UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                  SCHEDULE 13D
                        Under the Securities Act of 1934
                                (Amendment No. )

                         BROOKS AUTOMATION, INC. (BRKS)
                                (Name of Issuer)

                                  Common Stock
                         (Title of Class of Securities)

                                    114340102
                                 (CUSIP Number)

                                David Nierenberg

                               The D3 Family Funds

                               19605 NE 8th Street

                                 Camas, WA 98607

                                  360-604-8600

                  (Name, Address and Telephone Number of Person
                Authorized to Receive Notices and Communications)

                                  July 11, 2005
             (Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report
the acquisition that is the subject of this Schedule 13D and is filing this
schedule because of ss.ss.240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the
following box: |_|



--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Family Fund, L.P. (David Nierenberg is president of the General
     Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     USA
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    1,145,856 common shares (2.5%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           1,145,856
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     2,321,156 shares (5.1%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     5.1%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       2


--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Family Retirement Fund, L.P. (David Nierenberg is president of the
     General Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     USA
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    355,400 common shares (0.79%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           355,400
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     2,321,156 shares (5.1%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     5.1%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       3



--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Children's Fund, L.P. (David Nierenberg is president of the General
     Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     USA
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    85,400 common shares (0.19%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           85,400
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     2,321,156 shares (5.1%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     5.1%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       4



--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Offshore Fund, L.P. (David Nierenberg is president of the General
     Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     USA
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    558,900 common shares (1.23%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           558,900
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     2,321,156 shares (5.1%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     5.1%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       5



--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Family Bulldog Fund, L.P. ((David Nierenberg is president of the
     General Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     USA
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    175,600 common shares (0.39%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           175,600
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     2,321,156 shares (5.1%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     5.1%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       6


Item 1.     Security and Issuer.

            Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive ,
            Chelmsford, MA 01824-4111.

Item 2.     Identity and Background.

            The D3 Family Fund, L.P. is a Washington State limited partnership,
            whose principal business is investing in the equities of public
            micro-cap issuers. Located at 19605 N.E. 8th St., Camas, Washington
            98607. No convictions or administrative proceedings as described in
            2 (d) and (e).

Item 3.     Source and Amount of Funds or Other Consideration

            Source of funds is money invested in the partnership by its
            partners.

Item 4.     Purpose of Transaction

            We support the merger of Brooks Automation, Inc. and Helix
            Technology.

Item 5.     Interest in Securities of the Issuer.

            (a,b) The D3 Family Fund, L.P. owns and has sole voting and
            dispositive power over 1,145,856 common shares of BRKS.

            (c) Date            Shares Bought           Price
                ----            -------------           -----
                7/11/05         90,300                  14.66

            (d) N/A

            (e) N/A

Item 6.     Contracts, Arrangements, Understandings or Relationships with
            Respect to Securities of the Issuer.

            N/A

Item 7.     Material to be Filed as Exhibits

            N/A


                                       7



                                    SIGNATURE

      After reasonable inquiry and to the best of my knowledge and belief, each
of the undersigned certifies that the information set forth in the Statement is
true, complete and correct.

July 11, 2005                              /s/ DAVID NIERENBERG
-------------                              -------------------------------------
                                           David Nierenberg
                                           President
                                           Nierenberg Investment Management
                                           Company, Inc., the General Partner of
                                           The D3 Family Retirement Fund, L.P


                                       8


Item 1.     Security and Issuer.

            Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive,
            Chelmsford, MA 01824-4111.

Item 2.     Identity and Background.

            The D3 Family Retirement Fund, L.P. is a Washington State limited
            partnership, whose principal Business is investing in the equities
            of public micro-cap issuers. Located at 19605 N.E. 8th St., Camas,
            Washington 98607. No convictions or administrative proceedings as
            described in 2 (d) and (e).

Item 3.     Source and Amount of Funds or Other Consideration

            Source of funds is money invested in the partnership by its
            partners.

Item 4.     Purpose of Transaction

            We support the merger of Brooks Automation, Inc. and Helix
            Technology.

Item 5.     Interest in Securities of the Issuer.

            (a,b) The D3 Family Retirement Fund, L.P. owns and has sole voting
            and dispositive power over 355,400 common shares of BRKS.

            (c) Date           Shares Bought        Price
                ----           -------------        -----
                7/11/05        21.90                14.66

            (d) N/A

            (e) N/A

Item 6.     Contracts, Arrangements, Understandings or Relationships with
            Respect to Securities of the Issuer.

            N/A

Item 7.     Material to be Filed as Exhibits

            N/A


                                       9


Signature

After reasonable inquiry and to the best of my knowledge and belief, I certify
that the information set forth in this statement is true, complete and correct.


July 11, 2005                         /s/ DAVID NIERENBERG
-------------                         ------------------------------------------
Date                                  David Nierenberg
                                      President
                                      Nierenberg Investment Management Company,
                                      Inc., the General Partner of the D3 Family
                                      Retirement Fund, L.P.


                                       10


Item 1.     Security and Issuer.

            Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive ,
            Chelmsford, MA 01824-4111.

Item 2.     Identity and Background.

            The D3 Children's Fund, L.P. is a Washington State limited
            partnership, whose principal business is investing in the equities
            of public micro-cap Issuers. Located at 19605 N.E. 8th St.,
            Camas,Washington 98607. No convictions or administrative proceedings
            as described in 2 (d) and (e).

Item 3.     Source and Amount of Funds or Other Consideration

            Source of funds is money invested in the partnership by its
            partners.

Item 4.     Purpose of Transaction

            We support the merger of Brooks Automation, Inc. and Helix
            Technology.

Item 5.     Interest in Securities of the Issuer.

            (a,b) The D3 Children's Fund, L.P. owns and has sole voting and
            dispositive power over 175,600 common shares of BRKS.

            (c) Date           Shares Bought        Price
                ----           -------------        -----
                6/15/05        1,000                15.64
                7/11/05        14,000               14.66

            (d) N/A

            (e) N/A

Item 6.     Contracts, Arrangements, Understandings or Relationships with
            Respect to Securities of the Issuer.

            N/A

Item 7.     Material to be Filed as Exhibits

            N/A


                                       11


                                    SIGNATURE

      After reasonable inquiry and to the best of my knowledge and belief, each
of the undersigned certifies that the information set forth in the Statement is
true, complete and correct.


July 11, 2005                              /s/ DAVID NIERENBERG
-------------                              -------------------------------------
                                           David Nierenberg
                                           President
                                           Nierenberg Investment Management
                                           Company, Inc., the General Partner of
                                           The D3 Children's Fund, L.P.


                                       12


Item 1.     Security and Issuer.

            Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive ,
            Chelmsford, MA 01824-4111.

Item 2.     Identity and Background.

            The D3 Offshore Fund, L.P. is a Washington State limited
            partnership, whose principal business is investing in the equities
            of public micro-cap issuers. Located at 19605 N.E. 8th St., Camas,
            Washington 98607. No convictions or administrative proceedings as
            described in 2 (d) and (e).

Item 3.     Source and Amount of Funds or Other Consideration

            Source of funds is money invested in the partnership by its
            partners.

Item 4.     Purpose of Transaction

            We support the merger of Brooks Automation, Inc. and Helix
            Technology.

Item 5.     Interest in Securities of the Issuer.

            (a,b) The D3 Offshore Fund, L.P. owns and has sole voting and
            dispositive power over 558,900 common shares of BRKS.

            (c) Date             Shares Bought         Price
                ----             -------------         -----
                5/18/05           40,000               14.29
                5/23/05           30,000               14.42
                5/24/05            5,700               14.38
                5/25/05            7,000               14.28
                6/1/05            10,000               15.38
                6/2/05            10,000               15.62
                6/3/05            25,000               15.29
                6/6/05            43,500               15.05
                6/7/05            20,000               15.22
                6/8/05            15,000               15.29
                6/9/05             5,000               15.36
                6/13/05           10,000               15.73
                6/14/05           22,000               15.74
                6/15/05            4,400               15.62
                6/24/05           10,000               15.33
                7/11/05          102,300               14.66

            (d) N/A

            (e) N/A


                                       13


Item 6.     Contracts, Arrangements, Understandings or Relationships with
            Respect to Securities of the Issuer.

            N/A

Item 7.     Material to be Filed as Exhibits

            N/A

                                    SIGNATURE

      After reasonable inquiry and to the best of my knowledge and belief, each
of the undersigned certifies that the information set forth in the Statement is
true, complete and correct.

July 11, 2005                              /s/ DAVID NIERENBERG
-------------                              -------------------------------------
                                           David Nierenberg
                                           President
                                           Nierenberg Investment Management
                                           Company, Inc., the General Partner of
                                           the D3 Offshore Fund, L.P.


                                       14


Item 1.     Security and Issuer.

            Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive ,
            Chelmsford, MA 01824-4111.

Item 2.     Identity and Background.

            The D3 Family Bulldog Fund, L.P. is a Washington State limited
            partnership, whose principal business is investing in the equities
            of public micro-cap issuers. Located at 19605 N.E. 8th St.,
            Camas,Washington 98607. No convictions or administrative proceedings
            as described in 2 (d) and (e).

Item 3.     Source and Amount of Funds or Other Consideration

            Source of funds is money invested in the partnership by its
            partners.

Item 4.     Purpose of Transaction

            We support the merger of Brooks Automation, Inc. and Helix
            Technology.

Item 5.     Interest in Securities of the Issuer.

            (a,b) The D3 Family Bulldog Fund, L.P. owns and has sole voting and
            dispositive power over 175,600 common shares of BRKS.

            (c) Date          Shares Bought       Price
                ----          -------------       -----
                6/14/05       18,000              15.74
                7/11/05       20,800              14.66

            (d) N/A

            (e) N/A

Item 6.     Contracts, Arrangements, Understandings or Relationships with
            Respect to Securities of the Issuer.

            N/A

Item 7.     Material to be Filed as Exhibits

            N/A


                                       15


                                    SIGNATURE

      After reasonable inquiry and to the best of my knowledge and belief, each
of the undersigned certifies that the information set forth in the Statement is
true, complete and correct.


July 11, 2005                              /s/ DAVID NIERENBERG
-------------                              -------------------------------------
                                           David Nierenberg
                                           President
                                           Nierenberg Investment Management
                                           Company, Inc., the General Partner of
                                           The D3 Family Bulldog Fund, L.P.


                                       16