Document:

<PAGE>
                                                                   EXHIBIT 10.31
                          LOAN MODIFICATION AGREEMENT

     This Loan Modification Agreement is entered into as of September 9, 1999,
by and between Applied Imaging Corp. and Applied Imaging International Limited
(collectively, the "Borrower") and Silicon Valley Bank ("Bank").

1.   DESCRIPTION OF EXISTING INDEBTEDNESS:  Among other indebtedness which may
     ------------------------------------
be owing by Borrower to Bank, Borrower is indebted to Bank pursuant to, among
other documents, a Loan and Security Agreement, dated September 9, 1999, as may
be amended from time to time, (the "Loan Agreement").  The Loan Agreement
provided for, among other things, a Term Loan in the original principal amount
of Two Million Dollars ($2,000,000).  Defined terms used but not otherwise
defined herein shall have the same meanings as in the Loan Agreement.

Hereinafter, all indebtedness owing by Borrower to Bank shall be referred to as
the "Indebtedness."

2.   DESCRIPTION OF COLLATERAL AND GUARANTIES.  Repayment of the Indebtedness is
     ----------------------------------------
secured by the Collateral as described in the Loan Agreement.

Hereinafter, the above-described security documents and guaranties, together
with all other documents securing repayment of the Indebtedness shall be
referred to as the "Security Documents".  Hereinafter, the Security Documents,
together with all other documents evidencing or securing the Indebtedness shall
be referred to as the "Existing Loan Documents".

3.   DESCRIPTION OF CHANGE IN TERMS.
     ------------------------------

     A.   Modification(s) to Loan Agreement
          ---------------------------------

          1.   Section 10 of the Loan Agreement is hereby replaced with the
               following:

               Notices.

               Unless otherwise provided in this Agreement, all notices or
               demands by any party relating to this Agreement or any other
               agreement entered into in connection herewith shall be in writing
               and (except for financial statements and other informational
               documents which may be sent by first-class mail, postage prepaid)
               shall be personally delivered or sent by a recognized overnight
               delivery service, certified mail, postage prepaid, return receipt
               requested, or by telefacsimile to Borrower or to Bank, as the
               case may be, at its addresses set forth below:

                If to Borrower:

                Applied Imaging Corp.
                2380 Walsh Avenue, Bldg
                Santa Clara, CA 95051
                Attn: ____________________
                FAX: __________

                and to Applied Imaging International Limited
                ______________________________
                ______________________________
                Attn: ____________________
                FAX: __________
<PAGE>

               If to Bank:
                        Silicon Valley Bank
                        3003 Tasman Drive
                        Santa Clara, CA 95054-1191
                        Attn: Kathryn Lungaro
                        FAX: 408-654-1045

               Subrogation and Similar Rights.

               Notwithstanding any other provision of this Agreement or any
               other Loan Document, until payment to Bank in full and
               performance of all Obligations, each Borrower irrevocably waives
               all rights that it may have at law or in equity (including,
               without limitation, any law subrogating the Borrower to the
               rights of Bank under the Loan Documents) to seek contribution,
               indemnification, or any other form of reimbursement from any
               other Borrower, or any other Person now or hereafter primarily or
               secondarily liable for any of the Obligations, for any payment
               made by the Borrower with respect to the Obligations in
               connection with the Loan Documents or otherwise and all rights
               that it might have to benefit from, or to participate in, any
               security for the Obligations as a result of any payment made by
               the Borrower with respect to the Obligations in connection with
               the Loan Documents or otherwise.  Any agreement providing for
               indemnification, reimbursement or any other arrangement
               prohibited under this Section 10 shall be null and void.  If any
               payment is made to a Borrower in contravention of this Section
               10, such Borrower shall hold such payment in trust for Bank and
               such payment shall be promptly delivered to Bank for application
               to the Obligations, whether matured or unmatured.

               Waivers of Notice.

               Each Borrower waives notice of acceptance hereof; notice of the
               existence, creation or acquisition of any of the Obligations;
               notice of an Event of Default; notice of the amount of the
               Obligations outstanding at any time; notice of intent to
               accelerate; notice of acceleration; notice of any adverse change
               in the financial condition of any other Borrower or of any other
               fact that might increase the Borrower's risk; presentment for
               payment; demand; protest and notice thereof as to any instrument;
               default; and all other notices and demands to which the Borrower
               would otherwise be entitled.  Each Borrower waives any defense
               arising from any defense of any other Borrower, or by reason of
               the cessation from any cause whatsoever of the liability of any
               other Borrower.  Bank's failure at any time to require strict
               performance by any Borrower of any provision of the Loan
               Documents shall not waive, alter or diminish any right of Bank
               thereafter to demand strict compliance and performance therewith.
               Nothing contained herein shall prevent Bank from foreclosing on
               the Lien of any deed of trust, mortgage or other security
               instrument, or exercising any rights available thereunder, and
               the exercise of any such rights shall not constitute a legal or
               equitable discharge of any Borrower.  Each Borrower also waives
               any defense arising from any act or omission of Bank that changes
               the scope of the Borrower's risks hereunder.  Each Borrower
               hereby waives any right to assert against Bank any defense (legal
               or equitable), setoff, counterclaim, or claims that such Borrower
               individually may now or hereafter have against another Borrower
               or any other Person liable to

                                       2
<PAGE>

               Borrower with respect to the Obligations in any manner or
               whatsoever until the Obligations are paid in full to Bank.

               Subrogation Defenses.

               Until payment to Bank in full and performance of all Obligations,
               each Borrower hereby waives any defense based on impairment or
               destruction of its subrogation or other rights against any other
               Borrower and waives all benefits which might otherwise be
               available to it under California Civil Code Sections 2809, 2810,
               2819, 2839, 2845, 2848, 2850, 2899 and 3433 and California Code
               of Civil Procedure Sections 580a, 580b, 580d and 726, as those
               statutory provisions are now in effect and hereafter amended, and
               under any other similar statutes now and hereafter in effect.

               Right to Settle, Release.

               (a)  The liability of Borrower hereunder shall not be diminished
                    by (i) any agreement, understanding or representation that
                    any of the Obligations is or was to be guaranteed by another
                    Person or secured by other property, or (ii) any release or
                    unenforceability, whether partial or total, or rights, if
                    any, which Borrower may now or hereafter have against any
                    other Person, including another Borrower, or property with
                    respect to any of the Obligations.

               (b)  Without notice to any Borrower and without affecting the
                    liability of any Borrower hereunder, Bank may (i)
                    compromise, settle, renew, extend the time for payment,
                    change the manner or terms of payment, discharge the
                    performance of, decline to enforce, or release all or any of
                    the Obligations with respect to a Borrower, (ii) grant other
                    indulgences to a Borrower in respect of the Obligations,
                    (iii) modify in any manner any documents, relating to the
                    Obligations with respect to a Borrower, (iv) release,
                    surrender or exchange any deposits or other property
                    securing the Obligations, whether pledged by a Borrower or
                    any other Person, or (v) compromise, settle renew, or extend
                    the time for payment, discharge the performance of, decline
                    to enforce, or release all or any obligations of any
                    guarantor, endorser or other Person who is now or may
                    hereafter be liable with respect to any of the Obligations.

4.   CONSISTENT CHANGES.  The Existing Loan Documents are hereby amended
     ------------------
wherever necessary to reflect the changes described above.

5.   NO DEFENSES OF BORROWER.  Borrower (and each guarantor and pledgor signing
     -----------------------
below) agrees that, as of the date hereof, it has no defenses against the
obligations to pay any amounts under the Indebtedness.

6.   CONTINUING VALIDITY.  Borrower (and each guarantor and pledgor signing
     -------------------
below) understands and agrees that in modifying the existing Indebtedness, Bank
is relying upon Borrower's representations, warranties, and agreements, as set
forth in the Existing Loan Documents.  Except as expressly modified pursuant to
this Loan Modification Agreement, the terms of the Existing Loan Documents
remain unchanged and in full force and effect.  Bank's agreement to
modifications to the existing Indebtedness pursuant to this Loan Modification
Agreement in no way shall obligate Bank to make any future modifications to the
Indebtedness.  Nothing in this Loan Modification Agreement shall constitute a
satisfaction of the Indebtedness.  It is the intention of Bank and Borrower to
retain as liable parties all makers and endorsers of

                                       3
<PAGE>

Existing Loan Documents, unless the party is expressly released by Bank in
writing. No maker, endorser, or guarantor will be released by virtue of this
Loan Modification Agreement. The terms of this paragraph apply not only to this
Loan Modification Agreement, but also to all subsequent loan modification
agreements.

     This Loan Modification Agreement is executed as of the date first written
above.

BORROWER:                                BANK:

APPLIED IMAGING CORP.                    SILICON VALLEY BANK

By:                                      By:
   -----------------------                  --------------------------
Name:                                    Name:
     ---------------------                    ------------------------
Title:                                   Title:
      --------------------                     -----------------------

APPLIED IMAGING INTERNATIONAL LIMITED

By:
   -----------------------
Name:
     ---------------------
Title:
      --------------------

                                       4<PAGE>
                                                                   EXHIBIT 10.32

                          LOAN MODIFICATION AGREEMENT

     This Loan Modification Agreement is entered into as of June 22, 2000, by
and between Applied Imaging Corp. and Applied Imaging International Limited
(collectively, the "Borrower") and Silicon Valley Bank ("Bank").

1.   DESCRIPTION OF EXISTING INDEBTEDNESS:  Among other indebtedness which may
     ------------------------------------
be owing by Borrower to Bank, Borrower is indebted to Bank pursuant to, among
other documents, a Loan and Security Agreement, dated September 9, 1999, as may
be amended from time to time, (the "Loan Agreement").  The Loan Agreement
provided for, among other things, a Term Loan in the original principal amount
of Two Million Dollars ($2,000,000).  Defined terms used but not otherwise
defined herein shall have the same meanings as in the Loan Agreement.

Hereinafter, all indebtedness owing by Borrower to Bank shall be referred to as
the "Indebtedness."

2.   DESCRIPTION OF COLLATERAL AND GUARANTIES.  Repayment of the Indebtedness is
     ----------------------------------------
secured by the Collateral as described in the Loan Agreement.   Additionally,
Borrower has agreed with Bank not to mortgage, pledge, hypothecate, or otherwise
encumber any of its Intellectual Property, pursuant to a Negative Pledge
Agreement.

Hereinafter, the above-described security documents and guaranties, together
with all other documents securing repayment of the Indebtedness shall be
referred to as the "Security Documents".  Hereinafter, the Security Documents,
together with all other documents evidencing or securing the Indebtedness shall
be referred to as the "Existing Loan Documents".

3.   DESCRIPTION OF CHANGE IN TERMS.
     ------------------------------

     A.   Modification(s) to Loan Agreement
          ---------------------------------

          1.   The following Section 2.1.2 entitled Revolving Advances" is
               hereby incorporated to read as follows:

               2.1.2  Revolving Advances.
                      ------------------

               (a)    Bank will make Advances not exceeding the Committed
               Revolving Line. Amounts borrowed under this Section may be repaid
               and reborrowed during the term of this Agreement.

               (b)    To obtain an Advance, Borrower must notify Bank by
               facsimile or telephone by 3:00 p.m. Pacific time on the Business
               Day the Advance is to be made. Borrower must promptly confirm the
               notification by delivering to Bank the Payment/Advance Form. Bank
               will credit Advances to Borrower's deposit account. Bank may make
               Advances under this Agreement based on instructions from a
               Responsible Officer or his or her designee or without
               instructions if the Advances are necessary to meet Obligations
               which have become due. Bank may rely on any telephone notice
               given by a person whom Bank believes is a Responsible Officer or
               designee. Borrower will indemnify Bank for any loss Bank suffers
               due to that reliance.

               (c)    The Committed Revolving Line terminates on the Revolving
               Maturity Date, when all Advances are immediately payable.
<PAGE>

          2.   Sub letter (a) under Section 2.2 entitled "Interest Rate,
               Payments" is hereby amended in part to provide that Advances
               accrue interest on the outstanding principal balance at a per
               annum rate of 1.75 percentage points above the Prime Rate.
               Interest due on the Advances is payable on the 21st day of each
               month.

          3.   Sub-section (ii) "Tangible Net Worth" of Section 6.7 entitled
               "Financial Covenants" is hereby amended to read as follows:

               Tangible Net Worth of at least $3,500,000 for the 1st and 2nd
               month of each fiscal quarter and $4,000,000 for the 3rd month of
               each fiscal quarter.

          4.   Sub-section (iv) "Profitability" of Section 6.7 entitled
               "Financial Covenants" is hereby amended in part to provide for
               losses not to exceed $1,400,000 for the fiscal quarter ended
               March 31, 2000; and $575,000 for the quarter ending September 30,
               2000.

          5.   The following defined terms under Section 13.1 entitled
               "Definitions" are hereby amended and/or incorporated to read as
               follows:

               "Advance" or "Advances" is a loan advance (or advances) under the
               Committed Revolving Line.

               "Committed Revolving Line" is a Credit Extension of up to
               $500,000.

               "Revolving Maturity Date" is June 21, 2001.

               Sub-section (ii) "Tangible Net Worth" of the defined term "Tier 1
               Pricing Guideline" is hereby amended in part to provide for
               Tangible Net Worth of at least $3,500,000 for the 1st and 2nd
               month of each fiscal quarter and $4,000,000 for the 3rd month of
               each fiscal quarter.

               Sub-section (iv) "Profitability" of the defined term "Tier 1
               Pricing Guideline" is hereby amended in part to provide for
               losses not to exceed $1,400,000 for the fiscal quarter ended
               March 31, 2000; and $575,000 for the quarter ending September 30,
               2000.

4.   CONSISTENT CHANGES.  The Existing Loan Documents are hereby amended
     ------------------
wherever necessary to reflect the changes described above.

5.   PAYMENT OF LOAN FEE.  Borrower shall pay Bank a fee in the amount of Five
     -------------------
Thousand Dollars ($5,000) ("Loan Fee") plus all out-of-pocket expenses.

6.   NO DEFENSES OF BORROWER.  Borrower (and each guarantor and pledgor signing
     -----------------------
below) agrees that, as of the date hereof, it has no defenses against the
obligations to pay any amounts under the Indebtedness.

7.   CONTINUING VALIDITY.  Borrower (and each guarantor and pledgor signing
     -------------------
below) understands and agrees that in modifying the existing Indebtedness, Bank
is relying upon Borrower's representations, warranties, and agreements, as set
forth in the Existing Loan Documents.  Except as expressly modified pursuant to
this Loan Modification Agreement, the terms of the Existing Loan Documents
remain unchanged and in full force and effect.  Bank's agreement to
modifications to the existing Indebtedness pursuant to this

                                       2
<PAGE>

Loan Modification Agreement in no way shall obligate Bank to make any future
modifications to the Indebtedness. Nothing in this Loan Modification Agreement
shall constitute a satisfaction of the Indebtedness. It is the intention of Bank
and Borrower to retain as liable parties all makers and endorsers of Existing
Loan Documents, unless the party is expressly released by Bank in writing. No
maker, endorser, or guarantor will be released by virtue of this Loan
Modification Agreement. The terms of this paragraph apply not only to this Loan
Modification Agreement, but also to all subsequent loan modification agreements.

8.   CONDITIONS.  The effectiveness of this Loan Modification Agreement is
     ----------
conditioned upon payment of the Loan Fee.

     This Loan Modification Agreement is executed as of the date first written
above.

BORROWER:                                BANK:

APPLIED IMAGING CORP.                    SILICON VALLEY BANK

By:                                      By:
   ----------------------                   ------------------------
Name:                                    Name:
     --------------------                     ----------------------
Title:                                   Title:
      -------------------                      ---------------------

APPLIED IMAGING INTERNATIONAL LIMITED

By:
   ----------------------
Name:
     --------------------
Title:
      -------------------

                                       3
<PAGE>

                                   EXHIBIT C
                            COMPLIANCE CERTIFICATE

TO:       SILICON VALLEY BANK
          3003 Tasman Drive
          Santa Clara, CA 95054

FROM:     APPLIED IMAGING CORP.

     The undersigned authorized officer of Applied Imaging Corp. ("Borrower")
certifies that under the terms and conditions of the Loan and Security Agreement
between Borrower and Bank (the "Agreement"), (i) Borrower is in complete
compliance for the period ending _______________ with all required covenants
except as noted below and (ii) all representations and warranties in the
Agreement are true and correct in all material respects on this date.  Attached
are the required documents supporting the certification.  The Officer certifies
that these are prepared in accordance with Generally Accepted Accounting
Principles (GAAP) consistently applied from one period to the next except as
explained in an accompanying letter or footnotes.  The Officer acknowledges that
no borrowings may be requested at any time or date of determination that
Borrower is not in compliance with any of the terms of the Agreement, and that
compliance is determined not just at the date this certificate is delivered.

   Please indicate compliance status by circling Yes/No under "Complies" column.
<TABLE>
<CAPTION>
<S>                                        <C>                                 <C>                     <C>        <C>
        Reporting Covenant                            Required                                            Complies
        -----------------                             --------                                            --------
        Monthly financial statements + CC             Monthly within 20 days                            Yes       No
        Annual (Audited)                              FYE within 90 days                                Yes       No
        10-Q, 10-K and 8-K                            Within 5 days after filing with SEC               Yes       No

        Financial Covenant                            Required                     Actual                 Complies
        ------------------                            --------                     ------                 --------
        Tier 1 Pricing Guideline
        ------------------------
        Maintain on a Monthly Basis:
         Minimum Tangible Net Worth                   $3,500,000*                  $______              Yes       No
         Maximum Debt/Tangible Net Worth**            2.00:1.00                    ________:1.00        Yes       No
         Minimum Liquidity Coverage*                                                                    Yes       No

* For the 1st and 2nd months of each fiscal quarter and $4,000,000 for the 3rd month of each fiscal quarter.

        Profitability:                                Quarterly                    $_________           Yes       No

                        Losses not to exceed:         $1,400,000 for the fiscal quarter ending          Yes       No
                                                      March 31, 2000; $500,000 for the fiscal
                                                      quarter ending June 30, 2000; $575,000 for
                                                      the fiscal quarter ending September 30,
                                                      2000; $250,000 for the fiscal quarter
                                                      ending December 31, 2000; $100,000 for the
                                                      fiscal quarter ending March 31, 2001; and
                                                      $100,000 for the fiscal quarter ending
                                                      June 30, 2001.
</TABLE>
<PAGE>

<TABLE>
<CAPTION>
<S>                                        <C>                                 <C>                     <C>        <C>
Tier 2 Pricing Guideline (to be maintained for Tier 2 Pricing)
----------------------------------------------------------------
Maintain on a Monthly Basis:
 Minimum Tangible Net Worth                           $5,000,000                   $_______             Yes       No
 Maximum Debt/Tangible Net Worth**                    1.75:1.00
                                                      Decreasing to 1.50
                                                      beginning 4/30/2000
                                                      and thereafter               _____:1.00           Yes       No
 Minimum Liquidity Coverage*                                                                            Yes       No

Profitability:                                        Quarterly                    $_______             Yes       No

                        Losses not to exceed:         $800,000 for the fiscal quarter ending            Yes       No
                                                      March 31, 2000; $500,000 for the fiscal
                                                      quarter ending June 30, 2000; $500,000 for
                                                      the fiscal quarter ending September 30,
                                                      2000; and $250,000 for the fiscal quarter
                                                      ending December 31, 2000.
</TABLE>

*    Cash and cash equivalents plus 50% of accounts receivable in which the
account debtors primary office is located in the United States of not less than
the greater of either (a) 2 times the outstanding Credit Extension under the
Term Loan, or (b) 6 months of the Average Monthly Cash Losses, as determined as
determined during the most recent 3 month period (for calculation purposes,
Average Monthly Cash Losses means the average monthly change in cash from
operations in accordance with GAAP). At such time as Borrower maintains 2
consecutive fiscal quarters of a 3 month minimum Debt Service Coverage of 1.50
to 1.00, the Liquidity Coverage, above shall be replaced by a minimum Debt
Service Coverage ratio requirement of 1.50 to 1.00. For calculation purposes,
Debt Service Coverage is defined as the sum of earnings after tax plus interest
and non-cash expenses, divided by the sum of current portion of long term debt
plus interest.

**exclude deferred revenue from Total Liabilities

                                      -----------------------------------
                                                 BANK USE ONLY

                                      Received by:
                                                  -----------------------
                                                    AUTHORIZED SIGNER

                                      Date:
                                           ------------------------------

                                      Verified:
                                               --------------------------
                                                  AUTHORIZED SIGNER

                                      Date:
                                           ------------------------------
                                      Compliance Status:       Yes     No
                                      -----------------------------------

Comments Regarding Exceptions:  See Attached.

Sincerely,

Applied Imaging Corp.

---------------------------------
Signature

---------------------------------
Title

---------------------------------
Date

                                       2
<PAGE>

                              SILICON VALLEY BANK

                       PRO FORMA INVOICE FOR LOAN CHARGES

BORROWER:      Applied Imaging, Inc.
               Applied Imaging International Ltd.

LOAN OFFICER:  Kathryn Lungaro

DATE:          June 14, 2000

               Loan Fee                             $5,000.00
               Documentation Fee                       700.00

               Less Fee Paid                         5,000.00

               TOTAL FEE DUE                        $  700.00
               -------------                        =========

Please indicate the method of payment:

        {_} A check for the total amount is attached.

        {X} Debit DDA # 3300120647 for the total amount.
                        ----------

----------------------------------------------
Borrower                                (Date)

----------------------------------------------
Borrower                                (Date)

----------------------------------------------
Silicon Valley Bank                     (Date)
Account Officer's Signature

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