<PAGE>

                                                                     EXHIBIT 4.4

THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER
THE SECURITIES ACT OF 1933, AND HAVE BEEN ACQUIRED FOR INVESTMENT AND NOT WITH A
VIEW TO, OR IN CONNECTION WITH, THE SALE OR DISTRIBUTION THEREOF.  NO SUCH SALE
OR DISTRIBUTION MAY BE EFFECTED WITHOUT AN EFFECTIVE REGISTRATION STATEMENT
RELATED THERETO OR AN OPINION OF COUNSEL IN A FORM SATISFACTORY TO THE COMPANY
THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE SECURITIES ACT OF 1933.



Warrant No. ___________                      Date of Issuance:  ________________


                             APPLIED IMAGING CORP.

                         Common Stock Purchase Warrant

     APPLIED IMAGING CORP. (the "Company"), for value received, hereby certifies
that ____________________ or its registered assigns (the "Registered Holder"),
is entitled, subject to the terms set forth below, to purchase from the Company
________ shares of Common Stock of the Company (the "Warrant Stock") at an
exercise price per share of $_____ (the "Exercise Price").  The number of shares
of Warrant Stock issuable upon exercise of this Warrant and the Exercise Price
shall be adjusted from time to time pursuant to the provisions of this Warrant.

1.   Exercise.
     --------

     (a)  Manner of Exercise.  This Warrant may be exercised by the Registered
          ------------------
Holder, in whole or in part, by surrendering this Warrant, with the exercise
form appended hereto as Exhibit A duly executed by such Registered Holder or by
                        ---------
such Registered Holder's duly authorized attorney, and delivering the Exercise
Price therefor in immediately available funds, at the principal office of the
Company, or at such other office or agency as the Company may designate.

     (b)  Effective Time of Exercise.  Each exercise of this Warrant shall be
          --------------------------
deemed to have been effected immediately prior to the close of business on the
day on which this Warrant shall have been surrendered and the Exercise Price
therefor delivered to the Company as provided in Section 1(a) above.  At such
time, the person or persons in whose name or names any certificates for Warrant
Stock shall be issuable upon such exercise as provided in Section 1(d) below
shall be deemed to have become the holder or holders of record of the Warrant
Stock represented by such certificates.
<PAGE>

     (c)  Delivery to Registered Holder.  As soon as practicable after the
          -----------------------------
exercise of this Warrant in whole or in part, and in any event within 10 days
thereafter, the Company at its expense will cause to be issued in the name of,
and delivered to, the Registered Holder, or as such Registered Holder (upon
payment by such Registered Holder of any applicable transfer taxes) may direct:

          (i)  a certificate or certificates for the number of shares of Warrant
Stock to which such Registered Holder shall be entitled, and

          (ii) in case such exercise is in part only, a new warrant or warrants
(dated the date hereof) of like tenor, calling in the aggregate on the face or
faces thereof for the number of shares of Warrant Stock equal (without giving
effect to any adjustment therein) to the number of such shares called for on the
face of this Warrant minus the number of such shares purchased by the Registered
Holder upon such exercise as provided in Section 2(a) or 2(c) above.

3.   Warrant Repurchase.  The Company shall have the option to repurchase this
     ------------------
Warrant upon 30 day's written notice to each Registered Holder at a price per
share of $0.05 if the closing bid price of the Common Stock on the Nasdaq
National Market is at least $9.00 for 15 consecutive trading days at any time
after the date of the issuance of this Warrant, provided that the Warrant Stock
shall have been registered at or prior to such time under the Securities Act (as
defined below).  Nothing herein shall prohibit the Registered Holder from
exercising this Warrant during the notice period referenced in the prior
sentence.

4.   Adjustment Of Exercise Price And Number Of Shares.
     -------------------------------------------------

     The number of shares of Warrant Stock issuable upon exercise of this
Warrant (or any shares of stock or other securities or property receivable or
issuable upon exercise of this Warrant) and the Exercise Price are subject to
adjustment upon occurrence of the following events:

     (a)  Adjustment for Stock Splits, Stock Subdivisions or Combinations of
          ------------------------------------------------------------------
Shares.  The Exercise Price of this Warrant shall be proportionally decreased
------
and the number of shares of Warrant Stock issuable upon exercise of this Warrant
(or any shares of stock or other securities at the time issuable upon exercise
of this Warrant) shall be proportionally increased to reflect any stock split or
subdivision of the Company's Common Stock. The Exercise Price of this Warrant
shall be proportionally increased and the number of shares of Warrant Stock
issuable upon exercise of this Warrant (or any shares of stock or other
securities at the time issuable upon exercise of this Warrant) shall be
proportionally decreased to reflect any combination of the Company's Common
Stock.

     (b)  Adjustment for Dividends or Distributions of Stock or Other Securities
          ----------------------------------------------------------------------
or Property.  In case the Company shall make or issue, or shall fix a record
-----------
date for the determination of eligible holders entitled to receive, a dividend
or other distribution with respect to the Warrant Stock (or any shares of stock
or other securities at the time issuable upon exercise of the Warrant) payable
in (i) securities of the Company or (ii) assets (excluding cash dividends paid
or payable solely out of retained earnings), then, in each such case, the
Registered Holder of

                                       2
<PAGE>

this Warrant on exercise hereof at any time after the consummation, effective
date or record date of such dividend or other distribution, shall receive, in
addition to the shares of Warrant Stock (or such other stock or securities)
issuable on such exercise prior to such date, and without the payment of
additional consideration therefor, the securities or such other assets of the
Company to which such Registered Holder would have been entitled upon such date
if such Registered Holder had exercised this Warrant on the date hereof and had
thereafter, during the period from the date hereof to and including the date of
such exercise, retained such shares and/or all other additional stock available
by it as aforesaid during such period giving effect to all adjustments called
for by this Section 4.

     (c)  Adjustment for Capital Reorganization, Merger or Consolidation.  In
          --------------------------------------------------------------
case of any capital reorganization of the capital stock of the Company (other
than a combination, reclassification, exchange or subdivision of shares
otherwise provided for herein), or any merger or consolidation of the Company
with or into another corporation, or the sale of all or substantially all the
assets of the Company then, and in each such case, as a part of such
reorganization, merger, consolidation, sale or transfer, lawful provision shall
be made so that the Registered Holder of this Warrant shall thereafter be
entitled to receive upon exercise of this Warrant, during the period specified
herein and upon payment of the Exercise Price then in effect, the number of
shares of stock or other securities or property of the successor corporation
resulting from such reorganization, merger, consolidation, sale or transfer that
a holder of the shares deliverable upon exercise of this Warrant would have been
entitled to receive in such reorganization, consolidation, merger, sale or
transfer if this Warrant had been exercised immediately before such
reorganization, merger, consolidation, sale or transfer, all subject to further
adjustment as provided in this Section 4. The foregoing provisions of this
Section 4(c) shall similarly apply to successive reorganizations,
consolidations, mergers, sales and transfers and to the stock or securities of
any other corporation that are at the time receivable upon the exercise of this
Warrant. If the per-share consideration payable to the Registered Holder hereof
for shares in connection with any such transaction is in a form other than cash
or marketable securities, then the value of such consideration shall be
determined in good faith by the Company's Board of Directors. In all events,
appropriate adjustment (as determined in good faith by the Company's Board of
Directors) shall be made in the application of the provisions of this Warrant
with respect to the rights and interests of the Registered Holder after the
transaction, to the end that the provisions of this Warrant shall be applicable
after that event, as near as reasonably may be, in relation to any shares or
other property deliverable after that event upon exercise of this Warrant.

     (d)  Reclassification, Etc.  In case there occurs any reclassification or
          ---------------------
change of the outstanding securities of the Company or of any reorganization of
the Company (or any other corporation the stock or securities of which are at
the time receivable upon the exercise of this Warrant) or any similar corporate
reorganization on or after the date hereof, then and in each such case the
Registered Holder, upon the exercise hereof at any time after the consummation
of such reclassification, change, or reorganization shall be entitled to
receive, in lieu of the stock or other securities and property receivable upon
the exercise hereof prior to such consummation, the stock or other securities or
property to which such Registered Holder would have been entitled upon such
consummation if such Registered Holder had exercised this Warrant immediately
prior thereto, all subject to further adjustment pursuant to the provisions of
this Section 4.

                                       3
<PAGE>

     (e)  Other Issuances of Common Stock.
          -------------------------------

          (i)   If the Company shall at any time or from time to time issue or
     sell any additional shares of Common Stock without consideration or for a
     consideration per share less than the Exercise Price in effect immediately
     prior to such issuance, then the Exercise Price shall be adjusted to a
     price determined by dividing (A) an amount equal to the sum of (1) the
     product of (a) the number of shares of Common Stock outstanding immediately
     prior to such issue or sale multiplied by (b) the then existing Exercise
     Price plus (2) the consideration, if any, received by the Company upon such
     issue or sale by (B) the total number of shares of Common Stock outstanding
     immediately after such issue or sale.

          (ii)  In case the Company shall at any time or from time to time in
     any manner grant any rights to subscribe for or to purchase any options for
     the purchase of Common Stock or any stock or other securities convertible
     into or exchangeable for Common Stock (such rights, options, convertible or
     exchangeable stock or securities being herein called "Convertible
     Securities") and the price per share for which Common Stock is issuable
     upon the exercise of such rights or options or upon conversion or exchange
     of such Convertible Securities (the "Rights Price") (determined by dividing
     (A) the sum of (1) the total amount, if any, received or receivable by the
     Company as consideration for the granting of such rights or options, plus
     (2) the minimum aggregate amount of additional consideration payable to the
     Company upon the exercise of such rights or options, plus, (3) in the case
     of such Convertible Securities, the minimum aggregate amount of additional
     consideration, if any, payable upon the conversion or exchange thereof, by
     (B) the maximum number of shares of Common Stock issuable upon the exercise
     of such rights or options or upon the conversion or exchange of all such
     Convertible Securities issuable upon the exercise of such rights or
     options) shall be less than the Exercise Price in effect immediately prior
     to the time of the granting of such rights or options, then the maximum
     number of shares of Common Stock issuable upon the exercise of such rights
     or options or upon conversion or exchange of the maximum amount of such
     Convertible Securities issuable upon the exercise of such rights or options
     shall (as of the date of granting of such rights or options) be deemed to
     be outstanding and to have been issued for the Rights Price per share as so
     determined, if the Rights Price is less than the Exercise Price in effects
     immediately prior to such issuance, the Exercise Price shall be adjusted to
     a price determined by the calculation provided for in Section 4(e)(i)
     above; provided, that no further adjustment of the Exercise Price shall be
            --------
     made upon the actual issue of such Common Stock or of such Convertible
     Securities, upon exercise of such rights or options or upon the actual
     issue of such Common Stock or upon conversion or exchange of such
     Convertible Securities; and provided, further, that upon the expiration of
                                 --------  -------
     such rights or options, if any thereof shall not have been exercised, (x)
     the number of shares of Common Stock deemed to be issued and outstanding by
     reason of the fact that they were issuable upon the exercise of such rights
     or options or upon conversion or exchange of Convertible Securities so
     issuable, which rights or options were

                                       4
<PAGE>

     not exercised, shall no longer be deemed to be issued and outstanding, and
     (y) the Exercise Price shall forthwith be readjusted and thereafter the
     Exercise Price shall be the price which it would have been had adjustment
     been made on the basis of the issue only of the shares of Common Stock or
     of the Convertible Securities actually issued upon the exercise of such
     rights or options.

          (iii) Without limiting the generality of the foregoing provisions of
     this Section 4(e), the Company agrees that the provisions of this Section
     4(e) shall apply to the issuance of Additional Shares (as defined in the
     Stock Purchase Agreement, dated as of December 13, 2000 (the "Purchase
     Agreement"), by and among the Company and the Investors named therein)
     and/or additional warrants (as contemplated in the Purchase Agreement) by
     the Company at any Subsequent Closing (as defined in the Purchase
     Agreement).

          (iv)  Notwithstanding any provision herein to the contrary, the
     provisions of this Section 4(e) shall not apply to the issuance of options
     and Common Stock pursuant to the exercise of such options as a result of
     any Company sponsored option or stock purchase plan.

     (f)  Certain Events.  If (i) any event occurs of a type that would have an
          --------------
effect on the rights granted under this Warrant similar to the effect of any
event described by the other provisions of this Section 4 and (ii) such event is
not expressly provided for by such other provisions (including, without
limitation, the granting of stock appreciation rights, phantom stock rights and
other rights with equity features), then an appropriate adjustment in the
Exercise Price and the number of shares of Common Stock obtainable upon exercise
of this Warrant so as to protect the rights of the Registered Holder shall be
made.

     (g)  Adjustment Certificate.  When any adjustment is required to be made in
          ----------------------
the Warrant Stock pursuant to this Section 4, the Company shall promptly mail to
the Registered Holder a certificate setting forth (i) a brief statement of the
facts requiring such adjustment, (ii) the kind and amount of stock or other
securities or property into which this Warrant shall be exercisable after such
adjustment.

5.   Transfers.
     ---------

     (a)  Unregistered Security.  Each holder of this Warrant acknowledges that
          ---------------------
this Warrant, the Warrant Stock and the Common Stock of the Company have not
been registered under the Securities Act of 1933, as amended (the "Securities
Act"), and agrees not to sell, pledge, distribute, offer for sale, transfer or
otherwise dispose of this Warrant, any Warrant Stock issued upon its exercise or
any Common Stock issued upon conversion of the Warrant Stock in the absence of
(i) an effective registration statement under the Act as to this Warrant, such
Warrant Stock or such Common Stock and registration or qualification of this
Warrant, such Warrant Stock or such Common Stock under any applicable U.S.
federal or state securities law then in effect or (ii) an opinion of counsel,
satisfactory to the Company, that such registration and qualification are not
required.  Each certificate or other instrument for Warrant Stock issued upon
the exercise of this Warrant shall bear a legend substantially to the foregoing
effect.

                                       5
<PAGE>

     (b)  Transferability.  Subject to the provisions of Section 5(a) hereof,
          ---------------
this Warrant and all rights hereunder are transferable, in whole or in part,
upon surrender of the Warrant with a properly executed assignment (in the form
of Exhibit B hereto) at the principal office of the Company.
   ---------

     (c)  Warrant Register.  The Company will maintain a register containing the
          ----------------
names and addresses of the Registered Holders of this Warrant. Until any
transfer of this Warrant is made in the warrant register, the Company may treat
the Registered Holder of this Warrant as the absolute owner hereof for all
purposes; provided, however, that if this Warrant is properly assigned in blank,
          --------  -------
the Company may (but shall not be required to) treat the bearer hereof as the
absolute owner hereof for all purposes, notwithstanding any notice to the
contrary. Any Registered Holder may change such Registered Holder's address as
shown on the warrant register by written notice to the Company requesting such
change.

6.   No Impairment.  The Company will not, by amendment of its charter or
     -------------
through reorganization, consolidation, merger, dissolution, sale of assets or
any other voluntary action, 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.

7.   Termination.  This Warrant (and the right to purchase securities upon
     -----------
exercise hereof) shall terminate on the date which is three years after the date
of this Warrant.

8.  Reservation of Stock.  The Company will at all times reserve and keep
    --------------------
available, solely for the issuance and delivery upon the exercise of this
Warrant, such shares of Warrant Stock and other stock, securities and property,
as from time to time shall be issuable upon the exercise of this Warrant.

9.   Exchange of Warrants.  Upon the surrender by the Registered Holder of any
     --------------------
Warrant or Warrants, properly endorsed, to the Company at the principal office
of the Company, the Company will, subject to the provisions of Section 5 hereof,
issue and deliver to or upon the order of such Registered Holder, at the
Company's expense, a new Warrant or Warrants of like tenor, in the name of such
Registered Holder or as such Registered Holder (upon payment by such Registered
Holder of any applicable transfer taxes) may direct, calling in the aggregate on
the face or faces thereof for the number of shares of Warrant Stock called for
on the face or faces of the Warrant or Warrants so surrendered.

10.  Replacement of Warrants.  Upon receipt of evidence reasonably satisfactory
     -----------------------
to the Company of the loss, theft, destruction or mutilation of this Warrant and
(in the case of loss, theft or destruction) upon delivery of an indemnity
agreement (with surety if reasonably required) in an amount reasonably
satisfactory to the Company, or (in the case of mutilation) upon surrender and
cancellation of this Warrant, the Company will issue, in lieu thereof, a new
Warrant of like tenor.

                                       6
<PAGE>

11.  Mailing of Notices. All notices and other communications required or
     ------------------
permitted hereunder shall be in writing and shall be sent by personal delivery,
facsimile, overnight courier or mailed by certified or registered mail, postage
prepaid, return receipt requested, (a) if to the Registered Holder, to the
address or facsimile number of the Registered Holder most recently furnished in
writing to the Company and (b) if to the Company, to the following address or
facsimile number:

                Applied Imaging Corp.
                2380 Walsh Avenue, Building B
                Santa Clara, CA 95051
                Facsimile:  (408) 562-0264
                Attention:  President

          with a copy to:

                Georgopoulos Pahlavan & Prince, LLP
                935 Hamilton Avenue
                Menlo Park, CA 94025
                Facsimile:  (650) 473-9060
                Attention:  Paul G. Prince

or to such other facsimile number or address provided to the parties hereunder
in accordance with this Section 11.

                                       7
<PAGE>

Copies of all notices shall also be sent to:

                H.C. Wainwright & Co., Inc.
                One Boston Place
                Boston, MA 02108
                Facsimile: (617) 788-9520
                Attention: Edward P. Crouch, Managing Director and
                Anne Buckley, Counsel

Such notices or other communications shall be deemed delivered upon receipt, in
the case of overnight delivery, personal delivery or facsimile transmission (as
evidenced by the confirmation thereof), or 3 days after deposit in the mails (as
determined by reference to the postmark).

12.  No Rights as Stockholder.  Until the exercise of this Warrant, the
     ------------------------
Registered Holder of this Warrant shall not have or exercise any rights by
virtue hereof as a stockholder of the Company.

13.  No Fractional Shares.  No fractional shares of Common Stock will be issued
     --------------------
in connection with any exercise hereunder.  In lieu of any fractional shares
which would otherwise be issuable, the Company shall pay cash equal to the
product of such fraction multiplied by the closing bid price of Common Stock on
the trading date immediately prior to the exercise date, as quoted on the Nasdaq
National Market.

14.  Amendment or Waiver.  Any term of this Warrant may be amended or waived as
     -------------------
set forth in the Purchase Agreement, or upon written consent of the Company and
the holders of at least a majority of the shares of Common Stock issuable upon
exercise of outstanding warrants issued pursuant to the Purchase Agreement. Any
amendment or waiver effected in accordance with this Section 14 shall be binding
upon the Company, the Registered Holder and each transferee of this Warrant. By
acceptance hereof, the Registered Holder acknowledges that in the event the
required consent is obtained, any term of this Warrant may be amended or waived
with or without the consent of the Registered Holder.

15.  Headings.  The headings in this Warrant are for purposes of reference only
     --------
and shall not limit or otherwise affect the meaning of any provision of this
Warrant.

16.  Governing Law. This Warrant shall be governed, construed and interpreted in
     -------------
accordance with the laws of the State of New York.

                            [Signature Page Follows]

                                       8
<PAGE>

     The Company has executed this Warrant as of the date first written above.


                                         APPLIED IMAGING CORP.



                                         By _________________________________
                                            Name:   Barry Hotchkies
                                            Title:  Chief Financial Officer

                                       9
<PAGE>

                                   EXHIBIT A
                                   ---------

                                 EXERCISE FORM
                                 -------------

To:  Applied Imaging Corp.
     Dated:__________________

     The undersigned, pursuant to the provisions set forth in the attached
Warrant No. __, hereby irrevocably elects to receive _______________ shares of
the Common Stock covered by such Warrant.

     The undersigned acknowledges that it has reviewed the representations and
warranties contained in Section 3 of the Purchase Agreement (as defined in the
Warrant) and by its signature below hereby makes such representations and
warranties to the Company.  Defined terms contained in such representations and
warranties shall have the meanings assigned to them in the Purchase Agreement,
provided that the term "Investor" shall refer to the undersigned and the term
--------
"Securities" shall refer to Warrant Stock.


                                         ____________________________________
                                         (Investor)


                                         By _________________________________
                                            Name:
                                            Title:
<PAGE>

                                   EXHIBIT B
                                   ---------

                                ASSIGNMENT FORM
                                ---------------

FOR VALUE RECEIVED, _________________________________________ hereby sells,
assigns and transfers all of the rights of the undersigned under the attached
Warrant with respect to the number of shares of Common Stock covered thereby set
forth below, unto:

Name of Assignee            Address/Facsimile Number        No. of Shares
----------------            ------------------------        -------------





Dated:_________________      Signature: ___________________________________

                                        ___________________________________

                             Witness:   ___________________________________