.9 million. For the three months ended March 31, 2015 and 2014, revenue earned by the Company from YBA was $1.0 million and $2.1 million, respectively. For the six months ended March 31, 2015 and 2014, revenue earned by the Company from YBA was $2.1 million and $2.8 million, respectively. For the three months ended March 31, 2015 and 2014, the Company incurred charges from YBA for products or services of $0.5 million and $0.2 million, respectively. For the six months ended March 31, 2015 and 2014, the Company incurred charges from YBA for products or services of $0.9 million and $0.3 million, respectively. The amount due from YBA included in accounts receivable at March 31, 2015 and September 30, 2014 was $0.0 million and $2.1 million, respectively. At March 31, 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. The Company expects the YBA dissolution to be completed within the fourth 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. As such, the Company concluded that BioCision will not be consolidated in the Company's financial statements.

For the three and six months ended March 31, 2015, the Company recorded a loss associated with BioCision of $0.3 million and $0.5 million. At March 31, 2015, the carrying value of the investment in BioCision in the Company’s Consolidated Balance Sheet was $3.2 million.

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 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. The Company will re-measure the fair value of the BioCision convertible debt securities and warrants 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. As a result of the funding, the Company reconsidered whether BioCision represents a variable interest entity, which is subject to consolidation. 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 the Company's financial statements. As of March 31, 2015, the fair value of the convertible debt securities and warrants was $5.2 million and $70,000, respectively. For further information regarding the convertible debt securities and warrants, 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 March 31, 2015 and 2014, the Company recorded income associated with UCI of $16,000 and $0.5 million, respectively. For the six months ended March 31, 2015 and 2014, the Company recorded income associated with UCI of $0.4 million and $1.2 million, respectively. At March 31, 2015, the carrying value of UCI in the Company’s Consolidated Balance Sheet was $21.9 million. For each of the three months ended March 31, 2015 and 2014, management fee payments received by the Company from UCI were $0.2 million. For each of the six months ended March 31, 2015 and 2014, management fee payments received by the Company from UCI were $0.3 million. For the three months ended March 31, 2015 and 2014, the Company incurred charges from UCI for products or services of $46,000 and $37,000, respectively. For each of the six months ended March 31, 2015 and 2014, the Company incurred charges from UCI for products or services of $0.1 million. At March 31, 2015 and September 30, 2014, the Company owed UCI $46,000 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. 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 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 $0.2 million of income associated with YBA for the three months ended March 31, 2015, compared to $35,000, for the three months ended March 31, 2014. For the six months ended March 31, 2015 and 2014, the Company recorded income (expense) associated with YBA of $(0.5) million and $17,000, respectively. At March 31, 2015, the carrying value of YBA in the Company’s Consolidated Balance Sheet was $1.9 million. For the three months ended March 31, 2015 and 2014, revenue earned by the Company from YBA was $1.0 million and $2.1 million, respectively. For the six months ended March 31, 2015 and 2014, revenue earned by the Company from YBA was $2.1 million and $2.8 million, respectively. For the three months ended March 31, 2015 and 2014, the Company incurred charges from YBA for products or services of $0.5 million and $0.2 million, respectively. For the six months ended March 31, 2015 and 2014, the Company incurred charges from YBA for products or services of $0.9 million and $0.3 million, respectively.

The amount due from YBA included in accounts receivable at March 31, 2015 and September 30, 2014 was $0.0 million and $2.1 million, respectively. At March 31, 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. The Company expects the YBA dissolution to be completed within the fourth quarter of fiscal year 2015.