**Exhibit 3.1**

 

**AMENDED AND RESTATED CERTIFICATE OF INCORPORATION**

 

**XENOGEN CORPORATION**

 

Xenogen Corporation a corporation organized and existing under the laws of the State of Delaware, hereby certifies as follows: 

 

A. The corporation was originally incorporated under the name of XenogenCorporation and the original Certificate of Incorporation of the corporation was filed with the Secretary of State of the State of Delaware on September 6, 2000. 

 

B. Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware (the “**DGCL**”),this Amended and Restated Certificate of Incorporation restates and amends the provisions of the Amended and Restated Certificate of Incorporation of the corporation. 

 

C. This Amended and Restated Certificate of Incorporation has been duly approved by the Board of Directors of thecorporation in accordance with Sections 242 and 245 of the DGCL. 

 

D. This Amended and Restated Certificate of Incorporation has been duly approved by the written consent of the stockholders of the corporation in accordance with Sections 228, 242 and 245 of the DGCL. 

 

E. The Certificate of Incorporation of the corporation is hereby amended andrestated in its entirety to read as follows: 

 

**ARTICLE I**

 

The name of the corporation is Xenogen Corporation

 

**ARTICLE II**

 

The address of the corporation’s registered office in the State ofDelaware is Corporation Trust Center, 1209 Orange Street, Wilmington, New Castle County, Delaware 19801. The name of its registered agent at such address is The Corporation Trust Company. 

 

**ARTICLE III**

 

The purpose of the corporation is to engage in any lawful act or activity for which corporations may be organized under the DGCL. 

**ARTICLE IV**

 

The corporation shall have authority to issue shares as follows: 

 

100,000,000 shares of Common Stock, par value $0.001 per share. Each share of Common Stock shall entitle the holder thereofto one (1) vote on each matter submitted to a vote at a meeting of stockholders. 

 

5,000,000 shares of Preferred Stock, par value $0.001 per share, which may be issued from time to time in one or more series pursuant to a resolution or resolutions providing for such issue duly adopted by the Boardof Directors (authority to do so being hereby expressly vested in the Board of Directors). The Board of Directors is further authorized, subject to limitations prescribed by law, to fix by resolution or resolutions the designations, powers,preferences and rights, and the qualifications, limitations or restrictions thereof, of any wholly unissued series of Preferred Stock, including without limitation authority to fix by resolution or resolutions the dividend rights, dividend rate,conversion rights, voting rights, rights and terms of redemption (including sinking fund provisions), redemption price or prices, and liquidation preferences of any such series, and the number of shares constituting any such series and thedesignation thereof, or any of the foregoing. 

 

The Board ofDirectors is further authorized to increase (but not above the total number of authorized shares of the class) or decrease (but not below the number of shares of any such series then outstanding) the number of shares of any series, the number ofwhich was fixed by it, subsequent to the issuance of shares of such series then outstanding, subject to the powers, preferences and rights, and the qualifications, limitations and restrictions thereof stated in the Certificate of Incorporation orthe resolution of the Board of Directors originally fixing the number of shares of such series. If the number of shares of any series is so decreased, then the shares constituting such decrease shall resume the status which they had prior to theadoption of the resolution originally fixing the number of shares of such series. 

 

**ARTICLE V**

 

The number ofdirectors that constitutes the entire Board of Directors of the corporation shall be determined in the manner set forth in the Bylaws of the corporation. At each annual meeting of stockholders, directors of the corporation shall be elected to holdoffice until the expiration of the term for which they are elected and until their successors have been duly elected and qualified; except that if any such election shall not be so held, such election shall take place at a stockholders’ meetingcalled and held in accordance with the DGCL. 

 

The directors ofthe corporation shall be divided into three classes as nearly equal in size as is practicable, hereby designated Class I, Class II and Class III. The term of office of the initial Class I directors shall expire at the first annual meeting of thestockholders following the effective date of this corporation’s initial public offering (the “**Effective Date**”), the term of office of the initial Class II directors shall expire at the second annual meeting of the stockholdersfollowing the Effective Date and the term of office of the initial Class III directors shall expire at the third annual meeting of the stockholders following the Effective Date. At each annual meeting of stockholders, commencing with the firstannual meeting of stockholders following the Effective Date, each of the successors elected to replace the directors of a Class whose term shall have expired at such annual meeting shall be elected to hold office until the third annual meeting nextsucceeding his or her election and until his or her respective successor shall have been duly elected and qualified. 

Notwithstanding the foregoing provisions of this Article, each director shall serve until his or hersuccessor is duly elected and qualified or until his or her death, resignation, or removal. If the number of directors is hereafter changed, any newly created directorships or decrease in directorships shall be so apportioned among the classes as tomake all classes as nearly equal in number as is practicable, provided that no decrease in the number of directors constituting the Board of Directors shall shorten the term of any incumbent director. 

 

Any director may be removed from office by the stockholders of thecorporation only for cause. Vacancies occurring on the Board of Directors for any reason and newly created directorships resulting from an increase in the authorized number of directors may be filled by vote of a majority of the remaining members ofthe Board of Directors, although less than a quorum, or by a sole remaining director. A person so elected by the Board of Directors to fill a vacancy or newly created directorship shall hold office until the next election of the Class for which suchdirector shall have been chosen and until his or her successor shall have been duly elected and qualified. 

 

**ARTICLE VI**

 

In furtherance and not in limitation of the powers conferred by statute, the Board of Directors of the corporation is expressly authorized to adopt, amend or repeal the Bylaws of the corporation. 

 

**ARTICLE VII**

 

The election of directors need not be by written ballot unless the Bylaws ofthe corporation shall so provide. 

 

**ARTICLE VIII**

 

Any action allowed to be taken by the stockholders of thecorporation at an annual or special meeting of the stockholders called in accordance with the Bylaws, may be taken by the stockholders by written consent. 

 

**ARTICLE IX**

 

To the fullest extent permitted by the General Corporation Law of Delaware or any other applicable law as the same exists or may hereafter be amended, adirector of the corporation shall not be personally liable to the corporation or its stockholders and shall otherwise be indemnified by the corporation for monetary damages for any action taken, or any failure to take any action, as a director.

 

The corporation shall indemnify to the fullest extentpermitted by law any person made or threatened to be made a party to an action or proceeding, whether criminal, civil, administrative or investigative, by reason of the fact that he or she or his or her testator or intestate is or was a director orofficer of the corporation or any predecessor of the corporation or serves or served at any other enterprise as a director, officer, employee or agent at the request of the corporation or any predecessor to the corporation. To the fullest extentpermitted by applicable law, the corporation is authorized to provide indemnification of, and advancement of expenses to, directors, officers, employees, other agents of the corporation and any other persons to which the General Corporation Law ofDelaware permits the corporation to provide indemnification. 

Neither any amendment nor repeal of this Article IX, nor the adoption of any provision of thiscorporation’s Certificate of Incorporation inconsistent with this Article IX, shall eliminate or reduce the effect of this Article IX in respect of any matter occurring, or any cause of action, suit or claim accruing or arising or that, but forthis Article IX, would accrue or arise, prior to such amendment, repeal or adoption of an inconsistent provision. 

 

**ARTICLE X**

 

Except as provided in Article IX above, the corporation reserves the right to amend, alter, change or repeal any provision contained in this Certificate of Incorporation, in the manner now or hereafter prescribed by statute, and all rightsconferred upon stockholders herein are granted subject to this reservation. 

IN WITNESS WHEREOF, Xenogen Corporation has caused this Amended and Restated Certificate of Incorporationto be signed by the President of the corporation on this 21st day of July, 2004. 

 

By:
 
/s/ Pamela Reilly Contag
  Pamela Reilly Contag, Ph.D.  President