<PAGE>

                                                                     EXHIBIT 4.2

                            STOCK PURCHASE AGREEMENT
                            ------------------------

     THIS STOCK PURCHASE AGREEMENT (the "Agreement") is made as of the ______
day of ______, 1999, by and between Applied Imaging Corp., a Delaware
corporation, located at 2380 Walsh Road, Bldg. B, Santa Clara, CA  95051 (the
"Company"), and _______________ ("the Investor").

     1.  Purchase and Sale of Stock.  Subject to the terms and conditions of
         --------------------------
this Agreement, the Investor agrees to purchase at the Closing (as hereinafter
defined) and the Company agrees to sell and issue to the Investor at the Closing
__________shares of the Company's Common Stock at the purchase price of
$_________ per share (the "Purchase Price").

          1.1  Closing.  The purchase and sale of the Shares (the "Closing")
               -------
shall be held at the offices of Wilson Sonsini Goodrich & Rosati, 650 Page Mill
Road, Palo Alto, California, on ______, 1999 at 2:00 p.m., local time, or at
such other time and place upon which the Company and the Investor shall agree
(which date and time shall be referred to as the "Closing Date").

          1.2  Delivery.  Within three days of the Closing the Company shall
               --------
issue to the Investor a certificate registered in the Investor's names,
representing the number of Shares purchased by the Investor against payment
therefor. Such payment shall be paid to the Company by check payable to the
Company or by wire transfer.

     2.  Representations and Warranties of the Company.  The Company hereby
         ---------------------------------------------
represents and warrants to the Investor that, except as set forth in the
Schedule of Exceptions attached hereto as Exhibit A:
                                          ---------

          2.1  Organization and Standing.  The Company is a corporation duly
               -------------------------
organized and validly existing under the laws of the State of Delaware and is in
good standing under such laws. The Company has all requisite corporate power to
own and operate its properties and assets, and to carry on its business as
presently conducted. The Company is qualified to do business as a foreign
corporation in the State of California. Such qualification is not presently
required in any other jurisdiction where a failure to so qualify would have a
material adverse effect on the Company.

          2.2  Capitalization.  The authorized capital stock of the Company
               --------------
consists of 20,000,000 shares of Common Stock and 6,000,000 shares of Preferred
Stock. As of September 30, 1999, 14,040,373 shares of Common Stock are issued
and outstanding. No shares of Preferred Stock are issued and outstanding. All
such issued and outstanding shares have been duly authorized and validly issued,
and are fully paid and nonassessable. Options to purchase 1,037,944 shares of
the Company's Common Stock are outstanding under the Company's Amended and
Restated 1988 Incentive Stock Option Plan and no shares are available for future
grant. Options to purchase 657,500 shares of the Company's Common Stock are
outstanding under the Company's 1998 Stock Option Plan and 292,500 shares are
available for future grant.
<PAGE>

120,000 options to purchase shares of the Company's Common Stock are outstanding
under the Company's 1994 Director Option Plan and no shares are available for
future grant. The Company has reserved 200,000 shares of Common Stock for
issuance under its Employee Stock Purchase Plan, of which 158,534 are available
for future purchase. The Company also has warrants outstanding for 313,010
shares of the Company's Common Stock. Except as disclosed in the Company SEC
Documents (as defined below), there are no other options, warrants, conversion
privileges, or preemptive or other rights or agreements presently outstanding to
purchase or otherwise acquire any authorized but unissued shares of the capital
stock or other securities of the Company.

          2.3  Authority.  The Company has full power and authority to execute
               ---------
and deliver this Agreement, and to consummate the transactions contemplated by
this Agreement. All corporate action on the part of the Company, its officers,
directors and stockholders necessary for the execution and delivery of, and the
consummation of the transactions contemplated by this Agreement and the
performance of all obligations of the Company under this Agreement has been
taken. This Agreement, upon execution and delivery by the Company and assuming
the due and proper execution and delivery by Investor, constitutes a legal,
valid and binding obligation of the Company, enforceable in accordance with its
respective terms, except as may be limited by (i) applicable bankruptcy,
insolvency, reorganization or other laws of general application relating to or
affecting the enforcement of creditors rights generally, and (ii) the effect of
rules of law governing the availability of equitable remedies.

          2.4  Valid Issuance of Common Stock.  The Common Stock to be sold
               ------------------------------
hereby has been duly authorized and, when issued, delivered and paid for in the
manner set forth in this Agreement, will be duly authorized, validly issued,
fully paid and nonassessable, and will be free of restrictions on transfer other
than restrictions on transfer under this Agreement and under applicable state
and federal securities laws. No preemptive rights or other rights to subscribe
for or purchase exist with respect to the issuance and sale of the Common Stock
by the Company pursuant to this Agreement.

          2.5  Governmental Consents.  Other than compliance with the
               ---------------------
Securities Act of 1933, as amended (the "Act") and such filings as may be
required to be made with the National Association of Securities Dealers (the
"NASD"), no consent, approval, order or authorization of, or registration,
qualification, designation, declaration or filing with, any federal, state or
local governmental authority on the part of the Company is required in
connection with the consummation of the transactions contemplated by this
Agreement.

          2.6  Conflicts.  The execution and delivery of this Agreement will
               ---------
not conflict with or result in a material breach of the terms, conditions or
provisions of, or constitute a material default under, any contract, covenant or
instrument under which the Company is now obligated.

          2.7  SEC Documents; Material Contracts; Financial Statements.  The
               -------------------------------------------------------
Company has filed each statement, annual, quarterly and other report,
registration statement and definitive proxy statement ("Company SEC Documents")
required to be filed (other than preliminary material) by the Company with the
SEC subsequent to November 7, 1996 (the date of effectiveness of the Company's
registration statement on Form S-1 for the Company's initial

                                       2
<PAGE>

public offering of its Common Stock).  As of their respective filing dates, the
Company SEC Documents complied in all material respects with the requirements of
the Act or the Securities Exchange Act of 1934 (the "1934 Act"), as the case may
be, and none of the Company SEC Documents contained any untrue statement of a
material fact or omitted to state a material fact required to be stated therein
or necessary to make the statements made therein, in light of the circumstances
in which they were made, not misleading, except to the extent corrected by any
subsequently filed Company SEC Document.  The Company's Registration Statement
on Form S-1, which became effective on November 7, 1996 (the "Registration
Statement"), and the Company SEC Documents, include certain contracts as
required by the SEC's rules and regulations.  The contracts so described in the
Registration Statement and in the Company SEC Documents, are currently material
to the Company and its business, and are in full force and effect on the date
hereof.  Neither the Company nor any of its subsidiaries, nor to the Company's
knowledge, any other party is in breach of or default under any of such
contracts, except as to breaches or defaults which, in any single case or in the
aggregate would not have a material adverse effect on the Company taken as a
whole.

     The consolidated financial statements of the Company and its subsidiaries
included in the Company SEC Documents (the "Financial Statements") comply as to
form in all material respects with applicable accounting requirements and with
the published rules and regulations of the SEC with respect thereto.  The
Financial Statements have been prepared in accordance with generally accepted
accounting principles consistently applied and fairly present the consolidated
financial position of the Company and any subsidiaries at the dates thereof and
the consolidated results of operations and consolidated cash flows for the
periods then ended (subject, in the case of unaudited statements, to normal,
recurring adjustments).

          2.8  Changes.  Since June 30, 1999 (the date of the most recent
               -------
Financial Statements), there has not been any event or condition of any
character that might materially and adversely affect the business, properties,
prospects or financial condition of the Company (as such business is presently
conducted and as it is proposed to be conducted).

          2.9  Litigation.  There is no pending or threatened lawsuit,
               ----------
administrative proceeding, arbitration, labor dispute or governmental
investigation ("Litigation") to which the Company is a party or by which any
material portion of its assets, taken as a whole, may be bound and which
Litigation, if adversely determined, would have a material adverse effect on the
Company's assets, liabilities, financial condition or operations.

          2.10  Solvency; No Default.  As of the date of this Agreement, the
                --------------------
Company has sufficient funds and cash flow to pay its debts and other
liabilities, and the Company is not in default with respect to any material debt
or liability.

          2.11  Disclosure.  The Company has fully delivered or made available
                ----------
to the Investor or their counsel all of the information (including the Company
SEC Documents) that the Company reasonably believes is necessary for the
Investor's purchase decision. Neither this Agreement nor any agreement,
instrument or other documents delivered by the Company to the Investor in
connection herewith or filed with the SEC subsequent to November 1996, when read
together, contains any untrue statement of a material fact, or, to the knowledge
of the Company, omits to state a material fact necessary to be stated, when read
together, to make the statements

                                       3
<PAGE>

contained herein or therein not misleading in light of the circumstances in
which they were made.

     3.  Representations and Warranties of the Investor.  The Investor hereby
         ----------------------------------------------
represents and warrants that:

          3.1  Authorization.  The Investor has full power and authority to
               -------------
execute and deliver, and to consummate the transactions contemplated by the
Closing and this Agreement. All corporate action on the part of the Investor,
its officers, directors and stockholders necessary for (i) the execution and
delivery of, and the consummation of the transactions contemplated by, this
Agreement, and (ii) as of the Closing, the performance of all obligations of the
Investor under this Agreement, has been taken. This Agreement, upon execution
and delivery by the Investor and assuming the due and proper execution and
delivery by the Company, constitutes a legal, valid and binding obligation of
the Investor, enforceable in accordance with its terms, except as may be limited
by (i) applicable bankruptcy, insolvency, reorganization or other laws of
general application relating to or affecting the enforcement of creditors rights
generally, and (ii) the effect of rules of law governing the availability of
equitable remedies.

          3.2  Purchase Entirely for Own Account.  This Agreement is made with
               ---------------------------------
the Investor in reliance upon the Investor's representation to the Company,
which by the Investor's execution of this Agreement, the Investor hereby
confirms, that the Common Stock to be received by the Investor (collectively,
the "Securities") will be acquired for investment for the Investor's own account
and not with a view to the resale or distribution of any part thereof, and that
the Investor has no present intention of selling, granting any participation in,
or otherwise distributing the same. By executing this Agreement, the Investor
further represents that the Investor does not have any contract, undertaking,
agreement or arrangement with any person to sell, transfer or grant
participations to such person or to any third person, with respect to any of the
Securities.

          3.3  Disclosure of Information.  The Investor believes it has
               -------------------------
received all the information it considers necessary or appropriate for deciding
whether to purchase the Common Stock. The Investor further represents that it
has had an opportunity to ask questions and receive answers from the Company
regarding the terms and conditions of the offering of the Common Stock and the
business, properties, prospects and financial condition of the Company. The
foregoing, however, does not limit or modify the representations and warranties
of the Company in Section 2 of this Agreement or the right of the Investor to
rely thereon.

          3.4  Investment Experience.  The Investor is an investor in
               ---------------------
securities of companies in the development stage and acknowledges that it is
able to fend for itself, can bear the economic risk of its investment, and has
such knowledge and experience in financial or business matters that it is
capable of evaluating the merits and risks of the investment in the Common
Stock. The Investor has not been organized for the purpose of acquiring the
Common Stock.

          3.5  Accredited Investor.  The Investor is an "accredited investor"
               -------------------
within the meaning of SEC Rule 501 of Regulation D, as presently in effect.

                                       4
<PAGE>

          3.6  Restricted Securities.  The Investor understands that the
               ---------------------
Securities it is purchasing are characterized as "restricted securities" under
the federal securities laws inasmuch as they are being acquired from the Company
in a transaction not involving a public offering and that under such laws and
applicable regulations such securities may be resold without registration under
the Act, only in certain limited circumstances. In this connection, the Investor
represents that it is familiar with SEC Rule 144, as presently in effect, and
understands the resale limitations imposed thereby and by the Act.

          3.7  Further Limitations on Disposition.  Without in any way limiting
               ----------------------------------
the representations set forth above, the Investor further agrees not to make any
disposition of all or any portion of the Securities unless and until the
transferee has agreed in writing for the benefit of the Company to be bound by
this Section 3 provided and to the extent this Section is applicable, and:

               (a)  There is then in effect a Registration Statement under the
Act covering such proposed disposition and such disposition is made in
accordance with such Registration Statement; or

               (b)  If reasonably requested by the Company, the Investor 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 Act. It is agreed that the Company will not require opinions of
counsel for transactions made pursuant to Rule 144 except in unusual
circumstances.

          3.8  Legends.  Each certificate or instrument representing Shares
               -------
shall bear a legend in substantially the following form: "THE SECURITIES
REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES
ACT OF 1933 (THE 'SECURITIES ACT') AND ARE 'RESTRICTED SECURITIES' AS DEFINED IN
RULE 144 PROMULGATED UNDER THE SECURITIES ACT. THE SECURITIES MAY NOT BE SOLD OR
OFFERED FOR SALE OR OTHERWISE DISTRIBUTED EXCEPT (I) IN CONJUNCTION WITH AN
EFFECTIVE REGISTRATION STATEMENT FOR THE SECURITIES UNDER THE SECURITIES ACT, OR
(II) IN COMPLIANCE WITH RULE 144, OR (III) PURSUANT TO AN OPINION OF COUNSEL
SATISFACTORY TO THE ISSUER OF THESE SECURITIES THAT SUCH REGISTRATION OR
COMPLIANCE IS NOT REQUIRED AS TO SUCH SALE, OFFER OR DISTRIBUTION."

     The Company need not register a transfer of any Shares, and may also
instruct its transfer agent not to register a transfer of any Shares, unless the
conditions specified in the foregoing legends are satisfied to the extent
applicable.

     4.  Registration Rights.
         -------------------

          4.1  Request for Registration.
               ------------------------

               (a)  Following six months from the date of this Agreement, upon
written request by the Investor, the Company shall prepare and file with SEC as
soon as practicable but in no event later than 30 days following such written
request, a registration statement to register under the Act all Common Stock of
the Company acquired pursuant to this

                                       5
<PAGE>

Agreement held by the Investor. In addition, if the Company shall determine to
register any of its Common Stock for its own account or for the account of
others, other than a registration relating solely to employee benefit or a
registration relating solely to a Commission Rule 145 transaction, the Company
will give the Investor written notice thereof and include such registration all
shares held by the Investor that the Investor wishes to register. However, if
such registration is for a registered public offering involving an underwriting,
the Investor's right to participate will be subject to reduction or elimination,
if the underwriter determines that marketing forces requires a limitation of the
number of share to be underwritten.

               (b)  If the Investor intend to distribute the securities covered
by its request by means of an underwriting, the Investor shall so advise the
Company as a part of its request made pursuant to subsection (a) above. The
underwriter will be selected by the Company and shall be reasonably acceptable
to the Investor. The Investor shall (together with the Company) enter into an
underwriting agreement in customary form with the underwriter or underwriters
selected for such underwriting.

               (c)  Notwithstanding the foregoing, if the Company shall furnish
to the Investor a certificate signed by the Chief Executive Officer of the
Company stating that in the good faith judgment of the Board of Directors of the
Company, it would be seriously detrimental to the Company and its stockholders
for such registration statement to be filed, and it is therefore essential to
defer the filing of such registration statement, the Company shall have the
right to defer taking action with respect to such filing for a period of not
more than 90 days after receipt of the request of the Investor; provided,
however, that the Company may not utilize this right more than once in any
twelve-month period.

          4.2  Obligations of the Company.  Whenever required under this
               --------------------------
Section 4 to effect the registration of any securities, the Company shall, as
expeditiously as reasonably possible:

               (a)  Prepare and file with the SEC a registration statement with
respect to such securities and use commercially reasonable efforts to cause such
registration statement to become effective, and, keep such registration
statement effective for a period of up to two years, or such lesser period of
time as all of the Shares have been sold or can be sold without restriction
under Rule 144.

               (b)  Prepare and file with the SEC such amendments and
supplements to such registration statement and the prospectus used in connection
with such registration statement as may be necessary to comply with the
provisions of the Act with respect to the disposition of all securities covered
by such registration statement.

               (c)  Furnish to the Investor such numbers of copies of a
prospectus, including a preliminary prospectus, in conformity with the
requirements of the Act, and such other documents as they may reasonably request
in order to facilitate the disposition of securities.

               (d)  Use its best efforts to register and qualify the securities
covered by such registration statement under such other securities or Blue Sky
laws of such jurisdictions as

                                       6
<PAGE>

shall be reasonably requested by the Investor; provided that the Company shall
not be required in connection therewith or as a condition thereto to qualify to
do business or to file a general consent to service of process in any such
states or jurisdictions, unless the Company is already subject to service in
such jurisdiction and except as may be required by the Act.

               (e)  In the event of any underwritten public offering, enter
into and perform its obligations under an underwriting agreement, in usual and
customary form, with the managing underwriter of such offering, said form to be
agreeable to the Company and its counsel. The Investor shall also enter into and
perform its obligations under such an agreement.

               (f)  Notify the Investor at any time when a prospectus relating
to such registration statement is required to be delivered under the Act of the
happening of any event as a result of which the prospectus included in such
registration statement, as then in effect, includes an untrue statement of a
material fact or omits to state a material fact required to be stated therein or
necessary to make the statements therein not misleading in the light of the
circumstances then existing.

               (g)  Cause all such securities registered pursuant hereunder to
be listed on each securities exchange on which similar securities issued by the
Company are then listed.

               (h)  Furnish, at the request of the Investor, on the date that
securities are delivered to the underwriters for sale in connection with a
registration pursuant to this Section 4, if such securities are being sold
through underwriters, or, if such securities are not being sold through
underwriters, on the date that the registration statement with respect to such
securities becomes effective, (i) an opinion, dated such date, of the counsel
representing the Company for the purposes of such registration, in form and
substance as is customarily given to underwriters in an underwritten public
offering, addressed to the underwriters, if any, and to the Investor and (ii) a
letter dated such date, from the independent certified public accountants of the
Company, in form and substance as is customarily given by independent certified
public accountants to underwriters in an underwritten public offering, addressed
to the underwriters, if any, and to the Investor.

          4.3  Expenses of Registration.  All expenses, other than underwriting
               ------------------------
discounts and commissions incurred in connection with the requests for
registration pursuant to Section 4.1, and the reasonable fees and disbursements
of counsel to the Investor, including (without limitation) all registration,
filing and qualification fees, printers' and accounting fees, fees and
disbursements of counsel for the Company shall be borne by the Company.

     5.  Conditions of the Investor's Obligations at Closing.  The obligations
         ---------------------------------------------------
of the Investor under subsection 1.2 of this Agreement are subject to the
fulfillment on or before the Closing of each of the following conditions, the
waiver of which shall not be effective without the Investor's consent thereto:

          5.1  Representations and Warranties.  The representations and
               ------------------------------
warranties of the Company contained in Section 2 shall be true on and as of the
Closing with the same effect as though such representations and warranties had
been made on and as of the date of such Closing.

                                       7
<PAGE>

          5.2  Performance.  The Company shall have performed and complied with
               -----------
all agreements, obligations and conditions contained in this Agreement that are
required to be performed or complied with by it on or before the Closing.

          5.3  Qualifications.  All authorizations, approvals, or permits, if
               --------------
any, of any governmental authority or regulatory body of the United States or of
any state that are required in connection with the lawful issuance and sale of
the Securities pursuant to this Agreement shall be duly obtained and effective
as of the Closing.

          5.4  Proceedings and Documents.  All corporate and other proceedings
               -------------------------
in connection with the transactions contemplated at the Closing and all
documents incident thereto shall be reasonably satisfactory in form and
substance to the Investor, and it shall have received all such counterpart
original and certified or other copies of such documents as it may reasonably
request.

          5.5  Opinion of Company Counsel.  The Investor shall have received an
               --------------------------
opinion from counsel to the Company in form and substance reasonably
satisfactory to the Investor and attached hereto as Exhibit B.
                                                    ---------

     6.  Conditions of the Company's Obligations at Closing.  The obligations
         --------------------------------------------------
of the Company to the Investor under this Agreement are subject to the
fulfillment on or before the Closing of each of the following conditions by the
Investor:

          6.1  Representations and Warranties.  The representations and
               ------------------------------
warranties of the Investor contained in Section 3 shall be true on and as of the
Closing with the same effect as though such representations and warranties had
been made on and as of the Closing.

          6.2  Payment of Purchase Price.  The Investor shall have delivered
               -------------------------
the purchase price specified in Section 1.

          6.3  Qualifications.  All authorizations, approvals, or permits, if
               --------------
any, of any governmental authority or regulatory body of the United States or of
any state that are required in connection with the lawful issuance and sale of
the Securities pursuant to this Agreement shall be duly obtained and effective
as of the Closing.

     7.  Miscellaneous.
         -------------

          7.1  Survival of Warranties.  The warranties, representations and
               ----------------------
covenants of the Company and the Investor contained in or made pursuant to this
Agreement shall survive the execution and delivery of this Agreement and the
Closing and shall in no way be affected by any investigation of the subject
matter thereof made by or on behalf of the Investor or the Company.

          7.2  Assignment; Successors and Assigns.  No provision of this
               ----------------------------------
Agreement may be assigned (other than to an affiliate of the Investor), without
the prior written consent of the other parties hereto. Except as otherwise
provided herein, the terms and conditions of this Agreement shall inure to the
benefit of and be binding upon the respective successors and assigns of the
parties (including transferees of any Securities). Nothing in this Agreement,
express or implied, is intended to confer upon any party other than the parties
hereto or their

                                       8
<PAGE>

respective successors and assigns any rights, remedies, obligations, or
liabilities under or by reason of this Agreement, except as expressly provided
in this Agreement.

          7.3  Governing Law.  This Agreement shall be governed by and
               -------------
construed under the laws of the State of California as applied to agreements
among California residents entered into and to be performed entirely within
California.

          7.4  Expenses.  Irrespective of whether the Closing is effected, each
               --------
party shall pay all costs and expenses that it incurs with respect to the
negotiation, execution, delivery and performance of this Agreement.

          7.5  Amendments and Waivers.  Any term of this Agreement may be
               ----------------------
amended and the observance of any term of this Agreement may be waived (either
generally or in a particular instance and either retroactively or
prospectively), only with the written consent of the Company and the Investor.
Any amendment or waiver effected in accordance with this paragraph shall be
binding upon each holder of any securities purchased under this Agreement at the
time outstanding (including securities into which such securities are
convertible), each future holder of all such securities, and the Company.

          7.6  Notices, etc.  All notices and other communications required or
               ------------
permitted hereunder shall be in writing and shall be sent by personal delivery,
facimile, overnight courier or mailed by certified or registered mail, postage
prepaid, return receipt requested, to the facsimile number or address as
follows:


                   Company:    Applied Imaging Corp.
                               2380 Walsh Avenue, Building B
                               Santa Clara, California 95051
                               Telephone:  (408) 562-0250
                               Facsimile:  (408) 562-0264
                               Attention: President

                   with a copy (which will not constitute notice) to:

                               Wilson Sonsini Goodrich & Rosati
                               650 Page Mill Road
                               Palo Alto, California 94304-1050
                               Telephone:  (650) 493-9300
                               Facsimile:  (650) 493-6811
                               Attention:  David J. Saul

                   Investor:   ______________________________

                               ______________________________

                               ______________________________

                               ______________________________

                                       9
<PAGE>

                   with a copy (which will not constitute notice) to:

                               Antonio Valla, Esq.
                               Gilliss & Valla
                               180 Montgomery St. Suite 820
                               San Francisco, California 94104
                               Telephone:  (415) 782-3999
                               Facismile:  (415) 782-3998

     or to such other facsimile number or address provided to the parties to
this Agreement in accordance with this Section 7.6.  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 2 days after deposit in the mails (as determined by
reference to the postmark).

          7.8  Severability.  If one or more provisions of this Agreement are
               ------------
held to be unenforceable under applicable law, such provision shall be excluded
from this Agreement and the balance of the Agreement shall be interpreted as if
such provision were so excluded and shall be enforceable in accordance with its
terms.

          7.9  Entire Agreement.  This Agreement and the documents referred to
               ----------------
herein constitute the entire agreement among the parties and no party shall be
liable or bound to any other party in any manner by any warranties,
representations, or covenants except as specifically set forth herein or
therein.

                                       10
<PAGE>

     IN WITNESS WHEREOF, the parties have executed this Agreement as of the date
first above written.


COMPANY:                               INVESTOR:

APPLIED IMAGING CORP.                   _______________________________

By:______________________________      By:_____________________________

Title:_____________________________    Title:____________________________

                                       11