Document:

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                                                                    EXHIBIT 10.9

THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED, OR ANY STATE SECURITIES LAWS. THEY MAY NOT BE SOLD OR OFFERED FOR SALE
IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO THE SECURITIES UNDER
SAID ACT AND ANY APPLICABLE STATE SECURITIES LAWS OR THE AVAILABILITY OF AN
EXEMPTION FROM REGISTRATION UNDER SAID ACT AND ANY APPLICABLE STATE SECURITIES
LAWS.

                                      No.
                          STOCK SUBSCRIPTION WARRANT

                          To Purchase Common Stock of

                      XENOGEN CORPORATION (the "Company")

                   DATE OF INITIAL ISSUANCE: August 14, 1998

     THIS CERTIFIES THAT for value received, TRANSAMERICA BUSINESS CREDIT
CORPORATION or its registered assigns (hereinafter called the "Holder") is
entitled to purchase from the Company, at any time during the Term of this
Warrant, Seventy Six Thousand Nine Hundred Twenty-Three (76,923) shares of
common stock, no par value, of the Company (the "Common Stock"), at the Warrant
Price, payable as provided herein. The exercise of this Warrant shall be subject
to the provisions, limitations and restrictions herein contained, and may be
exercised in whole or in part.

SECTION 1. Definitions.
           -----------
     For all purposes of this Warrant, the following terms shall have the
meanings indicated:

     Common Stock - shall mean and include the Company's authorized Common
     ------------
Stock, no par value, as constituted at the date hereof.

     Exchange Act - shall mean the Securities Exchange Act of 1934, as amended
     ------------
from time to time.

     Securities Act. - the Securities Act of 1933, as amended.
     --------------

     Term of this Warrant - shall mean the period beginning on the date of
     --------------------
initial issuance hereof and ending on August 14, 2005.

     Warrants Price - $1.30 per share, subject to adjustment in accordance with
     --------------
Section 5 hereof.

     Warrant - this Warrant and any other Warrant or Warrants issued in
     -------
connection with a Commitment Letter dated July 17, 1998 executed by the Company
and Transamerica Business Credit Corporation (the "Commitment Letter") to the
original holder of this Warrant, or any transferees from such original holder or
this Holder.

     Warrant Shares - shares of Common Stock purchased or purchasable by the
     --------------
Holder of this Warrant upon the exercise hereof.
<PAGE>

SECTION 2. Exercise of Warrant.
           -------------------

     2.1.   Procedure for Exercise of Warrant.  To exercise this Warrant in
            ---------------------------------
whole or in part (but not as to any fractional share of Common Stock), the
Holder shall deliver to the Company as its office referred to in Section 12
hereof at any time and from time to time during the Term of this Warrant: (i)
the Notice of Exercise in the form attached hereto, (ii) cash, certified or
official bank check payable to the order of the Company, wire transfer of funds
to the Company's account, or evidence of any indebtedness of the Company to the
Holder (or any combination of any of the foregoing) in the amount of the Warrant
Price for each share being purchased, and (iii) this Warrant. Notwithstanding
any provisions herein to the contrary, if the Current Market Price (as defined
in Section 5) is greater than the Warrant Price (at the date of calculation, as
set forth below), in lieu of exercising this Warrant as hereinabove permitted,
the Holder may elect to receive shares of Common Stock equal to the value (as
determined below) of this Warrant (or the portion thereof being canceled) by
surrender of this Warrant at the office of the Company referred to in Section 12
hereof, together with the Notice of Exercise, in which event the Company shall
issue to the Holder that number of shares of Common Stock computed using the
following formula:

                              CS - WCS % (CMP-WP)
                                   --------------
                                      CMP

Where

     CS        equals the number of shares of Common Stock to be issued to the
               Holder

     WCS       equals the number of shares of Common Stock purchasable under the
               Warrant or, if only a portion of the Warrant is being exercised,
               the portion of the Warrant being exercised (at the date of such
               calculation)

     CMP       equals the Current Market Price (at the date of such calculation)

     WP        equals the Warrant Price (as adjusted to the date of such
               calculation)

In the event of any exercise of the rights represented by this Warrant, a
certificate or certificates for the shares of Common Stock so purchased,
registered in the name of the Holder or such other name or names as may be
designated by the Holder, shall be delivered to the Holder hereof within a
reasonable time, not exceeding fifteen (15) days, after the rights represented
by this Warrant shall have been so exercised; and, unless this Warrant has
expired, a new Warrant representing the number of shares (except a remaining
fractional share), if any, with respect to which this Warrant shall not then
have been exercised shall also be issued to the Holder hereof within such time.
The person in whose name any certificate for shares of Common Stock is issued
upon exercise of this Warrant shall for all purposes be deemed to have become
the holder of record of such shares on the date on which the Warrant was
surrendered and payment of the Warrant Price and any applicable taxes was made,
irrespective of the date of delivery of such certificate, except that, if the
date of such surrender and payment is a date when the stock transfer books of
the Company are closed, such person shall be deemed to have become
the holder of such shares at the close of business on the next succeeding date
on which the stock transfer books are open.

     2.2    Transfer Restriction Legend.  Each certificate for Warrant Shares
            ---------------------------
shall bear the following legend (and any additional legend required by (i) any
applicable state securities laws and (ii)

                                      -2-
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any securities exchange upon which such Warrant Shares may, at the time of such
exercise, be listed) on the face thereof unless at the time of exercise such
Warrant Shares shall be registered under the Securities Act:

       "The shares represented by this certificate have not been
       registered under the Securities Act of 1933, as amended,
       and may not be sold or transferred in the absence of such
       registration or an exemption therefrom under said Act."

Any certificate issued at any time in exchange or substitution for any
certificate bearing such legend (except a new certificate issued upon completion
of a public distribution under a registration statement of the securities
represented thereby) shall also bear such legend unless, in the opinion of
counsel for the holder thereof (which counsel shall be reasonably satisfactory
to counsel for the Company) the securities represented thereby are not, at such
time, required by law to bear such legend.

SECTION 3. Coverage as to Common Stock. The Company covenants and agrees that
           ---------------------------
all shares of Common Stock that may be issued upon the exercise of the rights
represented by this Warrant will,  upon issuance, be validly issued, fully paid
and nonassessable, and free from all taxes, liens and charges with respect to
the issue thereof. The Company further covenants and agrees that it will pay
when due and payable any and all federal and state taxes which may be payable in
respect of the issue of this Warrant or any Common Stock or certificates
therefor issuable upon the exercise of this Warrant. The Company further
covenants and agrees that the Company will at all times have authorized and
reserved, free from preemptive rights, a sufficient number of shares of Common
Stock to provide for the exercise of the rights represented by this Warrant. The
Company further covenants and agrees that if any shares of capital stock to be
reserved for the purpose of the issuance of shares upon the exercise of this
Warrant require registration with or approval of any governmental authority
under any federal or state law before such shares may be validly issued or
delivered upon exercise, then the Company will in good faith and as
expeditiously as possible endeavor to secure such registration or approval, as
the case may be. If and so long as the Common Stock issuable upon the exercise
of this Warrant is listed on any national securities exchange, the Company will,
if permitted by the rules of such exchange, list and keep listed on such
exchange, upon official notice of issuance, all shares of such Common Stock
issuable upon exercise of this Warrant.

SECTION 4. Adjustment of Number of Shares. Upon each adjustment of the Warrant
           ------------------------------
Price as provided in Section 5, the Holder shall thereafter be entitled to
purchase, at the Warrant Price resulting from such adjustment, the number of
shares (calculated to the nearest tenth of a share) obtained by multiplying the
Warrant Price in effect immediately prior to such adjustment by the number of
shares purchasable pursuant hereto immediately prior to such adjustment and
dividing the product thereof by the Warrant Price resulting from such
adjustment.

SECTION 5. Adjustment of Warrant Price. The Warrant Price shall be subject to
           ---------------------------
adjustment from time to time as follows:

     (i) If, at any time during the Term of this warrant, the number of shares
of Common Stock outstanding is increased by a stock dividend payable in shares
of Common Stock or by a subdivision or split-up of shares of Common Stock, then,
following the record date fixed for the determination of holders of Common Stock
entitled to receive such stock dividend, subdivision or split-up, the Warrant
Price shall be appropriately decreased so that the number of shares of Common
Stock issuable upon the exercise hereof shall be increased in proportion to such
increase in outstanding shares.

                                      -3-

<PAGE>

     (ii)  If, at any time during the Term of this Warrant, the number of shares
of Common Stock outstanding is decreased by a combination of the outstanding
shares of Common Stock, then, following the record date for such combination,
the Warrant Price shall appropriately increase so that the number of shares of
Common Stock issuable upon the exercise hereof shall be decreased in proportion
to such decrease in outstanding shares.

     (iii) In case, at any time during the Term of this Warrant, the Company
shall declare a cash dividend upon its Common Stock payable otherwise than out
of earnings or earned surplus or shall distribute to holders of its Common Stock
shares of its capital stock (other than Common Stock), stock or assets
(excluding cash dividends and distributions) or options or rights (excluding
options to purchase and rights to subscribe for Common Stock or other securities
of the Company convertible into or exchangeable for Common Stock), then, in each
such case, immediately following the record date fixed for the determination of
the holders of Common Stock entitled to receive such dividend or distribution,
the Warrant Price in effect thereafter shall be determined by multiplying the
Warrant Price in effect immediately prior to such record date by a fraction of
which the numerator shall be an amount equal to the difference of (x) the
Current Market Price of one share of Common Stock minus (y) the fair market
value (as determined by the Board of Directors of the Company, whose
determination shall be conclusive) of the stock, securities, evidences of
indebtedness, assets, options or rights so distributed in respect of one share
of Common Stock, and of which the denominator shall be such Current Market
Price.

     (iv)  All calculations under this Section 5 shall be made to the nearest
cent or to the nearest one-tenth (1/10) of a share, as the case may be.

     (v)   For the purpose of any computation pursuant to this Section 5, the
Current Market Price at any date of one share of Common Stock shall be deemed to
be the average of the daily closing prices for the 15 consecutive business days
ending on the last business day before the day in question (as adjusted for any
stock dividend, split, combination or reclassification that took effect during
such 15 business day period). The closing price for each day shall be the last
reported sales price regular way or, in case no such reported sales took place
on such day, the average of the last reported bid and asked prices regular way,
in either case on the principal national securities exchange on which the Common
Stock is listed or admitted to trading or as reported by Nasdaq (or if the
Common Stock is not at the time listed or admitted for trading on any such
exchange or if prices of the Common Stock are not reported by Nasdaq then such
price shall be equal to the average of the last reported bid and asked prices on
such day as reported by The National Quotation Bureau Incorporated or any
similar reputable quotation and reporting service, if such quotation is not
reported by The National Quotation Bureau Incorporated); provided, however, that
if the Common Stock is not traded in such manner that the quotations referred to
in this clause (v) are available for the period required hereunder, the Current
Market Price shall be determined in good faith by the Board of Directors of the
Company or, if such determination cannot be made, by a nationally recognized
independent investment banking firm selected by the Board of Directors of the
Company (or if such selection cannot be made, by a nationally recognized
independent investment banking firm selected by the American Arbitration
Association in accordance with its rules).

     (vi)  Whenever the Warrant Price shall be adjusted as provided in Section
5, the Company shall prepare a statement showing the facts requiring such
adjustment and the Warrant Price that shall be in effect after such adjustment.
The Company shall cause a copy of such statement to be sent by mail, first

                                      -4-
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class postage prepaid, to each Holder of this Warrant at its, his or her address
appearing on the Comany's records. Where appropriate, such copy may be given in
advance and may be included as part of the notice required to be mailed under
the provisions of subsection (viii) of this Section 5.

     (vii)   Adjustments made pursuant to clauses (i), (ii) and (iii) above
shall be made on the date such dividend, subdivision, split-up, combination or
distribution, as the case may be, is made, and shall become effective at the
opening of business on the business day next following the record date for the
determination of stockholders entitled to such dividend, subdivision, split-up,
combination or distribution.

     (viii)  In the event the Company shall propose to take any action of the
types described in clauses (i), (ii), or (iii) of this Section 5, the Company
shall forward, at the same time and in the same manner, to the Holder of this
Warrant such notice, if any, which the Company shall give to the holders of
capital stock of the Company.

     (ix)    In any case in which the provisions of this Section 5 shall require
that an adjustment shall become effective immediately after a record date for an
event, the Company may defer until the occurrence of such event issuing to the
Holder of all or any part of this Warrant which is exercised after such record
date and before the occurrence of such event the additional shares of capital
stock issuable upon such exercise by reason of the adjustment required by such
event over and above the shares of capital stock issuable upon such exercise
before giving effect to such adjustment exercise; provided, however, that the
Company shall deliver to such Holder a due bill or other appropriate instrument
evidencing such Holder's right to receive such additional shares upon the
occurrence of the event requiring such adjustment.

SECTION 6. Ownership.
           ---------

     6.1. Ownership of This Warrant. The Company may deem and treat the person
          -------------------------
in whose name this Warrant is registered as the holder and owner hereof
(notwithstanding any notations of ownership or writing hereon made by anyone
other than the Company) for all purposes and shall not be affected by any notice
to the contrary until presentation of this Warrant for registration of transfer
as provided in this Section 6.

     6.2  Transfer and Replacement. This Warrant and all rights hereunder are
          ------------------------
transferable in whole or in part upon the books of the Company by the Holder
hereof in person or by duly authorized attorney, and a new Warrant or Warrants,
of the same tenor as this Warrant but registered in the name of the transferee
or transferees (and in the name of the Holder, if a partial transfer is
effected) shall be made and delivered by the Company upon surrender of this
Warrant duly endorsed, at the office of the Company referred to in Section 12
hereof. Upon receipt by the Company of evidence reasonably satisfactory to it of
the loss, theft or destruction, and, in such case, of indemnity or security
reasonably satisfactory to it, and upon surrender of this Warrant if mutilated,
the Company will make and deliver a new Warrant of like tenor, in lieu of this
Warrant; provided that if the Holder hereof is an instrumentality of a state or
local government or an institutional holder or a nominee for such an
instrumentality or institutional holder an irrevocable agreement of indemnity by
such Holder shall be sufficient for all purposes of this Section 6, and no
evidence of loss or theft or destruction shall be necessary. This Warrant shall
be promptly cancelled by the Company upon the surrender hereof in connection
with any transfer or replacement. Except as otherwise provided above, in the
case of the loss, theft or destruction of a Warrant, the Company shall pay all
expenses, taxes and other charges payable in connection with any transfer or
replacement of this Warrant, other than stock tranfer taxes (if any) payable in
connection

                                      -5-

<PAGE>

with a transfer of this Warrant, which shall be payable by the Holder. Holder
will not transfer this Warrant and the rights hereunder except in compliance
with federal and state securities laws.

SECTION 7. Mergers, Consolidation, Sales. In the case of any proposed
           -----------------------------
consolidation or merger of the Company with another entity, or the proposed sale
of all or substantially all of its assets to another person or entity, or any
proposed reorganization or reclassification of the capital stock of the Company,
then, as a condition of such consolidation, merger, sale, reorganization or
reclassification, lawful and adequate provision shall be made whereby the Holder
of this Warrant shall thereafter have the right to receive upon the basis and
upon the terms and conditions specified herein, in lieu of the shares of the
Common Stock of the Company immediately theretofore purchasable hereunder, such
shares of stock, securities or assets as may (by virtue of such consolidation,
merger, sale, reorganization or reclassification) be issued or payable with
respect to or in exchange for the number of shares of such Common Stock
purchasable hereunder immediately before such consolidation, merger, sale,
reorganization or reclassification. In any such case appropriate provision shall
be made with respect to the rights and interests of the Holder of this Warrant
to the end that the provisions hereof shall thereafter be applicable as nearly
as may be, in relation to any shares of stock, securities or assets thereafter
deliverable upon the exercise of this Warrant.

SECTION 8. Notice of Dissolution or Liquidation. In case of distribution of the
           ------------------------------------
assets of the Company in dissolution or liquidation (except under circumstances
when the foregoing Section 7 shall be applicable), the Company shall give notice
thereof to the Holder hereof and shall make no distribution to shareholders
until the expiration of thirty (30) days from the date of mailing of the
aforesaid notice and, in any case, the Holder hereof may exercise this Warrant
within thirty (30) days from the date of the giving of such notice, and all
rights herein granted not so exercised within such thirty-day period shall
thereafter become null and void.

SECTION 9. Notice of Extraordinary Dividends. If the Board of Directors of the
           ---------------------------------
Company shall declare any dividend or other distribution on its Common Stock
except out of earned surplus or by way of a stock dividend payable in shares of
its Common Stock, the Company shall mail notice thereof to the Holder hereof not
less than thirty (30) days prior to the record date fixed for determining
shareholders entitled to participate in such dividend or other distribution, and
the Holder hereof shall not participates in such dividend or other distribution
unless this Warrant is exercised prior to such record date. The provisions of
this Section 9 shall not apply to distributions made in connection with
transactions covered by Section 7.

SECTION 10. Fractional Shares. Fractional shares shall not be issued upon the
            -----------------
exercise of this Warrant but in any case where the Holder would, except for the
provisions of this Section 10, be entitled under the terms hereof to receive a
fractional share upon the complete exercise of this Warrant, the Company shall,
upon the exercise of this Warrant for the largest number of whole shares then
called for, pay a sum in cash equal to the excess of the value of such
fractional share (determined in such reasonable manner as may be prescribed in
good faith by the Board of Directors of the Company) over the Warrant Price for
such fractional share.

SECTION 11. Special Arrangements of the Company. The Company covenants and
            -----------------------------------
agrees that during the Term of this Warrant, unless otherwise approved by the
Holder of this Warrant:

                                      -6-

<PAGE>

     11.1.   Will Reserve Shares. The Company will reserve and set apart and
             -------------------
have available for issuance at all times, free from preemptive or other
preferential rights, the number of shares of authorized but unissued Common
Stock deliverable upon the exercise of this Warrant.

     11.2.   Will Not Amend Certificate.  The Company will not amend its
             --------------------------
Certificate of Incorporation to eliminate as an authorized class of capital
stock that class denominated as "Common Stock" on the date hereof.

     11.3.   Will Bind Successors.  This Warrant shall be binding upon any
             --------------------
corporation or other person or equity succeeding to the Company by merger,
consolidation or acquisition of all or substantially all of the Company's
assets.

SECTION 12.  Notices.  Any notice or other document required or permitted to be
             -------
given or delivered to the Holder shall be delivered at, or sent by certified or
registered mail to, the Holder at Transamerica Technology Finance Division, 76
Batterson Park Road, Farmington, Connecticut 06032, Attention: Assistant Vice
President, Lease Administration, with a copy to the Lender at Riverway II, West
Office Tower, 9399 West Higgins Road, Rosemont, Illinois 60018, Attention: Legal
Department or to such other address as shall have been furnished to the Company
in writing by the Holder.  Any notice or other document required or permitted to
be given or delivered to the Company shall be delivered at, or sent by certified
or registered mail to, the Company at 860 Atlantic Avenue, Alameda, California,
94501, Attention: Chairman or to such other address as shall have been furnished
in writing to the Holder by the Company. Any notice so addressed and mailed by
registered or certified mail shall be deemed to be given when so mailed. Any
notice so addressed and otherwise delivered shall be deemed to be given when so
mailed. Any notice so addressed and otherwise delivered shall be deemed to be
given when actually received by the addressee.

SECTION 13.  No Rights as Stockholder; Limitation of Liability.  This Warrant
             -------------------------------------------------
shall not entitle the Holder to any of the rights of a shareholder of the
Company except upon exercise in accordance with the terms hereof.  No provision
hereof, in the absence of affirmative action by the Holder to purchase shares
of Common Stock, and no mere enumeration herein of the rights or privileges of
the Holder, shall give rise to any liability of the Holder for the Warrant Price
hereunder or as a shareholder of the Company, whether such liability is asserted
by the Company or by creditors of the Company.

SECTION 14.  Law Governing.  THE VALIDITY, INTERPRETATION, AND ENFORCEMENT OF
             -------------
THIS WARRANT SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF
THE STATE OF ILLINOIS WITHOUT GIVING EFFECT TO THE CONFLICT OF LAW PRINCIPLES
THEREOF.

SECTION 15.  Miscellaneous.  This Warrant and any provision hereof may be
             -------------
changed, waived, discharged or terminated only by an instrument in writing
signed by both parties (or any respective predecessor in interest thereof). The
headings in this Warrant are for purposes of reference only and shall not affect
the meaning or construction of any of the provision hereof

                                      -7-

<PAGE>

     IN WITNESS WHEREOF, the Company has caused this Warrant to be signed by its
duly authorized officer this 13th day of August, 1998.

                                             XENOGEN CORPORATION
[CORPORATE SEAL]
                                             By: /s/ Pamela Reilly Contag
                                                ----------------------------
                                             Title:  President/Co-CEO

                                      -8-
<PAGE>

                          FORM OF NOTICE OF EXERCISE

               [To be signed only upon exercise of the Warrant]

                    TO BE EXECUTED BY THE REGISTERED HOLDER
                        TO EXERCISE THE WITHIN WARRANT

     The undersigned hereby exercise the right to purchase ___________ shares of
Common Stock which the undersigned is entitled to purchase by the terms of the
within Warrant according to the conditions thereof, and herewith

[check one]
                              [_]  makes payment of $________ therefor; or

                              [_]  directs the Company to issue _______ shares,
                                   and to withhold ______ shares in lieu of
                                   payment of the Warrant Price, as described in
                                   Section 2.1 of the Warrant.

All shares to be issued pursuant hereto shall be issued in the name of and the
initial address of such person to be entered on the books of the Company shall
be:

     The shares are to be issued in certificates of the following denominations:

                                        ______________________________

                                        [Type Name of Holder]

                                        By:___________________________

                                        Title:________________________

Dated:____________________

                                      -9-
<PAGE>

                              FORM OF ASSIGNMENT
                                   (ENTIRE)

              [To be signed only upon transfer of entire Warrant]

                    TO BE EXECUTED BY THE REGISTERED HOLDER
                        TO TRANSFER THE WITHIN WARRANT

     FOR VALUE RECEIVED ________________hereby sells, assigns and transfers unto
________________all rights of the undersigned under and pursuant to the within
Warrant, and the undersigned does hereby irrevocably constitute and appoint
________________ Attorney to transfer the said Warrant on the books of the
Company, with full power of substitution.

                                                 ______________________________
                                                 [Type Name of Holder]

                                                 By: __________________________

                                                 Title: _______________________

Dated: ______________________

NOTICE

     The signature to the foregoing Assignment must correspond to the name as
written upon the face of the within Warrant in every particular, without
alteration or enlargement or any change whatsoever.

                                     -10-
<PAGE>

                              FORM OF ASSIGNMENT
                                   (PARTIAL)

             [To be signed only upon partial transfer of Warrant]

                   TO BE EXECUTED BY THE REGISTERED HOLDER
                        TO TRANSFER THE WITHIN WARRANT

     FOR VALUE RECEIVED ____________________ hereby sells, assigns and transfers
unto _____________________ (i) the rights of the undersigned to purchase _____
shares of Common Stock under and pursuant to the within Warrant, and (ii) on a
non-exclusive basis, all other rights of the undersigned under and pursuant to
the within Warrant, it being understood that the undersigned shall retain,
severally (and not jointly) with the transferee(s) named herein, all rights
assigned on such non-exclusive basis. The undersigned does hereby irrevocably
constitute and appoint __________________ Attorney to transfer the said Warrant
on the books of the Company, with full power of substitution.

                                                  ____________________________

                                                  [Type Name of Holder]

                                                  By:_________________________

                                                  Title: _____________________

Dated: _________________________

NOTICE

     The signature to the foregoing Assignment must correspond to the name as
written upon the face of the within Warrant in every particular, without
alteration or enlargement or any change whatsoever.

                                     -11-<PAGE>

                                                                   EXHIBIT 10.10

THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED. THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN THE
ABSENCE OF A REGISTRATION STATEMENT IN EFFECT WITH RESPECT TO THE SECURITIES
UNDER SUCH ACT OR AN EXEMPTION FROM SUCH REQUIREMENT UNDER SUCH ACT.

No. __________

                              XENOGEN CORPORATION
                              WARRANT CERTIFICATE

     THIS CERTIFIES that, for valued received, _______________________________,
or its registered successors and assigns, is the owner of Warrants to purchase
from XENOGEN CORPORATION, a California corporation (herein called the
"Company"), the security issued in the Company's next financing with gross
proceeds (excluding amounts received upon cancellation of indebtedness) in
excess of $________ (the "Next Financing"). For purposes of this Warrant
Certificate, the term "Shares" shall mean the security issued by the Company
in the Next Financing. The aggregate Exercise price of the Shares subject to
this Warrant Certificate is $______ (the "Aggregate Exercise Price"). The
aggregate number of Shares for which the Warrants may be exercised equals the
Aggregate Exercise Price divided by the price per share of the Shares, subject
to adjustment from time to time pursuant to the provisions of Section 2
hereof. Upon exercise of the Warrants, the holder hereof shall pay the
exercise price per Share equal to the per Share price paid in the Next
Financing.

1.   Exercise of Warrants.
     --------------------

     1.1  Cash Exercise. The Warrants evidenced hereby may be exercised at any
          -------------
time after the date of commencement of the Next Financing through November 13,
2007 (the "Expiration Date") by the registered holder hereof, in whole or in
part, by the surrender of this Warrant Certificate, duly endorsed (unless
endorsement is waived by the Company), at the time principal office of the
Company (or at such other office or agency of the Company as it may designate by
notice in writing to the registered holder hereof at such holder's last address
appearing on the books of the Company) and upon payment to the Company by check
payable to the order of the Company of the purchase price of the Shares
purchased. The certificates(s) for such Shares shall be delivered to the
registered holder hereof within a reasonable time, not exceeding ten (10) days,
after Warrants evidenced hereby shall have been so exercised and a new Warrant
Certificate evidencing the number of Warrants, if any, remaining unexercised
shall also be issued to the registered holder within such time unless such
Warrants have expired. The holder of the Warrants evidenced by this Certificate
shall have all the rights of a holder of Shares to be issued upon exercise of
the Warrants when such Warrant holder tenders payment of the Exercise Price (as
defined below) to the Company
<PAGE>

along with this Warrant Certificate duly endorsed in accordance with this
Section 1. No fractional Shares of the Company, or scrip for any such fractional
shares, shall be issued upon the exercise of any Warrants; but the holder hereof
shall be entitled to cash equal to such fraction multiplied by the then
effective Exercise Price (as defined below).

     1.2  Common Net Issue Exercise.
          -------------------------

          (a)  In lieu of exercising this Warrant and provided that the
Company's common stock (the "Common Stock") is then publicly traded, the holder
hereof may elect to receive shares of Common Stock equal to the value of this
Warrant (or the portion thereof being canceled) by surrender of this Warrant at
the principal office of the Company together with notice of such election in
which event the Company shall issue to the holder hereof a number of shares of
the Company's Common Stock computed using the following formula:

                                 X = Y (A - B)
                                     ---------
                                       A

Where     X -  The number of shares of Common Stock to be issued to Holder.

          Y -  The number of shares of Common Stock into which the Shares
               purchasable under this Warrant are then convertible.

          A -  The fair market value of one share of the Company's Common Stock.

          B -  Exercise Price (as adjusted to the date of such calculations).

          (b)  For purposes of this Section, fair market value of the Company's
Common Stock shall mean the average of the closing bid and asked prices of the
Company's Common Stock quoted in the over-the-counter market summary or the
closing price quoted on any exchange on which the Common Stock is listed,
whichever is applicable, as published in the Eastern Edition of The Wall Street
                                                                ---------------
Journal for the ten trading days prior to the date of determination of fair
-------
market value.

     1.3  Preferred Net Issue Exercise.
          ----------------------------

          In the event of a merger of the Company with or into another entity in
which the shareholders of the Company immediately prior to the merger own
immediately after the consummation of the merger less than a majority of the
outstanding voting securities of the surviving entity (or its parent) calculated
on a fully-diluted basis, then,

          (a)  In lieu of exercising this Warrant, the holder hereof may elect
     to receive Shares of the Company equal to the value of this Warrant (or the
     portion thereof being canceled) by surrender of this Warrant at the
     principal office of the company together

                                      -2-

<PAGE>

     with notice of such election, in which event the Company shall issue to the
     holder hereof a number of Shares of the Company computed using the
     following formula:

                                 X = Y (A - B)
                                     ---------
                                       A

Where     X -  The number of Shares to be issued to Holder.

          Y -  The number of Shares purchasable under this Warrant.

          A -  The fair market value of one Share of the Company's Preferred
               Stock.

          B -  Exercise Price (as adjusted to the date of such calculations).

          (b)  For purposes of this Section, fair market value of the Company's
     Preferred Stock shall mean the average of the closing bid and asked prices
     of the Company's Preferred Stock quoted in the over-the-counter market
     summary or the closing price quoted on any exchange on which the Preferred
     Stock is listed, whichever is applicable, as published in the Eastern
     Edition of The Wall Street Journal for the ten trading days prior to the
                -----------------------
     date of determination of fair market value. If the Preferred Stock is not
     traded over-the-counter or on an exchange, the fair market value shall be
     determined in good faith by the Board of Directors of the Company with the
     approval of the holder of this Certificate, which approval shall not be
     unreasonably withheld.

2.   Adjustment in Exercise Price and Number of Shares.  The applicable exercise
     -------------------------------------------------
price per share as set forth above shall be subject to adjustment from time to
time as hereinafter provided (such price, as last adjusted, being hereinafter
called the "Exercise Price").  Upon each adjustment of the Exercise Price, the
holder of this Warrant Certificate shall thereafter be entitled to purchase at
the Exercise Price resulting from such adjustment, the number of shares obtained
by dividing (1) the Aggregate Exercise Price by (2) the Exercise Price resulting
from such adjustment.

     2.1  Stock Dividends.  If and whenever at any time the Company shall
          ---------------
declare a dividend or make any other distribution upon any class or series of
stock of the Company payable in Shares or securities convertible into or
exercisable for Shares, the number of Shares to be obtained upon exercise of
this Warrant shall be proportionately adjusted (through a reduction of the
Exercise Price) to reflect the issuance of any such securities issuable in
payment of such dividend or distribution.

     2.2  Subdivision or Combination of Stock.  If and whenever the Company
          -----------------------------------
shall at any time subdivide its outstanding Common Shares into a greater number
of shares, the Exercise Price in effect immediately prior to such subdivision
shall be proportionately reduced, and conversely, in case the outstanding Common
Shares of the Company shall be

                                      -3-

<PAGE>

combined into a smaller number of shares, the Exercise Price in effect
immediately prior to such combination shall be proportionately increased.

     2.3  Reorganization, Reclassification. If any capital reorganization or
          --------------------------------
reclassification of the capital stock of the Company shall be effected, then, as
a condition of such reorganization or reclassification, lawful and adequate
provision shall be made whereby each holder of Warrants shall thereafter have
the right, but shall not be required, to purchase and receive upon the basis and
upon the terms and conditions herein specified and in lieu of the Shares
immediately theretofore issuable upon exercise of the Warrants, such shares of
stock, securities or properties (collectively, the "Substitute Securities") as
may be issuable or payable with respect to or in exchange for a number of
outstanding Shares equal to the number of Shares immediately theretofore
issuable upon exercise of the Warrants, had such reorganization or
reclassification taken place, and in any such case appropriate provision shall
be made with respect to the rights and interests of each holder of Warrants to
the end that the provisions hereof (including, without limitation, provisions
for adjustment of the Exercise Price) shall thereafter be applicable, as nearly
equivalent as may be practicable in relation to any Substitute Securities
thereafter deliverable upon the exercise thereof. The above provisions of this
Subsection 2.3 shall similarly apply to successive reorganizations or
reclassification.

3.   Other Notices. If any time prior to the Expiration Date of the Warrants
     -------------
evidenced hereby:

          (a)  The Company shall declare any dividend payable in shares of
     capital stock of the Company; or

          (b)  The Company shall authorize the issue of any options, warrants or
     rights entitling the recipient to subscribe for or purchase any shares of
     capital stock of the Company or to receive any other rights; or

          (c)  The Company shall authorize the distribution of evidences of its
     indebtedness or assets (including cash dividends or distributions paid out
     of retained earnings or retained surplus); or

          (d)  There shall occur any reclassification of the capital stock of
     the Company, or any consolidation or merger of the Company with or into
     another corporation (other than a consolidation or merger in which the
     Company is the continuing corporation and which does not result in any
     reclassification of the Shares) or a sale or transfer to another
     corporation of all or substantially all of the properties of the Company;
     or

          (e)  There shall occur the voluntary or involuntary liquidation,
     dissolution or winding up of the affairs of the Company;

                                      -4-
<PAGE>

then, and in each of such cases, the Company shall mail to the registered holder
hereof as its last address appearing on the books of the Company, as promptly as
practicable but in any event at least twenty days prior to the applicable record
date (or determination date) mentioned below, a notice stating, to the extent
such information is available, (I) the date on which a record is to be taken for
the purpose of such dividend, distribution or rights, if a record is not to be
taken, the date as of which the holders of Shares of record to be entitled to
such dividend, distribution or rights are to be determined, or (ii) the date on
which such liquidation, dissolution or winding up is expected to become
effective and the date as of which it is expected that holders of Shares of
record shall be entitled to exchange their Shares for securities or other
property deliverable upon such reclassification, consolidation, merger, sale,
transfer, liquidation, dissolution or winding up.

4.   Replacement of Warrants.  On receipt of evidence reasonably satisfactory to
     -----------------------
the Company of the loss, theft, destruction or mutilation of any Warrant, and in
the case of any such loss, theft or destruction of any Warrant, on delivery of
an indemnity agreement or security reasonable satisfactory in form and amount to
the Company or, in the case of any such mutilation, on surrender and
cancellation of such Warrant, unless the Company has received notice that any
such Warrant has been acquired by a bona fide purchaser, the Company at its
expense will execute and deliver, in lieu thereof, a new Warrant of like tenor;
provided, however, if any Warrant of which the original holder of this Warrant,
--------  -------
its nominee, or any of its affiliates is the registered holder is lost, stolen
or destroyed, the affidavit of the President, Vice President, Treasurer,
Secretary, or Clerk, of the registered holder setting forth the circumstances
with respect to such loss, theft or destruction shall be accepted as
satisfactory evidence thereof, and no indemnity bond or other security shall be
required as a condition to the execution and delivery by the Company of a new
Warrant in replacement of such lost, stolen or destroyed Warrant other than the
registered holder's written agreement to indemnify the Company.

5.   Registered Holder.  The registered holder of this Warrant Certificate shall
     -----------------
be deemed the owner hereof and of the Warrants evidenced hereby for all
purposes.  The registered holder of this Warrant Certificate shall not be
entitled by virtue of ownership of this Warrant Certificate to any rights
whatsoever as a shareholder of the Company.

6.   Amendments and Waivers.  Any provision in this Warrant Certificate to the
     ----------------------
contrary notwithstanding, changes in or additions to this Warrant Certificate
may be made and compliance with any covenant or provision herein set forth may
be omitted or waived if the Company shall obtain consent thereto in writing from
the holder of this Warrant Certificate.

7.   Transfer.  (a) This Warrant Certificate and the Warrants evidenced hereby
     --------
may not be sold, transferred, pledged, hypothecated or otherwise disposed of
unless and until:

                    (i)  There is then in effect a registration statement under
               the Securities Act of 1933, as amended (the "Securities Act"),
               covering such

                                      -5-
<PAGE>

          proposed disposition and such disposition is made in accordance with
          such registration statement and all applicable state securities laws;
          or

               (ii)  (A) The transferor shall have notified the Company of the
          proposed disposition and shall have furnished the Company with a
          statement of the circumstances surrounding the proposed disposition,
          (B) if reasonably requested by the Company, such transferor shall have
          furnished the Company with an opinion of counsel, reasonably
          satisfactory to the Company, that such disposition will not require
          registration of such shares under the Securities Act and that all
          requisite action has been or will, on a timely basis, be taken under
          any applicable state securities laws in connection with such
          disposition: (C) the proposed transferee shall have agreed in writing
          to be bound by the terms and provisions of this Section 8; and (D)
          provided, however, that only two such transfers pursuant to this
          Section 7(ii) may occur without the written consent of the Company.

          (b)  Notwithstanding the provisions of paragraphs (i) and (ii) above,
     no such registration statement or opinion of counsel shall be necessary and
     the provisions of subparagraph 7(ii)(a) shall not apply for a transfer to a
     partner, former partner, subsidiary, shareholder or affiliate of such
     transferor if the transferee agrees in writing to be subject to the terms
     hereof to the same extent as if such transferee were an original holder of
     this certificate or for transfers pursuant to Rule 144 or 144A promulgated
     under the Securities Act.

8.   Early Termination.  If at any time the Company proposes to merge with or
     -----------------
into any other entity, effect a reorganization or sell or convey all or
substantially all of its assets to any other entity in a transaction in which
the shareholders of the Company immediately prior to the transaction own
immediately after the transaction less than a majority of the outstanding voting
securities of the surviving entity (or its parent), then the Company shall give
the holder of this Warrant Certificate thirty days' prior written notice of the
effective date of the transaction and if the Warrants have not been exercised on
or prior to the effective date of such transaction the Warrants shall terminate.

                                      -6-
<PAGE>

     IN WITNESS WHEREOF, XENOGEN CORPORATION has caused this Warrant Certificate
to be signed by a duly authorized officer under its corporate seal, and this
Warrant Certificate to be dated November 13, 1997.

                                                  XENOGEN CORPORATION

                                                  By: _______________________
                                                      Name:
                                                      Title:

                                      -7-

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