Document:

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                                                                   EXHIBIT 10.11

THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED OR ANY STATE SECURITIES LAWS.  NO SALE OR DISPOSITION MAY BE EFFECTED
WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION
OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH
REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS FROM THE
APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE
PROVISIONS OF SECTION 7 OF THIS WARRANT.

                              XENOGEN CORPORATION

                          WARRANT TO PURCHASE SHARES
                                OF COMMON STOCK

     THIS CERTIFIES THAT, for value received, MEIER MITCHELL & COMPANY and its
assignees are entitled to subscribe for and purchase 24,706 shares of the fully
paid and nonassessable Common Stock (as adjusted pursuant to Section 4 hereof,
the "Shares") of XENOGEN CORPORATION, a California corporation (the "Company"),
at the price per share as determined pursuant to the next paragraph hereof (such
price and such other price as shall result, from time to time, from the
adjustments specified in Section 4 hereof is herein referred to as the "Warrant
Price"), subject to the provisions and upon the terms and conditions hereinafter
set forth.  As used herein, (a) the term "Date of Grant" shall mean April 28,
2000 and (b) the term "Other Warrants" shall mean any other warrants issued by
the Company in connection with the transaction with respect to which this
Warrant was issued, and any warrant issued upon transfer or partial exercise of
this Warrant. The term "Warrant" as used herein shall be deemed to include Other
Warrants unless the context clearly requires otherwise.

          In the event of a Liquidation (as defined in the Articles (as defined
below)), the Warrant Price shall be (i) $4.25 per share if the holders of all of
the applicable series preferred stock (Series A, B, C, D and E) are entitled to
receive a higher Converted Liquidation Amount (as defined in the Articles) in
lieu of the applicable Threshold Amount (as defined in the Articles) pursuant to
Section B.1.(c) of the Amended and Restated Articles of Incorporation of Xenogen
Corporation filed or to be filed on or about the Date of Grant with the
California Secretary of State (the "Articles"), or (ii) $0.00 per share if the
holders of all of the applicable series preferred stock (Series A, B, C and D)
are not entitled to receive a higher Converted Liquidation Amount (as defined in
the Articles) in lieu of the applicable Threshold Amount (as defined in the
Articles) pursuant to Section B.1.(c) of the Articles. In all other cases, the
Warrant Price shall be $4.25 per share.

     1.   Term. The purchase right represented by this Warrant is exercisable,
          ----
in whole or in part, at any time and from time to time from the Date of Grant
through the later of (i) ten (10) years after the Date of Grant, or (ii) five
(5) years after the closing of the Company's initial public offering of its
Common Stock (an "IPO") effected pursuant to a Registration Statement on form
S-1 (or its successor) filed under the Securities Act of 1933 (the "Act").

     2.   Method of Exercise; Payment; Issuance of New Warrant. Subject to
          ----------------------------------------------------
Section 1 hereof, the purchase right represented by this Warrant may be
exercised by the holder hereof, in whole or in part and from time to time, at
the election of the holder hereof, by (a) the surrender of this Warrant (with
the notice of exercise substantially in the form attached hereto as Exhibit A-1
duly completed and executed) at the principal office of the Company and by the
payment to the Company, by certified or bank check, or by wire

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transfer to an account designated by the Company (a "Wire Transfer") of an
amount equal to the then applicable Warrant Price multiplied by the number of
Shares then being purchased; (b) if in connection with a registered public
offering of the Company's securities, the surrender of this Warrant (with the
notice of exercise form attached hereto as Exhibit A-2 duly completed and
executed) at the principal office of the Company together with notice of
arrangements reasonably satisfactory to the Company for payment to the Company
either by certified or bank check or by Wire Transfer from the proceeds of the
sale of shares to be sold by the holder in such public offering of an amount
equal to the then applicable Warrant Price per share multiplied by the number of
Shares then being purchased; or (c) exercise of the "net issuance" right
provided for in Section 10.2 hereof. The person or persons in whose name(s) any
certificate(s) representing the Shares shall be issuable upon exercise of this
Warrant shall be deemed to have become the holders(s) of record of, and shall be
treated for all purposes as the record holder(s) of, the shares represented
thereby (and such shares shall be deemed to have been issued) immediately prior
to the close of business on the date or dates upon which this Warrant is
exercised. In the event of any exercise of the rights represented by this
Warrant, certificates for the shares of stock so purchased shall be delivered to
the holder hereof as soon as possible and in any event within thirty (30) days
after such exercise and, unless this Warrant has been fully exercised or
expired, a new Warrant representing the portion of the Shares, if any, with
respect to which this Warrant shall not then have been exercised shall also be
issued to the holder hereof as soon as possible and in any event within such
thirty-day period; provided, however, at such time as the Company is subject to
the reporting requirements of the Securities Exchange Act of 1934, as amended,
if requested by the holder of this Warrant, the Company shall cause its transfer
agent to deliver the certificate representing Shares issued upon exercise of
this Warrant to a broker or other person (as directed by the holder exercising
this Warrant) within the time period required to settle any trade made by the
holder after exercise of this Warrant.

     3.   Stock Fully Paid; Reservation of Shares.  All Shares that may be
          ---------------------------------------
issued upon the exercise of the rights represented by this Warrant will, upon
issuance pursuant to the terms and conditions herein, be fully paid and
nonassessable, and free from all taxes, liens and charges with respect to the
issue thereof.  During the period within which the rights represented by this
Warrant may be exercised, the Company will at all times have authorized, and
reserved for the purpose of the issue upon exercise of the purchase rights
evidenced by this Warrant, a sufficient number of shares of its Common Stock to
provide for the exercise of the rights represented by this Warrant.

     4.   Adjustment of Warrant Price and Number of Shares.  The number and kind
          ------------------------------------------------
of securities purchasable upon the exercise of this Warrant and the Warrant
Price shall be subject to adjustment from time to time upon the occurrence of
certain events, as follows:

     (a)  Reclassification or Merger.  In case of any reclassification or change
          --------------------------
of securities of the class issuable upon exercise of this Warrant (other than a
change in par value, or from par value to no par value, or from no par value to
par value, or as a result of a subdivision or combination), or in case of any
merger of the Company with or into another corporation (other than a merger with
another corporation in which the Company is the acquiring and the surviving
corporation and which does not result in any reclassification or change of
outstanding securities issuable upon exercise of this Warrant), or in case of
any sale of all or substantially all of the assets of the Company, the Company,
or such successor or purchasing corporation, as the case may be, shall duly
execute and deliver to the holder of this Warrant a new Warrant (in form and
substance satisfactory to the holder of this Warrant), or the Company shall make
appropriate provision without the issuance of a new Warrant, so that the holder
of this Warrant shall have the right to receive, at a total purchase price not
to exceed that payable upon the exercise of the unexercised portion of this
Warrant, and in lieu of the shares of Common Stock theretofore issuable upon
exercise of this Warrant, (i) the kind and amount of shares of stock, other
securities, money and property receivable upon such reclassification, change,

                                      -2-

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merger or a sale by a holder of the number of shares of Common Stock then
purchasable under this Warrant, or (ii) in the case of such a merger or sale in
which the consideration paid consists all or in part of assets other than
securities of the successor or purchasing corporation, at the option of the
holder of this Warrant, the securities of the successor or purchasing
corporation having a value at the time of the transaction equivalent to the
value of the Common Stock at the time of the transaction. Any new Warrant shall
provide for adjustments that shall be as nearly equivalent as may be practicable
to the adjustments provided for in this Section 4. The provisions of this
subparagraph (a) shall similarly apply to successive reclassifications, changes,
mergers and transfers.

     (b)  Subdivision or Combination of Shares.  If the Company at any time
          ------------------------------------
while this Warrant remains outstanding and unexpired shall subdivide or combine
its outstanding shares of Common Stock, the Warrant Price shall be
proportionately decreased and the number of Shares issuable hereunder shall be
proportionately increased in the case of a subdivision and the Warrant Price
shall be proportionately increased and the number of Shares issuable hereunder
shall be proportionately decreased in the case of a combination.

     (c)  Stock Dividends and Other Distributions.  If the Company at any time
          ---------------------------------------
while this Warrant is outstanding and unexpired shall (i) pay a dividend with
respect to Common Stock payable in Common Stock, then the Warrant Price shall
be adjusted, from and after the date of determination of shareholders entitled
to receive such dividend or distribution, to that price determined by
multiplying the Warrant Price in effect immediately prior to such date of
determination by a fraction (A) the numerator of which shall be the total number
of shares of Common Stock outstanding immediately prior to such dividend or
distribution, and (B) the denominator of which shall be the total number of
shares of Common Stock outstanding immediately after such dividend or
distribution; or (ii) make any other distribution with respect to Common Stock
(except any distribution specifically provided for in Sections 4(a) and 4(b)),
then, in each such case, provision shall be made by the Company such that the
holder of this Warrant shall receive upon exercise of this Warrant a
proportionate share of any such dividend or distribution as though it were the
holder of the Common Stock as of the record date fixed for the determination of
the shareholders of the Company entitled to receive such dividend or
distribution.

     (d)  Adjustment of Number of Shares.  Upon each adjustment in the Warrant
          ------------------------------
Price, the number of Shares purchasable hereunder shall be adjusted, to the
nearest whole share, to the product obtained by multiplying the number of Shares
purchasable immediately prior to such adjustment in the Warrant Price by a
fraction, the numerator of which shall be the Warrant Price immediately prior to
such adjustment and the denominator of which shall be the Warrant Price
immediately thereafter.

     (e)  Antidilution Rights.  The holder of this Warrant shall have the same
          -------------------
antidilution rights as afforded or granted to the Company's Series E Preferred
Stock. The other antidilution rights applicable to the Shares purchasable
hereunder are set in the Company's Articles, as amended through the Date of
Grant, a true and complete copy of which is attached hereto as Exhibit B (the
"Charter"). These antidilution rights shall not be restated, amended, modified
or waived in any manner that is adverse to the holder hereof without such
holder's prior written consent. The Company shall provide the holder hereof with
any restatement, amendment, modification or waiver of the Charter promptly after
same as been made.

     5.   Notice of Adjustments.  Whenever the Warrant Price or the number of
          ---------------------
Shares purchasable hereunder shall be adjusted pursuant to Section 4 hereof, the
Company shall make a certificate signed by its chief financial officer setting
forth, in reasonable detail, the event requiring the adjustment, the amount of
the adjustment, the method by which such adjustment was calculated, and the
Warrant Price and the number of

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Shares purchasable hereunder after giving effect to such adjustment, and shall
cause copies of such certificate to be mailed (without regard to Section 13
hereof, by first class mail, postage prepaid) to the holder of this Warrant at
such holder's last known address.

     6.   Fractional Shares.  No fractional shares of Common Stock will be
          -----------------
issued in connection with any exercise hereunder, but in lieu of such fractional
shares the Company shall make a cash payment therefor based on the fair market
value of the Common Stock on the date of exercise as reasonably determined in
good faith by the Company's Board of Directors.

     7.   Compliance with Act; Disposition of Warrant or Shares of Common Stock.
          ---------------------------------------------------------------------

     (a)  Compliance with Act.  The holder of this Warrant, by acceptance
          -------------------
hereof, agrees that this Warrant, and the Shares to be issued upon exercise
hereof are being acquired for investment and that such holder will not offer,
sell or otherwise dispose of this Warrant, or any Shares except under
circumstances which will not result in a violation of the Act or any applicable
state securities laws.  Upon exercise of this Warrant, unless the Shares being
acquired are registered under the Act and any applicable state securities laws
or an exemption from such registration is available, the holder hereof shall
confirm in writing that the Shares so purchased are being acquired for
investment and not with a view toward distribution or resale in violation of the
Act and shall confirm such other matters related thereto as may be reasonably
requested by the Company.  This Warrant and all Shares issued upon exercise of
this Warrant (unless registered under the Act and any applicable state
securities laws) shall be stamped or imprinted with a legend in substantially
the following form:

     "THE SECURITIES EVIDENCED HEREBY HAVE NOT BEEN REGISTERED UNDER
     THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES
     LAW. NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE
     REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF
     COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE
     COMPANY, THAT SUCH REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT
     OF NO-ACTION LETTERS FROM THE APPROPRIATE GOVERNMENTAL
     AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE PROVISIONS OF
     SECTION 7 OF THE WARRANT UNDER WHICH THESE SECURITIES WERE
     ISSUED, DIRECTLY OR INDIRECTLY."

Said legend shall be removed by the Company, upon the request of a holder, at
such time as the restrictions on the transfer of the applicable security shall
have terminated. In addition, in connection with the issuance of this Warrant,
the holder specifically represents to the Company by acceptance of this Warrant
as follow:

     (1)  The holder is aware of the Company's business affairs and financial
condition, and has acquired information about the Company sufficient to reach an
informed and knowledgeable decision to acquire this Warrant. The holder is
acquiring this Warrant for its own account for investment purposes only and not
with a view to, or for the resale in connection with, any "distribution" thereof
in violation of the Act.

     (2)  The holder understands that this Warrant has not been registered under
the Act in reliance upon a specific exemption therefrom, which exemption depends
upon, among other things, the bona fide nature of the holder's investment
intent as expressed herein.

                                      -4-

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     (3)  The holder further understands that this Warrant must be held
indefinitely unless subsequently registered under the Act and qualified under
any applicable state securities laws, or unless exemptions from registration and
qualification are otherwise available. The holder is aware of the provisions of
Rule 144, promulgated under the Act.

     (4)  The holder is an "accredited investor" as such term is defined in Rule
501 of Regulation D promulgated under the Act.

     (b)  Disposition of Warrant or Shares. With respect to any offer, sale or
          --------------------------------
other disposition of this Warrant or any Shares acquired pursuant to the
exercise of this Warrant prior to registration of such Warrant or Shares, the
holder hereof agrees to give written notice to the Company prior thereto,
describing briefly the manner thereof, together with a written opinion of such
holder's counsel, or other evidence, if reasonably satisfactory to the Company,
to the effect that such offer, sale or other disposition may be effected
without registration or qualification (under the Act as then in effect or any
federal or state securities law then in effect) of this Warrant or the Shares
and indicating whether or not under the Act certificates for this Warrant or the
Shares to be sold or otherwise disposed of require any restrictive legend as to
applicable restrictions on transferability in order to ensure compliance with
such law. Upon receiving such written notice and reasonably satisfactory
opinion or other evidence, the Company, as promptly as practicable but no later
than fifteen (15) days after receipt of the written notice, shall notify such
holder that such holder may sell or otherwise dispose of this Warrant or such
Shares, all in accordance with the terms of the notice delivered to the Company.
If a determination has been made pursuant to this Section 7(b) that the opinion
of counsel for the holder or other evidence is not reasonably satisfactory to
the Company, the Company shall so notify the holder promptly with details
thereof after such determination has been made. Nothwithstanding the foregoing,
this Warrant or such Shares may, as to such federal laws, be offered, sold or
otherwise disposed of in accordance with Rule 144 or 144A under the Act,
provided that the Company shall have been furnished with such information as the
Company may reasonably request to provide a reasonable assurance that the
provisions of Rule 144 or 144A have been satisfied. Each certificate
representing this Warrant or the Shares thus transferred (except a transfer
pursuant to Rule 144 or 144A) shall bear a legend as to the applicable
restrictions on transferability in order to ensure compliance with such laws,
unless in the aforesaid opinion of counsel for the holder, such legend is not
required in order to ensure compliance with such laws. The Company may issue
stop transfer instructions to its transfer agent in connection with such
restrictions.

     (d)  Applicability of Restrictions. Neither any restrictions of any legend
          -----------------------------
described in this Warrant nor the requirements of Section 7(b) above shall apply
to any transfer or grant of a security interest in, this Warrant (or the Common
Stock obtainable upon exercise thereof) or any part hereof (i) to a partner of
the holder if the holder is a partnership or to a member of the holder if the
holder is a limited liability company, (ii) to a partnership of which the holder
is a partner or to a limited liability company of which the holder is a member,
or (iii) to any affiliate of the holder if the holder is a corporation;
provided, however, in any such transfer, if applicable, the transferee shall on
--------  -------
the Company's request agree in writing to be bound by the terms of this Warrant
as if an original holder hereof.

     8.   Rights as Shareholders; Information. No holder of this Warrant, as
          -----------------------------------
such, shall be entitled to vote or receive dividends or be deemed the holder of
Shares, nor shall anything contained herein be construed to confer upon the
holder of this Warrant, as such, any of the rights of a shareholder of the
Company or any right to vote for the election of directors or upon any matter
submitted to shareholders at any meeting thereof, or to receive notice of
meetings, or to receive dividends or subscription rights or otherwise until this
Warrant shall have been exercised and the Shares purchasable upon the exercise
hereof shall have become deliverable, as provided herein. Notwithstanding the
foregoing, the Company will transmit to the holder of this warrant

                                      -5-

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such information, documents and reports as are generally distributed to the
holders of any class or series of the securities of the Company concurrently
with the distribution thereof to the shareholders.

     9.   [Reserved]
          ----------

     10.  Additional Rights.
          -------------------

     10.1 Acquisition Transactions. The Company shall provide the holder of this
          -----------------------
Warrant with at least twenty (20) days' written notice prior to closing thereof
of the terms and conditions of any of the following transactions (to the extent
the Company has notice thereof): (i) the sale, lease, exchange, conveyance or
other disposition of all or substantially all of the Company's property or
business, or (ii) its merger into or consolidation with any other corporation
(other than a wholly-owned subsidiary of the Company), or (iii) any transaction
(including a merger or other reorganization) or series of related transactions,
in which more than 50% of the voting power of the Company is disposed of.

     10.2 Right to Convert Warrant into Stock: Net Issuance.
          -------------------------------------------------

     (a)  Right to Convert. In addition to and without limiting the rights of
          ----------------
the holder under the terms of this Warrant, the holder shall have the right to
convert this Warrant or any portion thereof (the "Conversion Right") into shares
of Common Stock as provided in this Section 10.2 at any time or from time to
time during the term of this Warrant. Upon exercise of the Conversion Right with
respect to a particular number of shares subject to this Warrant (the "Converted
Warrant Shares"), the Company shall deliver to the holder (without payment by
the holder of any exercise price or any cash or other consideration) that number
of shares of fully paid and nonassessable Common Stock as is determined
according to the following formula:

                    X= B - A
                       -----
                         Y

     Where:    X =  the number of shares of Common Stock that shall be issued to
           the holder

               Y = the fair market value of one share of Common Stock

               A =  the aggregate Warrant Price of the specified number of
           Converted Warrant Shares immediately prior to the exercise of the
           Conversion Right (i.e., the number of Converted Warrant Shares
           multiplied by the Warrant Price)

               B =  the aggregate fair market value of the specified number of
           Converted Warrant Shares (i.e. the number of Converted Warrant Shares
           multiplied by the fair market value of one Converted Warrant Share)

No fractional shares shall be issuable upon exercise of the Conversion Right,
and, if the number of shares to be issued determined in accordance with the
foregoing formula is other than a whole number, the Company shall pay to the
holder an amount in cash equal to the fair market value of the resulting
fractional share on the Conversion Date (as hereinafter defined). For purposes
of Section 9 of this Warrant, shares issued pursuant to the Conversion Right
shall be treated as if they were issued upon the exercise of this Warrant.

     (b)  Method of Exercise. The Conversion Right may be exercised by the
          ------------------
holder by the surrender of this Warrant at the principal office of the Company
together with a written statement (which may be in the

                                      -6-

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form of Exhibit A-1 or Exhibit A-2 hereto) specifying that the holder thereby
intends to exercise the Conversion Right and indicating the number of shares
subject to this Warrant which are being surrendered (referred to in Section
10.2(a) hereof as the Converted Warrant Shares) in exercise of the Conversion
Right. Such conversion shall be effective upon receipt by the Company of this
Warrant together with the aforesaid written statement, or on such later date as
is specified therein (the "Conversion Date"), and, at the election of the holder
hereof, may be made contingent upon the closing of the sale of the Company's
Common Stock to the public in a public offering pursuant to a Registration
Statement under the Act (a "Public Offering"). Certificates for the shares
issuable upon exercise of the Conversion Right and, if applicable, a new warrant
evidencing the balance of the shares remaining subject to this Warrant, shall be
issued as of the Conversion Date and shall be delivered to the holder within
thirty (30) days following the Conversion Date.

     (c)  Determination of Fair Market Value. For purposes of this Section 10.2,
          ----------------------------------
"fair market value" of a share of Common Stock as of a particular date (the
"Determination Date") shall mean:

          (i)  If the Conversion Right is exercised in connection with and
contingent upon a Public Offering, and if the Company's Registration Statement
relating to such Public Offering ("Registration Statement") has been declared
effective by the Securities and Exchange Commission, then the initial "Public to
Public" specified in the final prospectus with respect to such offering.

          (ii) If the Conversion Right is not exercised in connection with and
contingent upon a Public Offering, then as follows:

                    (A)  If traded on a securities exchange, the fair market
     value of the Common Stock shall be deemed to be the average of the closing
     prices of the Common Stock on such exchange over the 30-day period ending
     five business days prior to the Determination Date;

                    (B)  If traded on the Nasdaq Stock Market or other over-the-
     counter system, the fair market value of the Common Stock shall be deemed
     to be the average of the closing bid prices of the Common Stock over the
     30-day period ending five business days prior to the Determination Date;
     and

                    (C)  If there is no public market for the Common Stock,
     then fair market value shall be determined by mutual agreement of the
     holder of this Warrant and the Company.

     10.3 Exercise Prior to Expiration. To the extent this Warrant is not
          ----------------------------
previously exercised as to all of the Shares subject hereto, and if the fair
market value of one share of the Common Stock is greater than the Warrant Price
then in effect, this Warrant shall be deemed automatically exercised pursuant to
Section 10.2 above (even if not surrendered) immediately before its expiration.
For purposes of such automatic exercise, the fair market value of one share of
Common Stock upon such expiration shall be determined pursuant to Section
10.2(c). To the extent this Warrant or any portion thereof is deemed
automatically exercised pursuant to this Section 10.3, the Company agrees to
promptly notify the holder of the number of Shares, if any, the holder hereof is
to receive by reason of such automatic exercise.

     11.  Representations and Warranties. The Company represents and warrants to
          ------------------------------
the holder of this Warrant as follows:

     (a)  This Warrant has been duly authorized and executed by the Company and
is a valid and binding obligation of the Company enforceable in accordance with
its terms, subject to laws of general

                                      -7-

<PAGE>

application relating to bankruptcy, insolvency and the relief of debtors and
the rules of law or principles at equity governing specific performance,
injunctive relief and other equitable remedies;

     (b)  The Shares have been duly authorized and reserved for issuance by the
Company and, when issued in accordance with the terms hereof, will be validly
issued, fully paid and non-assessable;

     (c)  The execution and delivery of this Warrant are not, and the issuance
of the Shares upon exercise of this Warrant in accordance with the terms hereof
will not be, inconsistent with the Company's Articles, or by-laws, do not and
will not contravene any law, governmental rule or regulation, judgment or order
applicable to the Company, and do not and will not conflict with or contravene
any provision of, or constitute a default under, any indenture, mortgage,
contract or other instrument of which the Company is a party or by which it is
bound or require the consent or approval of, the giving of notice to, the
registration or filing with or the taking of any action in respect of or by, any
Federal, state or local government authority or agency or other person, except
for the filing of notices pursuant to federal and state securities laws, which
filings will be effected by the time required thereby;

     (d)  There are no actions, suits, audits, investigations or proceedings
pending or, to the knowledge of the Company, threatened against the Company in
any court or before any governmental commission, board or authority which, if
adversely determined, will have a material adverse effect on the ability of the
Company to perform its obligations under this Warrant; and

     (e)  The number of shares of Common Stock of the Company outstanding on the
date hereof, on a fully diluted basis (assuming the conversion of all
outstanding convertible securities and the exercise of all outstanding options
and warrants) does not exceed outstanding is not more than 18,979,000 shares
(not counting this Warrant or any Series E Preferred Stock).

     12.  Modification and Waiver. This Warrant and any provision hereof may be
          -----------------------
changed, waived, discharged or terminated only by an instrument in writing
signed by the party against which enforcement of the same is sought.

     13.  Notices. Any notice, request, communication or other document required
          -------
or permitted to be given or delivered to the holder hereof or the Company shall
be delivered, or shall be sent by certified or registered mail, postage prepaid,
to each such holder at its address as shown on the books of the Company or to
the Company at the address indicated therefor on the signature page of this
Warrant.

     14.  Binding Effect on Successors. This Warrant shall be binding upon any
          ----------------------------
corporation succeeding the Company by merger, consolidation or acquisition of
all or substantially all of the Company's assets, and all of the obligations of
the Company relating to the Shares issuable upon the exercise or conversion of
this Warrant shall survive the exercise, conversion and termination of this
Warrant and all of the covenants and agreements of the Company shall inure to
the benefit of the successors and assigns of the holder hereof.

     15.  Lost Warrants or Stock Certificates. The Company covenants to the
          -----------------------------------
holder hereof that, upon receipt of evidence reasonably satisfactory to the
Company of the loss, theft, destruction or mutilation of this Warrant or any
stock certificate and, in the case of any such loss, theft or destruction, upon
receipt of an indemnity reasonably satisfactory to the Company, or in the case
of any such mutilation upon surrender and cancellation of such Warrant or stock
certificate, the Company will make and deliver a new Warrant or stock
certificate, of like tenor, in lieu of the lost, stolen, destroyed or mutilated
Warrant or stock certificate.

                                      -8-
<PAGE>

     16.  Descriptive Headings.  The descriptive headings of the several
          --------------------
paragraphs of this Warrant are inserted for convenience only and do not
constitute a part of this Warrant.  The language in this Warrant shall be
construed as to its fair meaning without regard to which party drafted this
Warrant.

     17.  Governing Law.  This Warrant shall be construed and enforced in
          -------------
accordance with, and the rights of the parties shall be governed by, the laws
of the State of California.

     18.  Survival of Representations, Warranties and Agreements.  All
          ------------------------------------------------------
representations and warranties of the Company and the holder hereof contained
herein shall survive the Date of Grant, the exercise or conversion of this
Warrant (or any part hereof) or the termination or expiration of rights
hereunder.  All agreements of the Company and the holder hereof contained herein
shall survive indefinitely until, by their respective terms, they are no longer
operative.

     19.  Remedies.  In case any one or more of the convenants and agreements
          --------
contained in this Warrant shall have been breached, the holders hereof (in the
case of a breach by the Company), or the Company (in the case of a breach by a
holder), may proceed to protect and enforce their or its rights either by suit
in equity and/or by action at law, including, but not limited to, an action for
damages as a result of any such breach and/or an action for specific performance
of any such covenant or agreement contained in this Warrant.

     20.  No Impairment of Rights.  The Company will not, by amendment of its
          -----------------------
Charter or through any other means, avoid or seek to avoid the observance or
performance of any of the terms of this Warrant, but will at all times in good
faith assist in the carrying out of all such terms and in the taking of all such
action as may be necessary or appropriate in order to protect the rights of the
holder of this Warrant against impairment.

     21.  Severability.  The invalidity or unenforceability of any provision of
          ------------
this Warrant in any jurisdiction shall not affect the validity or enforceability
of such provision in any other jurisdiction, or affect any other provision of
this Warrant, which shall remain in full force and effect.

     22.  Recovery of Litigation Costs.  If any legal action or other
          ----------------------------
proceeding is brought for the enforcement of this Warrant, or because of an
alleged dispute, breach, default, or misrepresentation in connection with any of
the provisions of this Warrant, the successful or prevailing party or parties
shall be entitled to recover reasonable attorneys' fees and other costs incurred
in that action or proceeding, in addition to any other relief to which it or
they may be entitled.

     23.  Entire Agreement; Modification.  This Warrant constitutes the entire
          ------------------------------
agreement between the parties pertaining to the subject matter contained in it
and supersedes all prior and contemporaneous agreements, representations, and
undertakings of the parties, whether oral or written, with respect to such
subject matter.

           [The remainder of this page is intentionally left blank.]

                                      -9-

<PAGE>

     The Company has caused this Warrant to be duly executed and delivered as of
the Date of Grant specified above.

                                                XENOGEN CORPORATION

                                                By: /s/ Kevin Birtchnell
                                                   -------------------------
                                                Name: Kevin Birtchnell
                                                     -----------------------
                                                Title: CFO & VP.
                                                      ----------------------

                                                Address: 860 Atlantic Avenue
                                                         Alameda, CA 94501

                                     -10-
<PAGE>

                                  EXHIBIT A-1

                              NOTICE OF EXERCISE

     To: XENOGEN CORPORATION (the "Company")

     1.   The undersigned hereby:

     ___  elects to purchase ___ shares of Common Stock of the Company pursuant
          to the terms of the attached Warrant, and tenders herewith payment of
          the purchase price of such shares in full, or

     ___  elects to exercise its net issuance rights pursuant to Section 10.2 of
          the attached Warrant with respect to __ shares of Common stock.

     2.   Please issue a certificate or certificates representing ____ shares in
the name of the undersigned or in such other name or names as are specified
below:

          _____________________________________________ (Name)

          _____________________________________________
          _____________________________________________ (Address)

     3.   The undersigned represents that the aforesaid shares are being
acquired for the account of the undersigned for investment and not with a view
to, or for resale in connection with, the distribution thereof and that the
undersigned has no present intention of distributing or reselling such shares,
all except as in compliance with applicable securities laws.

                                   __________________________ (Signature)

     Date:_____________________

                                     -11-

<PAGE>

EXHIBIT A-2

                              NOTICE OF EXERCISE

     To: XENOGEN CORPORATION (the "Company")

     1.   Contingent upon and effective immediately prior to the closing (the
"Closing") of the Company's public offering contemplated by the Registration
Statement on Form S, filed, __________, 19__, the undersigned hereby:

     ___  elects to purchase __ shares of Common Stock of the Company (or such
          lesser number of shares as may be sold on behalf of the undersigned at
          the Closing) pursuant to the terms of the attached Warrant, or

     ___  elects to exercise its net issuance rights pursuant to Section 10.2 of
          the attached Warrant with respect to __ Shares of Common Stock.

     2.   Please deliver to the custodian for the selling shareholders a stock
certificate representing such _________ shares.

     3.   The undersigned has instructed the custodian for the selling
shareholders to deliver to the Company $___________ or, if less, the net
proceeds due the undersigned from the sale of shares in the aforesaid public
offering. If such net proceeds are less than the purchase price for such shares,
the undersigned agrees to deliver the difference to the Company prior to the
Closing.

                                  ____________________________ (Signature)

     Date:____________________

                                     -12-

<PAGE>

                                   EXHIBIT B

                                    CHARTER

                                     -13-<PAGE>

                                                                   EXHIBIT 10.12

[CONFIDENTIAL TREATMENT REQUESTED. CONFIDENTIAL PORTIONS OF THIS AGREEMENT HAVE
       BEEN REDACTED AND HAVE BEEN SEPARATELY FILED WITH THE COMMISSION.]

                                   AGREEMENT

Effective as of May 5, 2000 ("Effective Date"), THE BOARD OF TRUSTEES OF THE
LELAND STANFORD JUNIOR UNIVERSITY, a body having corporate powers under the laws
of the State of California ("STANFORD"), and Xenogen Corporation, a California
corporation, having a principal place of business at 860 Atlantic Avenue,
Alameda, CA  94501 ("LICENSEE"), agree as follows:

1.   BACKGROUND
---------------

1.1  STANFORD has an assignment of the invention entitled "Using Light to Detect
     and Track Pathogens in Living Hosts", from the laboratory of Dr.
     Christopher Contag ("Invention[s]"), as described in Stanford Docket S94-
     044, and any Licensed Patent(s), as hereinafter defined, which may issue to
     such Invention(s).

1.2  STANFORD desires to have the Invention(s) perfected and marketed at the
     earliest possible time in order that products resulting therefrom may be
     available for public use and benefit.

1.3  LICENSEE desires a license under said Invention(s), Licensed Materials and
     Licensed Patent(s) to develop, make, have made, use, import, offer for sale
     and sell Licensed Product(s) in the Licensed Field of Use, and/or to
     sublicense said Invention(s), Licensed Materials and Licensed Patent(s) in
     the Licensed Field of Use.

1.4  LICENSEE and STANFORD have a prior agreement and amendments to the prior
     agreement for Invention(s), Licensed Materials and Licensed Patent(s).  The
     parties acknowledge that pursuant to the prior agreement, (i) LICENSEE has
     paid to STANFORD a noncreditable, nonrefundable license issue royalty of
     *** Dollars (***), and (ii) LICENSEE has paid to STANFORD *** for
     reimbursement of past patent expenses.  The prior agreement and amendments
     are superseded by this Agreement.

1.5  The Invention(s) was made in the course of research supported by one or
     more of the following: the American Foundation for AIDS Research, the
     National Institutes of Health, The United States Public Health Service, and
     the Office of Naval Research.

2.   DEFINITIONS
----------------

2.1  "Licensed Patent(s)" means any (i) U.S. patent application Serial Number
     270,631 filed July 1, 1994 (issued on July 22, 1997 as U.S. Patent Number
     5,650,135), (ii) all divisions, substitutions, and continuations in whole
     or part of any of the preceding,  (iii) all foreign patent applications
     corresponding to or claiming priority from (including International
     Application Number PCT/US95/15040 and all national applications claiming
     priority therefrom), and (iv) all U.S. and foreign patents issuing on any
     of the preceding, including patents of addition, reexaminations, reissues
     and extensions.

*** Confidential treatment requested
<PAGE>

2.2  "Licensed Materials" means those biological materials listed in Exhibit A,
     and such other agreed materials as STANFORD may provide to LICENSEE during
     the term of this Agreement, which shall be added to Exhibit A.

2.3  "Licensed Product(s)" means any product or part thereof in the Licensed
     Field of Use, the manufacture, use, or sale of which:

          (a)  Is covered by a valid claim of an issued, unexpired Licensed
               Patent(s) directed to the Invention(s). A claim of an issued,
               unexpired Licensed Patent(s) shall be presumed to be valid unless
               and until it has been held to be invalid or unenforceable by a
               final judgment of a court of competent jurisdiction from which no
               appeal can be or is taken or is disclaimed, or rejected or found
               invalid or unenforceable in a reissue application or re-
               examination proceeding or otherwise;

          (b)  Is covered by any claim being prosecuted in a pending application
               directed to the Invention(s); or

          (c)  Incorporates any of the Licensed Materials.

2.4  "Net Sales" means the gross revenue derived by LICENSEE from Licensed
     Product(s), less the following items but only insofar as they actually
     pertain to the disposition of such Licensed Product(s) by LICENSEE, are
     included in such gross revenue, and are separately billed:

          (a)  Import, export, excise and sales taxes, and custom duties;

          (b)  Costs of insurance, packing, and transportation from the place of
               manufacture to the customer's premises or point of installation;

          (c)  Costs of installation at the place of use; and

          (d)  Credit for returns, allowances, or trades.

2.5  "Licensed Field of Use" means all uses.

2.6  "Licensed Territory" means worldwide.

2.7  "Exclusive" means that, subject to Article 4, STANFORD shall not grant
     further licenses in the Licensed Territory in the Licensed Field of Use.

3.   GRANT
----------

3.1  STANFORD hereby grants and LICENSEE hereby accepts an Exclusive license
     under the Licensed Patents and Licensed Materials to make, have made,
     import, use, lease, sell and offer for sale and otherwise commercialize and
     exploit Licensed Products in the Licensed Territory, and practice any
     method process or procedure within the Licensed Patents in the Licensed
     Territory.

3.2  Said license is Exclusive, including the right to sublicense pursuant to
     Article 13, in the Licensed Field of Use for a term commencing as of July
     1, 1997 and ending on the expiration of the last to expire of the Licensed
     Patent(s).

3.3  STANFORD shall have the right to practice the Invention(s) and use the
     Technology for its own bona fide research, including sponsored research and
     collaborations.  STANFORD shall have the right to publish any information
     included in Licensed Materials and Licensed Patent(s).

3.4  Not withstanding Section 3.1 above, the license granted to XENOGEN for
     those Licensed Materials which are ***, shall be non-exclusive.  This
     Section 3.4 shall have no effect on the Exclusive License granted herein
     for (i) the Licensed Patents and (ii) all Licensed Materials and/or
     Licensed Product(s) other than the ***.

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                                      -2-
<PAGE>

4.   GOVERNMENT RIGHTS
----------------------

This Agreement is subject to all of the terms and conditions of Title 35 United
States Code Sections 200 through 204, including an obligation that Licensed
Product(s) sold or produced in the United States be "manufactured substantially
in the United States," and LICENSEE agrees to take all reasonable action
necessary on its part as licensee to enable STANFORD to satisfy its obligation
thereunder, relating to Invention(s), provided that STANFORD has provided
LICENSEE with written notice of each such obligation STANFORD must meet and a
description of each act LICENSEE must take to comply with such obligation.

5.   DILIGENCE
--------------

5.1  As an inducement to STANFORD to enter into this Agreement, LICENSEE agrees
     to use all reasonable efforts and diligence to sublicense the Licensed
     Patent(s) and/or to proceed with the development, manufacture, and sale or
     lease of Licensed Product(s).  LICENSEE further agrees to diligently
     develop markets for the Licensed Patent(s) and/or Licensed Product(s).
     LICENSEE agrees that STANFORD may terminate this Agreement if, prior to
     July 1, 2000, LICENSEE has neither sublicensed the Licensed Patent(s) nor
     made a Licensed Product(s) available for commercial sale.  LICENSEE further
     agrees that STANFORD may terminate this Agreement if, for any period of ***
     after first sublicense or commercial sale, LICENSEE has neither maintained
     at least one sublicense in force nor sold any Licensed Product(s).

5.2  Progress Report - On or before September 1 of each year until LICENSEE
     ---------------
     markets a Licensed Product(s) or grants a sublicense under the Licensed
     Patent(s), LICENSEE shall make a written annual report to STANFORD covering
     the preceding year ending June 30, regarding the progress of LICENSEE
     toward commercial use of Licensed Product(s) or sublicensing of Licensed
     Patent(s).  Such report shall include, as a minimum, information sufficient
     to enable STANFORD to satisfy reporting requirements of the U.S. Government
     and for STANFORD to ascertain progress by LICENSEE toward meeting the
     diligence requirements of this Article 5.

5.3  In the event that LICENSEE fails to make available for commercial sale a
     Licensed Product based on a particular Licensed Material listed in Exhibit
     A for any period of *** after July 1, 2000, STANFORD may convert the
     Exclusive License granted to LICENSEE solely with respect to that
     particular Licensed Material (hereinafter, the "Uncommercialized Material")
     to a non-exclusive license, provided that STANFORD gives LICENSEE written
     notice of such intent and LICENSEE fails to commercialize the
     Uncommercialized Material within ninety (90) days of such notice.  STANFORD
     agrees that nothing in this Section 5.3 shall have any effect on the
     Exclusive License granted to LICENSEE under any Licensed Material(s) or
     Licensed Product(s) other than the Uncommercialized Material.  STANFORD
     further agrees that nothing in this Section 5.3 shall have any effect on
     the Exclusive License granted to LICENSEE under the Licensed Patent(s) in
     Article 3 herein.

6.   ROYALTIES
--------------

6.1  Beginning July 1, 2000, and each July 1 thereafter, LICENSEE shall pay to
     STANFORD a yearly royalty of ***.  Said yearly royalty payments are
     nonrefundable, but they are creditable against earned royalties to the
     extent provided in Paragraph 6.4.

6.2  In addition, LICENSEE shall pay STANFORD earned royalties of *** of Net
     Sales.

*** Confidential treatment requested

                                      -3-
<PAGE>

6.3  In the event that a Licensed Product is sold in combination with or
     containing one or more products or components, then Net Sales on the
     combination product shall be calculated using one of the following methods:

          (a)  By multiplying the net selling price of the combination product
               by the fraction A/A+B, where A is the gross selling price, during
               the royalty-paying period being considered, of the Licensed
               Product sold separately, and B is the gross selling price, during
               the royalty period in question, of the other products or
               components sold separately; or

          (b)  In the event that no such separate sales are made of the Licensed
               Product, Net Sales on the combination product for royalty
               determination shall be as reasonably allocated between such
               Licensed Product and the other active products or components,
               based on their relative importance and proprietary protection, as
               agreed by the parties. If the parties fail to reach agreement
               such allocation shall be submitted to binding arbitration.

6.4  Creditable payments under this Agreement shall be an offset to LICENSEE
     against up to *** of each earned royalty payment which LICENSEE would be
     required to pay pursuant to Paragraph 6.2 until the entire credit is
     exhausted.

6.5  If this Agreement is not terminated in accordance with other provisions
     hereof, LICENSEE's obligation to pay royalties hereunder shall continue for
     so long as LICENSEE, by its activities would, but for the license granted
     herein, infringe a valid claim of an unexpired Licensed Patent(s) of
     STANFORD covering said activity.

6.6  The royalty on sales in currencies other than U.S. Dollars shall be
     calculated using the appropriate foreign exchange rate for such currency
     quoted by the Bank of America (San Francisco) foreign exchange desk, on the
     close of business on the last banking day of each calendar quarter.
     Royalty payments to STANFORD shall be in U.S. Dollars.  All non-U.S. taxes
     related to royalty payments shall be paid by LICENSEE and are not
     deductible from the payments due STANFORD.

7.   ROYALTY REPORTS, PAYMENTS, AND ACCOUNTING
----------------------------------------------

7.1  Quarterly Earned Royalty Payment and Report - Beginning with the first sale
     -------------------------------------------
     of a Licensed Product(s) or the first sublicense, LICENSEE shall make
     written reports (even if there are no sales or sublicenses) and earned
     royalty payments to STANFORD within thirty (30) days after the end of each
     calendar quarter.  This report shall state the number, description, and
     aggregate Net Sales of Licensed Product(s) during such completed calendar
     quarter, and resulting calculation pursuant to Paragraph 6.2 of earned
     royalty payment due STANFORD for such completed calendar quarter.  The
     report shall also state the number and description of, and fees due under,
     sublicenses issued by Xenogen during such completed calendar quarter, and
     resulting calculation pursuant to Paragraph 13.5 of earned royalty payment
     due STANFORD for such completed calendar quarter.  Concurrent with the
     making of each such report, LICENSEE shall include payment due STANFORD of
     royalties for the calendar quarter covered by such report.

7.2  Accounting - LICENSEE agrees to keep and maintain records for a period of
     ----------
     three (3) years showing the sublicenses granted and the manufacture, sale,
     use, and other

*** Confidential treatment requested

                                      -4-
<PAGE>

     disposition of products sold or otherwise disposed of under the license
     herein granted. Such records will include general ledger records showing
     cash receipts and expenses, and records which include production records,
     customers, serial numbers, and related information in sufficient detail to
     enable the royalties payable hereunder by LICENSEE to be determined.
     LICENSEE further agrees to permit its books and records to be examined by
     STANFORD from time to time to the extent necessary to verify reports
     provided for in Paragraph 7.1. Such examination is to be made by STANFORD
     or its designee, at the expense of STANFORD, except in the event that the
     results of the audit reveal an underreporting of royalties due STANFORD of
     five percent (5%) or more, then the audit costs shall be paid by LICENSEE.

8.   NEGATION OF WARRANTIES
---------------------------
8.1  Nothing in this Agreement is or shall be construed as:

          (a)  A warranty or representation by STANFORD as to the validity or
               scope of any Licensed Patent(s);

          (b)  A warranty or representation that anything made, used, sold, or
               otherwise disposed of under any license granted in this Agreement
               is or will be free from infringement of patents, copyrights, and
               other rights of third parties;

          (c)  An obligation to bring or prosecute actions or suits against
               third parties for infringement, except to the extent and in the
               circumstances described in Article 12;

          (d)  Granting by implication, estoppel, or otherwise any licenses or
               rights under patents or other rights of STANFORD or other persons
               other than Licensed Patent(s), regardless of whether such patents
               or other rights are dominant or subordinate to any Licensed
               Patent(s); or

          (e)  An obligation to furnish any technology or technological
               information.

8.2  Except as expressly set forth in this Agreement, STANFORD MAKES NO
     REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESS OR
     IMPLIED.  THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY OR
     FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE LICENSED
     PRODUCT(S) WILL NOT INFRINGE ANY PATENT, COPYRIGHT, TRADEMARK, OR OTHER
     RIGHTS OR ANY OTHER EXPRESS OR IMPLIED WARRANTIES.

8.3  LICENSEE agrees that nothing in this Agreement grants LICENSEE any express
     or implied license or right under or to U.S. Patent 4,656,134
     "Amplification of Eucaryotic Genes" or any patent application corresponding
     thereto.

9.   INDEMNITY
--------------

9.1  LICENSEE agrees to indemnify, hold harmless, and defend STANFORD, Stanford
     Hospital and Clinics and Stanford Health Services and their respective
     trustees, officers, employees, students, and agents against any and all
     claims for death, illness, personal injury, property damage, and improper
     business practices arising out of the manufacture, use, sale, or other
     disposition of Invention(s), Licensed Patent(s), Licensed Product(s), or
     Licensed Materials by LICENSEE or sublicensee(s), or their customers.

9.2  STANFORD shall not be liable for any indirect, special, consequential or
     other damages whatsoever, whether grounded in tort (including negligence),
     strict liability, contract or

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                                      -5-
<PAGE>

     otherwise. STANFORD shall not have any responsibilities or liabilities
     whatsoever with respect to Licensed Products(s).

9.3  LICENSEE shall at all times comply, through insurance or self-insurance,
     with all statutory workers' compensation and employers' liability
     requirements covering any and all employees with respect to activities
     performed under this Agreement.

9.4  In addition to the foregoing, LICENSEE shall maintain, during the term of
     this Agreement, Comprehensive General Liability Insurance, including
     Products Liability Insurance, with reputable and financially secure
     insurance carrier(s) to cover the activities of LICENSEE and its
     sublicensee(s).  Commencing with the introduction of Licensed Product(s)
     into humans for any purpose, including clinical trials, such insurance
     shall provide minimum limits of liability of Five Million Dollars
     ($5,000,000) and shall include STANFORD, Stanford University Hospital,
     their trustees, directors, officers, employees, students, and agents as
     additional insureds.  Such insurance shall be written to cover claims
     incurred, discovered, manifested, or made during or after the expiration of
     this Agreement.  At STANFORD's request, LICENSEE shall furnish a
     Certificate of Insurance evidencing primary coverage and requiring thirty
     (30) days prior written notice of cancellation or material change to
     STANFORD.  LICENSEE shall advise STANFORD, in writing, that it maintains
     excess liability coverage (following form) over primary insurance for at
     least the minimum limits set forth above.  All such insurance of LICENSEE
     shall be primary coverage; insurance of STANFORD or Stanford Health
     Services shall be excess and noncontributory.

10.  MARKING
------------

10.1 Prior to the issuance of any patents on any Licensed Products, LICENSEE
     agrees to mark all Licensed Products (or their containers or labels)
     covered by such patents and made, sold, or otherwise disposed of by
     LICENSEE under the license granted in this Agreement with the words "Patent
     Pending," and following the issuance of one or more patents, with the
     numbers of such patent(s).

10.2 STANFORD agrees to provide LICENSEE with notice of all STANFORD patent
     applications filed (and all STANFORD patents issuing) on any Licensed
     Products based on Licensed Materials listed in Exhibit A within 30 days of
     (i) the filing of such patent applications, and (ii) issuance of such
     patents. No such notice is required from STANFORD to LICENSEE for patents
     and patent applications that are included in the Licensed Patent(s).

11.  STANFORD NAMES AND MARKS
-----------------------------

Except in connection with the identification of the source of Invention(s),
Licensed Patent(s) and Licensed Products(s), LICENSEE agrees not to identify
STANFORD in any promotional advertising or other promotional materials to be
disseminated to the public or any portion thereof or to use the name of any
STANFORD faculty member, employee, or student or any trademark, service mark,
trade name, or symbol of STANFORD or the Stanford Health Services, or that is
associated with either of them, without STANFORD's prior written consent.
Notwithstanding the above, LICENSEE may use in any manner it deems fit the
name(s) of STANFORD faculty members or employees who are inventors on the
Inventions, Licensed Patents and/or Licensed Products, and who are employees of
or have a consulting agreement with LICENSEE ("Affiliates"), provided that
LICENSEE obtains the voluntary consent of the Affiliates for such

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                                      -6-
<PAGE>

use. STANFORD agrees that the names of the Affiliates and Affiliates' connection
with STANFORD will appear in disclosure documents required by securities laws,
and in other regulatory and administrative filings in the ordinary course of
LICENSEE'S business. Any use of STANFORD's name shall be limited to statements
of fact and shall not imply endorsement of LICENSEE's products or services.

12.  PATENT PROTECTION AND INFRINGEMENT
---------------------------------------

12.1 LICENSEE shall have the primary responsibility for the prosecution, filing
     and maintenance of all Licensed Patents, including the conduct of all
     interference, opposition, nullity and revocation proceedings, using counsel
     of its choice; provided, however, that STANFORD shall have reasonable
     opportunity to advise and consult with LICENSEE on such matters and may
     instruct LICENSEE to take such action as STANFORD reasonably believes
     necessary to protect the Licensed Patent(s).  Should LICENSEE elect to
     abandon any patent or patent application in any country, it shall give
     timely notice to STANFORD, who may continue prosecution or maintenance, at
     its sole expense and LICENSEE shall have not further rights with respect to
     such patent application or patent in such country.  In the event that a
     conflict arises with respect to patent counsel selected by LICENSEE,
     STANFORD may, with just cause and after consulting with LICENSEE, select
     new patent counsel reasonably acceptable to LICENSEE.

12.2 Payment of all reasonable fees and costs relating to the filing,
     prosecution and maintenance of all patent applications and patents within
     the Licensed Patent(s), including interference and/or opposition, nullity
     and revocation proceedings, shall be the responsibility of LICENSEE.
     STANFORD shall direct the patent counsel to send invoices for such fees and
     costs directly to LICENSEE with a copy to STANFORD, and LICENSEE shall pay
     such patent counsel directly amounts due.

12.3 STANFORD shall promptly inform LICENSEE of any suspected infringement of
     any Licensed Patent by a third party and any declaratory judgment filed
     with respect to any Licensed Patent.  LICENSEE shall have the initial right
     but not the obligation, at its expense, to initiate and control any
     proceeding relating to any infringement by a third party of any Licensed
     Patents, any declaratory action alleging invalidity or noninfringement of
     any Licensed Patents, or any interference, opposition, nullity or
     revocation proceeding relating to any Licensed Patents ("a Protective
     Action").  In pursuing any such Protective Action, LICENSEE shall provide
     STANFORD with material information related to the Protective Action, and
     shall have the right, but not the obligation, to join STANFORD as a party
     to the Protective Action, at LICENSEE's expense.  STANFORD shall have the
     right to participate in the Protective Action with its own counsel at its
     own expense.  If LICENSEE brings a Protective Action it may  enter into a
     settlement, consent judgment or other voluntary final disposition of such
     Protective Action, at its sole option, and any damages recovered by a
     Protective Action shall be used first to reimburse LICENSEE for the costs
     (including attorney's and expert fees) of such Protective Action actually
     paid by LICENSEE, and the remainder, if any, shall be retained by LICENSEE,
     except LICENSEE shall pay STANFORD two percent (2%) of said remainder,
     provided, if STANFORD joins in any Protective Action at its inception and
     shares equally in the costs (including attorney's and expert fees) incurred
     in its

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                                      -7-
<PAGE>

     conduct, in the event of any recovery each party shall be reimbursed for
     its expenses incurred in such Protective Action and STANFORD and LICENSEE
     shall equally share any remainder.

12.4 If LICENSEE, or its sublicensee pursuant to Section 13.6, decides not to
     bring a Protective Action after LICENSEE receives notice from STANFORD
     pursuant to Section 12.3, LICENSEE shall inform STANFORD and STANFORD may
     institute a Protective Action.  In such event, STANFORD shall control such
     Protective Action, including any settlement, consent judgment or other
     voluntary final disposition thereof at its sole option, and shall bear the
     entire cost of such Protective Action and shall be entitled to retain the
     entire amount of any recovery or settlement.  STANFORD may, at its expense,
     join LICENSEE as a party to such a Protective Action and LICENSEE shall
     cooperate reasonably with STANFORD in any such Protective Action, at
     STANFORD's expense.

12.5 Should either party commence a Protective Action under this Section 12 and
     thereafter elect to abandon the same, it shall give timely notice to the
     other party who may continue prosecution of such Protective Action;
     provided, however, that the sharing of past and future expenses and any
     recovery in such Protective Action shall be as mutually agreed by the
     parties.

12.6 In any Protective Action under this Section 12, the other party hereto
     shall, at the request and expense of the party initiating such Protective
     Action, cooperate in all respects and, to the extent possible, have its
     employees testify when requested and make available relevant records,
     papers, information, samples and the like.

13.  SUBLICENSE(S)
------------------

13.1 LICENSEE may grant sublicense(s) during the Exclusive period.  LICENSEE
     may sublicense all or a portion of the rights granted to it pursuant to
     this Agreement, subject to the conditions of this Article 13.  A "Patent
     Sublicense" means a sublicense which grants all or a portion of the rights
     under the Licensed Patent(s) to practice any method, process or procedure
     claimed therein in all or a part of the Licensed Territory.  It is
     understood that a Patent Sublicense shall not grant any rights to lease,
     sublicense, sell, offer for sale, or otherwise commercially dispose of any
     Licensed Products in any part of the Licensed Territory.  A "Products
     Sublicense" means a sublicense which grants all or a portion of the rights
     to lease, sell, offer for sale and otherwise commercially exploit Licensed
     Products in all or a part of the Licensed Territory.  It is understood that
     a Products Sublicense may also include rights under the Licensed Patent(s).

13.2 If LICENSEE is unable or unwilling to serve or develop a potential market
     or market territory for which there is a willing sublicensee(s), LICENSEE
     will, at STANFORD's request, negotiate in good faith a sublicense(s)
     hereunder.

13.3 Any sublicense(s) granted by LICENSEE under this Agreement shall be
     subject and subordinate to terms and conditions of this Agreement, except:

          (a)  Sublicense terms and conditions shall reflect that any
               sublicensee(s) shall not further sublicense without the written
               consent of STANFORD, which consent shall not be unreasonably
               withheld; and

          (b)  The earned royalty rate specified in the sublicense(s) may be at
               higher rates

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               than the rates in this Agreement

     Such sublicense(s) (including, without limitation, any non-exclusive
     sublicenses) shall remain in effect in the event of any termination of this
     Agreement, provided that upon request by STANFORD, such sublicensee agrees
     in writing to be bound by the applicable terms of this Agreement.  All
     Products Sublicenses shall expressly include the provisions of Articles 7,
     8, and 9 for the benefit of STANFORD.  All Patent Sublicenses granted to
     commercial or for-profit entities shall expressly include the provisions of
     Articles 8 and 9 for the benefit of STANFORD.

13.4 LICENSEE agrees to provide STANFORD a copy of any sublicense granted
     pursuant to this Article 13.

13.5 LICENSEE will pay to STANFORD *** of all non-equity payments received by
     LICENSEE from its sublicensee(s) for the grant of a sublicense to practice
     the Licensed Patent(s), excluding those made under consulting or service
     agreements.  In addition, LICENSEE shall pay to STANFORD *** of all earned
     royalty income received by LICENSEE from each sublicense from the sale of
     Licensed Product(s); provided however, that LICENSEE shall pay to STANFORD
     no less than *** and no more than *** of such royalty income.

13.6 With the prior written consent of LICENSEE, and the prior written consent
     of STANFORD, which shall not be unreasonably withheld, a sublicensee may
     bring a Protective Action, subject to the provisions of Section 12.3.

14.  TERMINATION
----------------

14.1 LICENSEE may terminate this Agreement by giving STANFORD notice in writing
     at least thirty (30) days in advance of the effective date of termination
     selected by LICENSEE.

14.2 STANFORD may terminate this Agreement if LICENSEE:

          (a)  Is in default in payment of royalty or providing of reports;

          (b)  Is in breach of any provision hereof; or

          (c)  Provides any false report;

     and LICENSEE fails to remedy any such default, breach, or false report
     within thirty (30) days after written notice thereof by STANFORD.

14.3 In the event of any termination of this Agreement, LICENSEE shall provide
     for the transfer to STANFORD of all obligations accrued or accruable after
     such termination in any active sublicense(s) issued pursuant to Section 13.
     Such obligations shall include the payment of any royalties specified in
     such sublicense(s) that have accrued after termination of this Agreement.

14.4 Surviving any termination are:

          (a)  LICENSEE's obligation to pay royalties accrued or accruable;

          (b)  Any cause of action or claim of LICENSEE or STANFORD, accrued or
               to accrue, because of any breach or default by the other party;
               and

          (c)  The provisions of Articles 7, 8, 9, 16 and 20, Sections 13.3,
               14.3, and 14.4 and any other provisions that by their nature are
               intended to survive.

15.  ASSIGNMENT
---------------

Neither party may assign this Agreement or any part hereof without the express
written consent of the other, which consent shall not be unreasonably withheld;
provided, however, LICENSEE

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may assign this Agreement or any portion hereof to an affiliate or to a
successor of all or substantially all its business relating to the Licensed
Patent(s) without the written consent of STANFORD and shall provide STANFORD
notice of any such assignment.

16.  ARBITRATION
----------------

16.1 Any controversy arising under or related to this Agreement, and any
     disputed claim by either party against the other under this Agreement
     excluding any dispute relating to patent validity or infringement arising
     under this Agreement, shall be settled by arbitration in accordance with
     the Licensing Agreement Arbitration Rules of the American Arbitration
     Association.

16.2 Upon request by either party, arbitration will be by a third party
     arbitrator mutually agreed upon in writing by LICENSEE and STANFORD within
     thirty (30) days of such arbitration request.  Judgment upon the award
     rendered by the arbitrator shall be final and nonappealable and may be
     entered in any court having jurisdiction thereof.

16.3 The parties shall be entitled to discovery in like manner as if the
     arbitration were a civil suit in the California Superior Court.  The
     Arbitrator may limit the scope, time and/or issues involved in discovery.

16.4 Any arbitration shall be held at Stanford, California, unless the parties
     hereto mutually agree in writing to another place.

17.  NOTICES
------------

All notices under this Agreement shall be deemed to have been fully given when
done in writing and deposited in the United States mail, registered or
certified, and addressed as follows:

               To STANFORD:   Office of Technology Licensing
                              Stanford University
                              900 Welch Road, Suite 350
                              Palo Alto, CA 94304-1850

                              Attention:  Director

               To LICENSEE:   Xenogen Corporation
                              860 Atlantic Avenue
                              Alameda, CA 94501

                              Attention:  President

Either party may change its address upon written notice to the other party.

18.  WAIVER
-----------

None of the terms of this Agreement can be waived except by the written consent
of the party waiving compliance.

19.  APPLICABLE LAW
-------------------

This Agreement shall be governed by the laws of the State of California
applicable to agreements negotiated, executed and performed wholly within
California.

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20.  CONFIDENTIALITY
--------------------

STANFORD shall maintain this Agreement and the reports and any information
provided by LICENSEE to STANFORD pursuant to Articles 5, 7 and 13 in confidence
and shall be treated with at least the same degree of care as used to maintain
secrecy of STANFORD's other confidential information.  STANFORD may, however,
disclose to third parties total annual royalty payments and general statistical
information regarding payments made hereunder in the context of disclosing
statistical information pertaining to the performance of the STANFORD Office of
Technology Licensing.

21.  Entire Agreement
---------------------

This Agreement constitutes the entire agreement between LICENSEE and STANFORD
and supersedes all prior communications, understandings and agreements with
respect to the subject matter of this Agreement.  This Agreement may not be
amended except with a written agreement signed by LICENSEE and STANFORD.

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          IN WITNESS WHEREOF, the parties hereto have executed this Agreement in
duplicate originals by their duly authorized officers or representatives.

          THE BOARD OF TRUSTEES OF THE LELAND
          STANFORD JUNIOR UNIVERSITY

          Signature /s/ Katharine Ku
                   --------------------------
          Name  Katharine Ku
              -------------------------------
          Title Director
               ------------------------------
          Date  Technology License
              -------------------------------

          LICENSEE

          Signature /s/ David W. Carter
                   --------------------------
          Name      David W. Carter
              -------------------------------
          Title     Chairman and Co-CEO
               ------------------------------
          Date
              -------------------------------

Exhibit A:  Licensed Materials

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                                   Exhibit A

                                      ***

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