COMPENSATION AND INDEMNIFICATION AGREEMENT

Exhibit 10.1

COMPENSATION AND INDEMNIFICATION AGREEMENT

This COMPENSATION AND INDEMNIFICATION AGREEMENT is made as of this 2nd day of December, 2007 (this “Agreement”) by and among Bruker BioSciences Corporation, a Delaware corporation (the “Corporation”), and each of William A. Linton, Collin D’Silva and Richard D. Kniss (each, a “Director” and collectively, the “Directors”).

WHEREAS, the Corporation’s Board of Directors (the “Board of Directors”), at a meeting held on August 1, 2007, appointed the Directors as members of a Special Committee of the Board of Directors of the Corporation (the “Special Committee”) to consider, evaluate, investigate, negotiate the terms and conditions of, recommend to the entire Board of Directors if it considers it in the best interests of the stockholders of the Corporation unaffiliated with the Laukien family to do so, and reject it if it considers it in the best interests of the stockholders to do so, an acquisition by the Corporation of Bruker BioSpin Inc., a Delaware corporation, Bruker BioSpin Invest AG, a Swiss corporation, Bruker Physik GmbH, a German limited liability company and Techneon AG, a Swiss corporation (the “Transaction”), and to make such reports to the entire Board of Directors at such times and in such manner as the Special Committee considers appropriate with respect to such possible transaction;

WHEREAS, in order to induce the Directors to serve on the Special Committee and to accept the additional duties, responsibilities and burdens of such service, the Corporation wishes to provide them with the compensation and indemnification arrangements set forth herein; and

WHEREAS, the Directors are willing to serve and continue to serve on the Special Committee on the terms set forth herein.

NOW, THEREFORE, in consideration of the foregoing, the parties hereto do hereby agree as follows:

Section 1.               Service on the Special Committee. Each Director hereby agrees to serve as a member of the Special Committee on the terms provided for herein so long as such appointment by the Board shall remain in effect. Each Director may, however, resign from such position at any time and for any reason. The Corporation’s obligation to indemnify each such Director as set forth in this Agreement shall continue in full force and effect notwithstanding any such termination of appointment or resignation.

Section 2.               Compensation and Expense Reimbursement. In return for his services as a member of the Special Committee, each Director shall be entitled to receive from the Corporation compensation in the amount of $80,000 ($100,000 in the case of Mr. Linton, Chairman of the Special Committee). In addition, each Director shall be reimbursed by the Corporation for his reasonable out-of-pocket travel and other expenses incurred in connection with his service on the Special Committee.

Section 3.            General Indemnification.

(a)           Article 10 of the Corporation’s By-Laws currently provides members of the Board of Directors with the following general right to indemnification:

The Corporation shall indemnify any person who was or is a party or is threatened to be made a party to any threatened, pending or completed action, suit or proceeding, whether civil, criminal, administrative or investigative (other than an action by or in the right of the Corporation) by reason of the fact that he is or was a Director, officer, employee or agent of the Corporation, or is or was serving at the request of the Corporation as a director, officer, employee or agent of another corporation, partnership, joint venture, trust or other enterprise, against expenses (including attorney’s fees), judgments, fines and amounts paid in settlement actually and reasonably incurred by him in connection with such action, suit or proceeding if he acted in good faith and in a manner he reasonably believed to be in or not opposed to the best interests of the Corporation, and, with respect to any criminal action or proceeding, had no reasonable cause to believe his conduct was unlawful. The termination of any action, suit or proceeding by judgment, order, settlement, conviction, or upon plea of nolo contendere or its equivalent, shall not, of itself, create a presumption that the person did not act in good faith and in a manner which he reasonably believed to be in or not opposed to the best interests of the Corporation, and, with respect to any criminal action or proceeding, had reasonable cause to believe that his conduct was unlawful.

(b)           The Corporation hereby confirms that the rights conferred upon the members of its Board of Directors pursuant to Article 10 of its By-Laws are fully applicable to the Directors in their capacity as members of the Special Committee. Any subsequent amendment to such By-Laws which is intended to diminish, or has the effect of diminishing, the rights of directors to indemnification shall not be applicable to the Directors for their service on the Special Committee, whether such service was rendered before or after the adoption of such amendment.

(c)           The Corporation hereby agrees to indemnify and hold harmless (including, without limitation, by advancement of expenses) each Director with respect to his service on, and any matter or transaction considered by, the Special Committee to the fullest extent authorized or permitted by law.

(d)           In addition to (but not in duplication of) the general right to indemnification set forth in Article 10 of its By-Laws and this Section 3, and any other rights to indemnification to which the Directors are entitled under applicable law or otherwise, the Corporation hereby agrees to provide each Director with respect to his service on, and any matter or transaction considered by, the Special Committee the specific rights to indemnification set forth in Section 4 through Section 11 of this Agreement.

2

Section 4.            Indemnification for a Proceeding, etc.

(a)           Proceedings Other Than Proceedings by or in the Right of the Corporation. Each Director shall be entitled to the rights of indemnification provided in this Section 4(a) if, by reason of his status as a person who is or was a member of the Special Committee or was otherwise a director of the Company (“Corporate Status”), he is, or is threatened to be made, a party to or participant in any Proceeding (as hereinafter defined) other than a Proceeding by or in the right of the Corporation. Pursuant to this Section 4(a), each Director shall be indemnified against all expenses, judgments, penalties, fines and amounts paid in settlement actually and reasonably incurred by him or on his behalf in connection with such Proceeding or any claim, issue or matter therein, if he acted in good faith and in a manner he reasonably believed to be in or not opposed to the best interests of the Corporation and, with respect to any criminal Proceeding, had no reasonable cause to believe his conduct was unlawful. For purposes of this Agreement, “fines” shall include, without limitation, excise taxes assessed against the Director with respect to an employee benefit plan.

(b)           Proceedings by or in the Right of the Corporation. Each Director shall be entitled to the rights of indemnification provided in this Section 4(b) if, by reason of his Corporate Status, he is, or is threatened to be made, a party to or participant in any Proceeding brought by or in the right of the Corporation to procure a judgment in its favor. Pursuant to this Section 4(b), each Director shall be indemnified against all expenses actually and reasonably incurred by him or on his behalf in connection with such Proceeding if he acted in good faith and in a manner he reasonably believed to be in or not opposed to the best interests of the Corporation; provided, however, that, if applicable law so provides, no indemnification against such expenses shall be made in respect of any claim, issue or matter in such Proceeding as to which such Director shall have been finally adjudged to be liable to the Corporation unless and to the extent that the Court of Chancery of the State of Delaware shall determine that such indemnification may be made.

(c)           Indemnification for Expenses of a Party Who is Wholly or Partly Successful. Notwithstanding any other provision of this Agreement, to the extent that a Director is, by reason of his Corporate Status, a party to and is successful, on the merits or otherwise, in any Proceeding, he shall be indemnified to the maximum extent permitted by law against all expenses actually and reasonably incurred by him or on his behalf in connection therewith. If a Director is not wholly successful in such Proceeding, but is successful, on the merits or otherwise, as to one or more, but less than all claims, issues or matters in such Proceeding, the Corporation shall indemnify such Director against all expenses actually and reasonably incurred by him or on his behalf in connection with each successfully resolved claim, issue or matter. For purposes of this Section and without limitation, the termination of any claim, issue or matter in such a Proceeding by dismissal, with or without prejudice, shall be deemed to be a successful result as to such claim, issue or matter.

(d)           Additional Indemnity. In addition to, and without regard to any limitations on, the indemnification provided for in Section 4(a)-(c), the Corporation shall

3

and hereby does indemnify and hold harmless each Director against all expenses, judgments, penalties, fines and amounts paid in settlement actually and reasonably incurred by him or on his behalf if, by reason of his Corporate Status he is, or is threatened to be made, a party to or participant in any Proceeding (including, without limitation, a Proceeding by or in the right of the Corporation). The only limitation that shall exist upon the Corporation’s obligations pursuant to this Agreement shall be that the Corporation shall not be obligated to make any payment to a Director that is finally determined (under the procedures, and subject to the presumptions, set forth in Sections 6, 7 and 8 hereof) to be unlawful under Delaware law.

(e)           Contribution in the Event of Joint Liability.

(i)    Whether or not the indemnification provided in Section 4(a)-(d) hereof is available, in respect of any threatened, pending or completed action, suit or proceeding in which Corporation is jointly liable with any Director (or would be if joined in such action, suit or proceeding), Corporation shall pay, in the first instance, the entire amount of any judgment or settlement of such action, suit or proceeding without requiring such Director to contribute to such payment and the Corporation hereby waives and relinquishes any right of contribution it may have against such Director. The Corporation shall not enter into any settlement of any action, suit or proceeding in which the Corporation is jointly liable with a Director (or would be if joined in such action, suit or proceeding) unless such settlement provides for a full and final release of all claims asserted against such Director.

(ii)   Without diminishing or impairing the obligations of the Corporation set forth in the preceding subparagraph, if, for any reason, a Director shall elect or be required to pay all or any portion of any judgment or settlement in any threatened, pending or completed action, suit or proceeding in which Corporation is jointly liable with such Director (or would be if joined in such action, suit or proceeding), the Corporation shall contribute to the amount of expenses, judgments, fines and amounts paid in settlement actually and reasonably incurred and paid or payable by such Director in proportion to the relative benefits received by the Corporation and all officers, directors or employees of the Corporation other than such Director who are jointly liable with him (or would be if joined in such action, suit or proceeding), on the one hand, and the Director, on the other hand, from the transaction from which such action, suit or proceeding arose; provided, however, that the proportion determined on the basis of relative benefit may, to the extent necessary to conform to law, be further adjusted by reference to the relative fault of the Corporation and all officers, directors or employees of the Corporation other than such Director who are jointly liable with the Director (or would be if joined in such action, suit or proceeding), on the one hand, and the Director, on the other hand, in connection with the events that resulted in such expenses, judgments, fines or settlement amounts, as well as any other equitable considerations which the law may require to be considered. The relative fault of the Corporation and all officers, directors or employees of the Corporation other than the Director who are jointly liable with him (or would be if joined in such action, suit or proceeding), on the one hand, and the Director, on the other hand, shall be determined by reference to, among other things, the degree to which their actions were motivated by intent to gain personal profit

4

or advantage, the degree to which their liability is primary or secondary, and the degree to which their conduct is active or passive.

(iii)  The Corporation hereby agrees to fully indemnify and hold each Director harmless from any claims of contribution which may be brought by officers, directors or employees of the Corporation who may be jointly liable with such Director.

Section 5.               Advancement of Expenses and Costs. If a Director is made or threatened to be made a party to a Proceeding, the Director is entitled, upon written request to the Corporation, to payment or reimbursement by the Corporation, within ten (10) days of receipt of the request, of all reasonable expenses, including, without limitation, attorneys’ fees and disbursements, incurred by the Director, whether prior to or after the final disposition of the Proceeding. Such request shall reasonably evidence the expenses incurred by the Director and shall include or be preceded or accompanied by an undertaking by or on behalf of such Director to repay any expenses advanced if it shall ultimately be determined that such Director is not entitled to such expenses. Any advances and undertakings to repay pursuant to this Section 5 shall be unsecured and interest free and shall be accepted without reference to financial ability to make the repayment. A Director’s entitlement to such expenses shall include those incurred in connection with any Proceeding by such Director seeking an adjudication pursuant to this Agreement.

Section 6.               Determination of Entitlement to Indemnification or Advances. It is the intent of this Agreement to secure for each Director rights of indemnity that are as favorable as may be permitted under the law and public policy of the State of Delaware. Accordingly, the parties agree that the following procedures and presumptions shall apply in the event of any question as to whether a Director is entitled to indemnification under this Agreement:

(a)           To obtain indemnification (including, without limitation, the advancement of expenses and contribution by the Corporation) under this Agreement, a Director shall submit to the Corporation a written request, including therein or therewith such documentation and information as is reasonably available to such Director and is reasonably necessary to determine whether and to what extent a Director is entitled to indemnification. The Secretary of the Corporation shall, promptly upon receipt of such a request for indemnification, advise the Board of Directors in writing that such Director has requested indemnification.

(b)           Upon written request by a Director for indemnification pursuant to the first sentence of Section 6(a) hereof, a determination, if required by applicable law, with respect to a Director’s entitlement thereto shall be made in the specific case by one of the following three methods, which shall be at the election of such Director:  (i) by a majority vote of the Disinterested Directors, even though less than a quorum, or (ii) by Independent Legal Counsel in a written opinion or (iii) by the stockholders.

(c)           If the determination of entitlement to indemnification is to be made by Independent Legal Counsel pursuant to Section 6(b) hereof, the Independent Legal

5

Counsel shall be selected as provided in this Section 6(c). The Corporation and its Board of Directors agree that, in the event of an election to use an Independent Legal Counsel under Section 6(b), that such election shall, by virtue of, among other things, their approval of this Agreement, be deemed at the direction of the directors of the Corporation. The Independent Legal Counsel shall be selected by the Director (unless such Director shall request that such selection be made by the Board of Directors). Such Director or the Corporation, as the case may be, may, within ten (10) days after such written notice of selection shall have been given, deliver to the Corporation or to the Director, as the case may be, a written objection to such selection; provided, however, that such objection may be asserted only on the ground that the Independent Legal Counsel so selected does not meet the requirements of “Independent Legal Counsel” as defined in Section 16(b) of this Agreement, and the objection shall set forth with particularity the factual basis of such assertion. Absent a proper and timely objection, the person so selected shall act as Independent Legal Counsel. If a written objection is made and substantiated, the Independent Legal Counsel selected may not serve as Independent Legal Counsel unless and until such objection is withdrawn or a court has determined that such objection is without merit. If, within thirty (30) days after submission by a Director of a written request for indemnification pursuant to Section 6(a) hereof, no Independent Legal Counsel shall have been selected and not objected to, either the Corporation or the Director may petition the Court of Chancery of the State of Delaware or other court of competent jurisdiction for resolution of any objection which shall have been made by the Corporation or such Director to the other’s selection of Independent Legal Counsel and/or for the appointment as Independent Legal Counsel of a person selected by the court or by such other person as the court shall designate, and the person with respect to whom all objections are so resolved or the person so appointed shall act as Independent Legal Counsel under Section 6(b) hereof. The Corporation shall pay any and all reasonable fees and expenses of Independent Legal Counsel incurred by such Independent Legal Counsel in connection with acting pursuant to Section 6(b) hereof, and the Corporation shall pay all reasonable fees and expenses incident to the procedures of this Section 6(c), regardless of the manner in which such Independent Legal Counsel was selected or appointed.

(d)           The Corporation acknowledges that a settlement or other disposition short of final judgment may be successful if it permits a party to avoid expense, delay, distraction, disruption and uncertainty. In the event that any action, claim or proceeding to which a Director is a party is resolved in any manner other than by adverse judgment against such Director (including, without limitation, settlement of such action, claim or proceeding with or without payment of money or other consideration) it shall be presumed (unless there is a preponderance of competent evidence to the contrary) that such Director has been successful on the merits or otherwise in such action, suit or proceeding.

(e)           Each Director shall reasonably cooperate with the person, persons or entity making such determination with respect to such Director’s entitlement to indemnification, including providing to such person, persons or entity upon reasonable advance request any documentation or information which is not privileged or otherwise protected from disclosure and which is reasonably available to such Director and

6