Applied Precision, Inc. Sample Contracts

FORM OF INDEMNIFICATION AGREEMENT
Indemnification Agreement • June 30th, 2006 • Applied Precision, Inc. • Delaware

Both the Company and Indemnitee recognize that highly competent persons have become more reluctant to serve publicly-held corporations as directors or in other capacities unless they are provided with adequate protection through insurance or adequate indemnification against inordinate risks of claims and actions against them arising out of their service to and activities on behalf of the corporation.

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Amended and Restated Loan and Security Agreement (Exim Program)
Loan and Security Agreement • June 30th, 2006 • Applied Precision, Inc. • California

THIS AMENDED AND RESTATED LOAN AND SECURITY AGREEMENT is entered into on the above date between SILICON VALLEY BANK (“Silicon”), whose address is 3003 Tasman Drive, Santa Clara, California 95054 and the borrower(s) named above (jointly and severally, the “Borrower”), whose chief executive office is located at the above address (“Borrower’s Address”). The Amended and Restated Schedule to this Agreement (the “Schedule”) shall for all purposes be deemed to be a part of this Agreement, and the same is an integral part of this Agreement. (Definitions of certain terms used in this Agreement are set forth in Section 8 below.)*

EMPLOYMENT AGREEMENT
Employment Agreement • June 30th, 2006 • Applied Precision, Inc. • Washington

THIS EMPLOYMENT AGREEMENT (“Agreement”) is made this 18th day of January, 2002 (the “Effective Date”) between Applied Precision, LLC, a Delaware limited liability company (“Employer”), and Ronald C. Seubert (“Executive”).

Lease Date: January 3, 1996 Landlord: CWO/TCEP II Joint Venture #1, a Texas joint venture Address of Landlord: c/o Trammell Crow Company 626 120th Avenue N.E., Suite B104 Bellevue, WA 98005 Tenant: Applied Precision, Inc., a Washington corporation...
Lease Agreement • June 30th, 2006 • Applied Precision, Inc.

THIS LEASE AGREEMENT, made and entered into by and between CWO/TCEP II Joint Venture #1, a Texas joint venture, hereinafter referred to as “Landlord”, and Applied Precision, Inc., a Washington corporation , hereinafter referred to as “Tenant”;

FIRST AMENDMENT TO LEASE
Lease Agreement • June 30th, 2006 • Applied Precision, Inc.

THIS FIRST AMENDMENT TO LEASE (the “First Amendment”) is made this 10th day of June, 1996, by and between CWO/TCEP II Joint Venture #1, a Texas joint venture (the “Landlord”) and Applied Precision, Inc., a Washington corporation (the “Tenant”).

Limited Waiver and Amendment to Loan Documents
Loan Agreement • June 30th, 2006 • Applied Precision, Inc.

THIS LIMITED WAIVER AND AMENDMENT TO LOAN DOCUMENTS is entered into between Silicon Valley Bank (“Silicon”) and the borrower named above (“Borrower”).

Amended and Restated Mutual Subordination Agreement (Debt and Security Interest)
Mutual Subordination Agreement • June 30th, 2006 • Applied Precision, Inc.

This Amended and Restated Mutual Subordination Agreement is executed by the above-named Creditor (“Creditor”) in favor of Silicon Valley Bank (“Silicon”), whose address is 3003 Tasman Drive, Santa Clara, California 95054, with respect to the above-named Borrower (“Borrower”) and amends and restates in its entirety that certain Mutual Subordination Agreement between Subordinating Creditor and Silicon and dated February 28, 2003. In order to induce Silicon to extend or continue to extend financing to the Borrower (but without obligation on Silicon’s part to do so), the Creditor hereby agrees as follows:

Re: [*] Distributor Agreement dated July 18, 2001-
Distributor Agreement • June 30th, 2006 • Applied Precision, Inc.

Please accept this letter as confirmation of renewal for the above referenced distributor agreement. Per the agreement, this renewal is for an additional term of three years from July 18, 2006 to July 18, 2009.

June 1, 2006
Exclusive License Agreement • June 30th, 2006 • Applied Precision, Inc.
SECURITY AGREEMENT
Security Agreement • June 30th, 2006 • Applied Precision, Inc. • Washington

THIS SECURITY AGREEMENT (“Agreement”) is made and entered into as of February 28, 2003, by Applied Precision, LLC, a Delaware limited liability company (“Borrower”), for the benefit of Lakeside Management Financial, LLC (“Lender”).

Distribution Agreement with John P. Kummer AG
Distribution Agreement • June 30th, 2006 • Applied Precision, Inc. • Washington

This Distributor Agreement (“Agreement”) is made as of this eighteenth day of July, by and between Applied Precision, Inc., a Washington corporation with its principal place of business at 1040 12th Avenue NW, Issaquah, Washington 98027 (hereinafter referred to as “API”) and John P. Kummer AG, a corporation duly organized under the laws of Switzerland with its principal place of business at Zimmelstrasse 48, CH-63 14 Unterageri, Switzerland, (hereinafter referred to as “the Distributor”).

EXCLUSIVE LICENSE AGREEMENT FOR THE OPTICAL SECTIONING MICROSCOPE
Exclusive License Agreement • June 30th, 2006 • Applied Precision, Inc. • California

THIS LICENSE AGREEMENT is made and is effective this by and between THE REGENTS OF THE UNIVERSITY OF CALIFORNIA, a California nonprofit corporation having its statewide administrative offices at 300 Lakeside Drive, 22nd Floor, Oakland, California 94612–3550, (hereinafter referred to as “The Regents”), and APPLIED PRECISION, INC., having a principal place of business at 8505 S.E. 68th Street, Mercer Island, Washington 98040, (hereinafter referred to as the “Licensee”).

Contract
Secured Promissory Note • June 30th, 2006 • Applied Precision, Inc.

THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “1933 ACT”) OR THE SECURITIES LAWS OF ANY STATE, AND MAY NOT BE SOLD, TRANSFERRED, ASSIGNED OR HYPOTHECATED UNLESS PURSUANT TO SEC RULE 144 OR UNLESS THERE IS AN EFFECTIVE REGISTRATION STATEMENT UNDER THE 1933 ACT AND THE SECURITIES LAWS OF ANY STATE COVERING SUCH SECURITIES OR THE COMPANY RECEIVES AN OPINION OF COUNSEL FOR THE HOLDER OF THE SECURITIES REASONABLY SATISFACTORY TO THE COMPANY, STATING THAT SUCH SALE, TRANSFER, ASSIGNMENT OR HYPOTHECATION IS EXEMPT FROM THE REGISTRATION AND PROSPECTUS DELIVERY REQUIREMENTS OF THE 1933 ACT AND THE SECURITIES LAWS OF ANY STATE.

Amended and Restated Loan and Security Agreement
Loan and Security Agreement • June 30th, 2006 • Applied Precision, Inc. • California

THIS AMENDED AND RESTATED LOAN AND SECURITY AGREEMENT is entered into on the above date between SILICON VALLEY BANK (“Silicon”), whose address is 3003 Tasman Drive, Santa Clara, California 95054 and the borrower(s) named above (jointly and severally, the “Borrower”), whose chief executive office is located at the above address (“Borrower’s Address”). The Amended and Restated Schedule to this Agreement (the “Schedule”) shall for all purposes be deemed to be a part of this Agreement, and the same is an integral part of this Agreement. (Definitions of certain terms used in this Agreement are set forth in Section 8 below.)*

AMENDMENT NO. 1 TO SECOND AMENDED AND RESTATED LIMITED LIABILITY COMPANY AGREEMENT OF APPLIED PRECISION HOLDINGS, LLC
Limited Liability Company Agreement • June 30th, 2006 • Applied Precision, Inc.

This Amendment No. 1 to the Second Amended and Restated Limited Liability Company Agreement of Applied Precision Holdings, LLC (the “Company”) is entered into as of June 23, 2006 by and among (i) a Majority of the Common Members and (ii) a Majority of the Preferred Members.

MANAGEMENT AGREEMENT
Management Agreement • June 30th, 2006 • Applied Precision, Inc. • Massachusetts

This Management Agreement is made as of January 18, 2002 by and between Applied Precision, LLC, a Delaware limited liability company (“APLLC”), and Riverside Partners, Inc., a Delaware Corporation (“Riverside”). Capitalized terms used but not otherwise defined herein shall have the meanings ascribed to such terms in the Amended and Restated Limited Liability Company Agreement of Applied Precision Holdings, LLC (“APHLLC”) dated the date hereof (the “LLC Agreement”).

SECOND AMENDED AND RESTATED LIMITED LIABILITY COMPANY AGREEMENT OF APPLIED PRECISION HOLDINGS, LLC
Limited Liability Company Agreement • June 30th, 2006 • Applied Precision, Inc. • Delaware

This Second Amended and Restated Limited Liability Company Agreement of Applied Precision Holdings, LLC (the “Company”) is entered into as of March 31, 2005 by and among (i) AP Stock Company (“API”), f/k/a Applied Precision Incorporated, (ii) Donald Snow (“Snow”), Ronald Seubert (“Seubert”) and John Stewart (“Stewart”, and collectively with Snow and Seubert, the “Founders”), (iii) Riverside Fund II, L.P. (“Riverside”), (iv) DRW Venture Partners LP (“DRW”) and (v) each other Person admitted as a Member from time to time and listed on Exhibit A hereto.

SECOND AMENDMENT TO LEASE
Lease Agreement • June 30th, 2006 • Applied Precision, Inc.

THIS SECOND AMENDMENT TO LEASE is made and entered into as of March , 2006, by and between 12th & NEWPORT PARTNERS LLC, a Washington limited liability company (“Landlord”), and APPLIED PRECISION, LLC, a Washington limited liability company (“Tenant”).

WARRANT TO PURCHASE SECURITIES
Warrant Agreement • June 30th, 2006 • Applied Precision, Inc. • Delaware

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE STATE SECURITIES LAW OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION. EXCEPT AS OTHERWISE PROVIDED FOR HEREIN, THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED WITHOUT COMPLIANCE WITH THE TERMS OF THE AMENDED AND RESTATED LIMITED LIABILITY COMPANY AGREEMENT OF THE COMPANY.

REGISTRATION RIGHTS AGREEMENT
Registration Rights Agreement • June 30th, 2006 • Applied Precision, Inc. • Delaware

This Agreement is entered into as of January 18, 2002 by and among (i) Applied Precision Holdings, LLC (“APHLLC”), (ii) Applied Precision, LLC (“APLLC”), (iii) Applied Precision, Inc. (“API”), (iv) Donald Snow (“Snow”), Ronald Seubert (“Seubert”) and John Stewart (“Stewart”, and collectively with Snow and Seubert, the “Founders”), each of whom is a principal shareholder of API, (v) Riverside Fund II, L.P. (“Riverside”) and (vi) DRW Venture Partners LP (“DRW “). API, Snow, Seubert, Stewart, Riverside, DRW and any person or entity who hereafter becomes a party to or bound by this Agreement are collectively referred to herein as, the “Holders”.

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