Document:

exv10w4

 

Exhibit 10.4

Agreement No. 98-0228

LICENSE
AGREEMENT

     This Agreement is made effective the 22nd day of February 1999, by and between Wisconsin Alumni
Research Foundation (hereinafter called “WARF”), a nonstock, nonprofit Wisconsin corporation, and
TomoTherapy Incorporated (hereinafter called “TomoTherapy”), a corporation organized and existing
under the laws of Wisconsin;

     WHEREAS, WARF owns certain inventions that are described in the “Licensed Patents” defined below
and WARF previously granted a license to TomoTherapy under the Licensed Patents in an agreement,
Agreement No. 98-0025, between the parties dated March 1, 1998 (the “Prior License Agreement”); and

     WHEREAS, WARF and TomoTherapy desire to supersede the Prior License Agreement as set forth herein.

     NOW, THEREFORE, in consideration of the mutual covenants and agreements set forth below, the
parties covenant and agree as follows:

     Section 1. Definitions.

     For the purpose of this Agreement, the Appendix A definitions shall apply.

     Section 2. Grant.

          A. License.

     WARF hereby grants to TomoTherapy an exclusive license, limited to the Licensed Field, under the
Licensed Patents to make, have made, use, sell and otherwise distribute Products anywhere in the
world. Such license shall be exclusive except for the rights granted
to [  *  ] prior to the date of this
Agreement. WARF will not broaden or renew rights to [  *  ] outside those
previously rights granted to [  *  ] under the license agreement existing as of the date of this
Agreement.

          B. Sublicenses.

               (i) TomoTherapy may grant written, nonexclusive sublicenses to third parties. Any agreement
granting a sublicense shall state that the sublicense is subject to the termination of this
Agreement and TomoTherapy shall incorporate relevant terms of this Agreement in the sublicense.
TomoTherapy shall have the same responsibility for the activities of any sublicensee as if the
activities were directly those of TomoTherapy.

               (ii) In respect to sublicenses granted by TomoTherapy under this Section 2B, TomoTherapy shall pay
to WARF [  *  ] percent
([  *  ]%) of all fees, royalties and other payments received from such
sublicense(s) in the manner specified in Section 3F. At a minimum, TomoTherapy shall require its
sublicensee(s) to pay an upfront license fee of
$[  *  ] patent reimbursement of $[  *  ] and
minimum royalties of at least $[  *  ] per year beginning three years from the date of the
sublicense. In addition, TomoTherapy shall require sublicensees to pay royalties at a rate equal to
or exceeding the rate set forth in Section 3D. TomoTherapy shall provide WARF with a copy of all
sublicense agreements to

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Confidential
treatment has been requested for portions of this exhibit. The copy
filed herewith omits the information subject to the confidentiality
request. Omissions are designated as
[  *  ]. A complete version of this
exhibit has been filed separately with the Securities and Exchange
Commission.

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allow WARF to verify the proper revenue sharing arrangement under such sublicense. WARF shall keep
all such information confidential as provided under Section 14. TomoTherapy shall not receive from
sublicensees anything of value in lieu of cash payments in consideration for any sublicense under
this Agreement without the express prior written permission of WARF. Any strategic partners of
TomoTherapy who are not granted a right to make or have made and sell Products under the Licensed
Patents shall not be considered a sublicensee under this Agreement and shall not be subject to
income sharing under this Section 2B. Strategic partners of TomoTherapy who, in addition to funding
Product development, are granted a right to make or have made and sell Products shall be considered
sublicensees under this Section 2B and shall be subject to minimum fee and royalty requirements as
set forth herein; however, WARF shall not share in any fees for services provided by TomoTherapy or
in any funding which TomoTherapy represents in good faith is not consideration for sublicense
rights granted to such strategic partner.

               (iii) Agreements with third parties which permit such third party to purchase Products from
TomoTherapy and resell such Products shall be considered distribution agreements and not sublicense
agreements subject to this Section 2B. Under any such distribution agreement, TomoTherapy shall pay
royalties to WARF on the sale of Products to such third party in accordance with Section 3D and
such agreements shall not be subject to the fee and royalty requirements of Section 2B(ii).

     Section
3. Consideration.

          A. Development.

     TomoTherapy agrees to and warrants that: it has, or will obtain, the expertise necessary to
independently evaluate the inventions of the Licensed Patents; it will establish and actively and
diligently pursue the development plan (see Appendix E) to the
end that the inventions of the
Licensed Patents will be utilized to provide Products for sale in the retail market; and within one
month following the end of each calendar quarter ending on March 31, June 30, September 30 and
December 31 and until the date of first commercial sale of Products, it will supply WARF with a
written Development Report. All development activities and strategies and all aspects of Products
design and decisions to market and the like are entirely at the discretion of TomoTherapy, and
TomoTherapy shall rely entirely on its own expertise with respect thereto. WARF’s review of
TomoTherapy’s development plan is solely to verify the existence of TomoTherapy’s commitment to
development activity and to assure compliance with TomoTherapy’s obligations to utilize the
inventions of the Licensed Patents for the marketplace, as set forth above.

          B. License Fee.

     TomoTherapy
agrees to pay to WARF a license fee of
$[  *  ] of which
$[  *  ] was paid under the
terms of the Prior License Agreement leaving a balance of
$[  *  ] due to WARF hereunder. In lieu
of a cash payment of these license fees, TomoTherapy agrees to issue to WARF and WARF agrees to
accept shares of TomoTherapy’s Common Stock under the terms the Equity Agreement between WARF and
TomoTherapy of even date herewith.

          C. Patent Reimbursement.

     TomoTherapy
agrees to reimburse WARF for [  *  ]% of the actual costs WARF incurs in
filing, prosecuting and maintaining the Licensed Patents. In lieu of a cash payment of patent
reimbursement due hereunder, TomoTherapy agrees to issue and WARF agrees to accept shares of
TomoTherapy Common Stock under the terms of the Equity Agreement referred to above, as a one time,
full and final payment of TomoTherapy’s obligations under this Section 3C to pay a portion of
WARF’s

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patent
costs. Such shares are included in the
[  *  ]% total of equity securities
TomoTherapy agrees to issue WARF under Section 2A of the Equity Agreement. WARF shall have sole
discretion to make or maintain any patent filing of the Licensed Patents. However, if WARF fails to
maintain the Licensed Patents, TomoTherapy may elect to maintain them in WARF’s name at
TomoTherapy’s own expense. In such case, TomoTherapy may credit
[  *  ]% of such patent
expense against royalties due under Section 3D.

          D. Royalty.

               (i) In addition to the Section 3B license fee, TomoTherapy agrees to pay to WARF as “earned
royalties” a royalty per Product Unit sold or leased by TomoTherapy at a rate determined in
accordance with the following table based on the cumulative number of Product Units sold or leased
by TomoTherapy before and including the sale or lease of the applicable Product Unit:

	 	 	 	 	 
	Cumulative Product Units Sold	 	Royalty Per
	or Leased	 	Product Unit
	[  *  ]
	 	 	
$[  *  ]	 
	[  *  ]
	 	 	$[  *  ]	 
	[  *  ]
	 	 	$[  *  ]	 

               (ii) A Product Unit is deemed sold or leased and a royalty is deemed earned under this
Agreement as of the date the Product Unit is actually sold and at least one third of the total
purchase price has been received by TomoTherapy in the case of a sale, or one third of the annual
lease payments for the first year of a lease have been so received by TomoTherapy.

               (iii) WARF is exempt from paying income taxes under U.S. law. Therefore, all payments due under
this Agreement shall be made without deduction for taxes, assessments, or other charges of any kind
which may be imposed on WARF by any government outside of the United States or any political
subdivision of such government with respect to any amounts payable to WARF pursuant to this
Agreement. All such taxes, assessments, or other charges shall be assumed by TomoTherapy.

          E. Minimum Royalty.

     TomoTherapy further agrees to pay to WARF a minimum royalty per calendar year or part thereof
during which this Agreement is in effect starting in calendar year 2000, against which any earned
royalty paid by TomoTherapy or WARF’s share of TomoTherapy’s sublicensee(s) payments for the same
calendar year will be credited. The minimum royalty shall be $[  *  ] in calendar year 2000, $[  *  ]
in 2001, $[  *  ] in 2002, and $[  *  ] in 2003 and each calendar year thereafter. The minimum
royalty for a given year shall be due at the time payments are due for the calendar quarter ending
on December 31. It is understood that the minimum royalties will apply on a calendar year basis,
and that sales of Products requiring the payment of earned royalties made during a prior or
subsequent calendar year shall have no effect on the annual minimum royalty due WARF for any given
calendar year.

          F.
Accounting; Payments.

               (i) Amounts owing to WARF under Section 3D shall be paid on a quarterly basis, with such
amounts due and received by WARF on or before the thirtieth day following the end of

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the calendar quarter ending on March 31, June 30, September 30 or December 31 in which such amounts
were earned. The balance of any amounts which remain unpaid more than thirty (30) days after they
are due to WARF shall accrue interest until paid at the rate of the lesser of one percent (1%) per
month or the maximum amount allowed under applicable law. However, in no event shall this
interest provision be construed as a grant of permission for any payment delays.

               (ii) Except as otherwise directed, all amounts owing to WARF under this Agreement shall be paid in
U.S. dollars to WARF at the address provided in Section 16(a). All royalties owing with respect to
selling prices stated in currencies other than U.S. dollars shall be converted at the rate shown in
the Federal Reserve Noon Valuation — Value of Foreign Currencies
on the day preceding the payment.

               (iii) A full accounting showing how any amounts owing to WARF under Section 3D have been calculated
shall be submitted to WARF on the date of each such payment. Such accounting shall be on a
per-country and product line, model or tradename basis and shall be summarized on the form shown in
Appendix C of this Agreement. In the event no payment is owed to WARF, a statement setting forth
that fact shall be supplied to WARF.

     Section 4. Certain Warranties of WARF.

          A. WARF warrants that except as otherwise provided under Section 13 of this Agreement with
respect to U.S. Government interests, it is the owner of the Licensed Patents or otherwise has the
right to grant the licenses granted to TomoTherapy in this Agreement. However, nothing in this
Agreement shall be construed as:

               (i) a warranty or representation by WARF as to the validity or scope of any of the Licensed
Patents;

               (ii) a warranty or representation that anything made, used, sold or otherwise disposed of under the
license granted in this Agreement will or will not infringe patents of third parties; or

               (iii) an obligation to furnish any know-how not provided in the Licensed Patents or any services
other than those specified in this Agreement.

          B. WARF MAKES NO REPRESENTATIONS, EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESS OR
IMPLIED, AND ASSUMES NO RESPONSIBILITIES WHATSOEVER WITH RESPECT TO USE, SALE, OR OTHER DISPOSITION
BY TOMOTHERAPY OR ITS VENDEES OR OTHER TRANSFEREES OF PRODUCTS INCORPORATING OR MADE BY USE OF
INVENTIONS LICENSED UNDER THIS AGREEMENT.

     Section 5. Recordkeeping.

          A. TomoTherapy shall keep books and records sufficient to verify the accuracy and
completeness of TomoTherapy’s accounting referred to above, including without limitation inventory,
purchase and invoice records relating to the Products or their manufacture. Such books and records
shall be preserved for a period not less than six (6) years after they are created during and after
the term of this Agreement.

          B. TomoTherapy shall take all steps necessary so that WARF may within sixty (60) days of
its request review and copy all the books and records at a single U.S. location to verify the
accuracy of TomoTherapy’s accounting. Such review may be performed by any employee of WARF as

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well as by any attorney or registered CPA designated by WARF at WARF’s expense, upon reasonable
notice and during regular business hours. TomoTherapy shall have the right to approve WARF’s
outside auditors and to reject them for bona fide conflicts of interest. TomoTherapy shall further
have the right to require audit participants to sign a reasonable non-disclosure agreement, but
such agreement may not compromise the auditor’s confidential communications of finding with WARF.

          C. If a royalty payment deficiency is determined, TomoTherapy shall pay the royalty
deficiency outstanding within forty-five (45) days of receiving written notice thereof, plus
interest on outstanding amounts as described in Section 3F(i). Should TomoTherapy contest the
royalty payment deficiency, TomoTherapy shall notify WARF of such contest within forty-five (45)
days of receiving notice and shall remit any uncontested amount plus interest within this same time
period. WARF’s acceptance of such payment shall not signify acceptance of this amount as a
settlement of the contested amount.

          D. If a royalty payment deficiency for a calendar year exceeds five percent (5%) of the
royalties paid for that year, then TomoTherapy shall be responsible
for paying WARF’s out-of-pocket
expenses incurred with respect to such review.

     Section 6. Term and Termination.

          A. The term of this license shall begin on the effective date of this Agreement and
continue until this Agreement is terminated as provided herein or until the earlier of the date
that no Licensed Patent remains an enforceable patent or the payment of earned royalties under
Section 3D, once begun, ceases for more than eight (8) consecutive calendar quarters.

          B. TomoTherapy may terminate this Agreement at any time by giving at least ninety (90)
days’ written and unambiguous notice of such termination to WARF. Such a notice shall be
accompanied by a statement of the reasons for termination.

          C. If TomoTherapy at any time defaults in the timely payment of any monies due to WARF or
the timely submission to WARF of any Development Report, fails to actively pursue the development
plan, or commits any breach of any other covenant herein contained, and TomoTherapy fails to remedy
any such breach or default within ninety (90) days after written notice thereof by WARF, or if
TomoTherapy commits any act of bankruptcy, becomes insolvent, is unable to pay its debts as they
become due, files a petition under any bankruptcy or insolvency act, or has any such petition filed
against it which is not dismissed within sixty (60) days, or offers any component of the Licensed
Patents to its creditors, WARF may, at its option, terminate this Agreement by giving notice of
termination to TomoTherapy.

          D. Upon the termination of this Agreement, TomoTherapy shall remain obligated to provide an
accounting for and to pay royalties earned up to the date of the termination and any minimum
royalties shall be prorated as of the date of termination by the number of days elapsed in the
applicable calendar year.

     Section 7.
Assignability.

     This Agreement may not be transferred or assigned by TomoTherapy except with the prior written
consent of WARF or except upon sale of substantially all the assets of TomoTherapy to a third
party. In such event, TomoTherapy shall ensure that the third party assignee has agreed to be bound
by all the obligations of this Agreement as part of such assignment and TomoTherapy shall provide
WARF with written notice, including the address and contact person, of the assignee.

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     Section 8. Contest of Validity.

     In the event TomoTherapy contests the validity of any Licensed Patent, TomoTherapy shall continue
to pay royalties with respect to that patent as if such contest were not underway until the patent
is adjudicated invalid or unenforceable by a court of last resort.

     Section 9. Enforcement and Defense of Patents.

          A. WARF intends to protect the Licensed Patents against infringers or otherwise act to eliminate
infringement, when, in WARF’s sole judgment, such action may be reasonably necessary, proper, and
justified. In the event that TomoTherapy believes there is infringement of any Licensed Patent
under this Agreement which is to TomoTherapy’s substantial detriment, TomoTherapy shall provide WARF
with written notice that such infringement is occurring including reasonable evidence of the
infringement. WARF shall have the right to determine the best course of action to resolve such
infringement, including but not limited to, the right to settle such infringement by negotiating a
license with such infringer. The license terms, fees and royalties shall be on terms no more
favorable in the aggregate to the Licensee than (those contained in the sublicense most favorable to
TomoTherapy granted by TomoTherapy. In the event that WARF licenses such infringer WARF shall share
the income from such license with TomoTherapy as set forth in this Section 9A. Upon request by
WARF, TomoTherapy shall take action, join in an action, and otherwise provide WARF with such
assistance and information as may be useful to WARF in connection with WARF’s taking such action
(if the cause of action arose during the term of this Agreement and WARF reimburses TomoTherapy for
TomoTherapy’s reasonable out-of-pocket expenses). Any recovery or damages for infringement or
license fees or royalties obtained through any settlement of infringement claims, except enhanced
damages, derived through WARF taking such action shall be applied as follows: (a) first, to WARF to
reimburse WARF for expenses incurred in litigation or negotiating a settlement, including
reasonable attorneys’ fees, (b) second, to TomoTherapy to reimburse TomoTherapy for its reasonable
expenses in assisting with same, including reasonable attorneys’ fees, and (c) the balance of any
recovery or damages shall be divided
[  *  ] percent
([  *  ]%) to TomoTherapy and
[  *  ] percent
([  *  ]%) to
WARF. If WARF does not take action to abate the infringement of the Licensed Patents within [  *  ] of receiving the notice described above, TomoTherapy may request that WARF do so and WARF
will comply as long as TomoTherapy reimburses WARF each month for
[  *  ] percent
([  *  ]%) of WARF’s
actual expenses incurred in bringing such action. Such expenses may be billed by WARF as frequently
as monthly and shall be paid by TomoTherapy to WARF on a net thirty (30) days basis. Late payments
shall be subject to the interest provisions set forth in Section 3F(i) for late payments.
TomoTherapy shall be reimbursed for its contribution to the cost of litigation or settlement from
the proceeds of such action as described in this Section 9A. TomoTherapy shall not have the right
to bring any infringement action or enforce the Licensed Patents without WARF’s prior, written
consent.

          B. In the event of a declaratory judgment action brought by a third party, WARF shall have
the exclusive right to defend the Licensed Patents by litigation or settlement, including the right
to grant licenses to third parties bringing such action. In the event that WARF licenses such third
party WARF shall share the income from such license with TomoTherapy as set forth in Section 9A.

          C. WARF agrees that if it determines to resolve any infringement or litigation by the grant
of a license to the infringer or third party litigant, it will first offer in writing to allow
TomoTherapy to negotiate a sublicense with such party. If TomoTherapy is not successful in
negotiating a sublicense agreement within six (6) months of such notification or if time becomes of
the essence in negotiating a license agreement to settle the infringement litigation, WARF may
directly negotiate and grant such a

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license to such third party and will share any revenue generated by such license with TomoTherapy
in accordance with Section 9A.

     Section 10. Patent Marking.

     TomoTherapy shall insure that it applies patent markings that meet all requirements of U.S. law, 35
U.S.C. 287, with respect to all Products subject to this Agreement.

     Section 11.
Product Liability; Conduct of Business.

     TomoTherapy shall, at all times during the term of this Agreement and thereafter, indemnify, defend
and hold WARF and the inventors of the Licensed Patents harmless against all claims and expenses,
including legal expenses and reasonable attorneys fees, arising out of the death of or injury to
any person or persons or out of any damage to property and against any other claim, proceeding,
demand, expense and liability of any kind whatsoever (other than patent infringement claims)
resulting from the production, manufacture, sale, use, lease, consumption or advertisement of
Products arising from any right or obligation of TomoTherapy hereunder. WARF at all times reserves
the right to select and retain counsel of its own to defend WARF’s interests.

     Section 12. Use of Names.

     TomoTherapy shall not use WARF’s name, the name of any inventor of inventions governed by this
Agreement, or the name of the University of Wisconsin in sales promotion, advertising, or any other
form of publicity without the prior written approval of the entity or person whose name is being
used.

     Section 13. United States Government Interests.

     It is understood that if the United States Government (through any of its agencies or otherwise)
has funded research, during the course of or under which any of the inventions of the Licensed
Patents were conceived or made, the United States Government is entitled, as a right, under the
provisions of 35 U.S.C. § 200-212 and applicable regulations of Chapter 37 of the Code of Federal
Regulations, to a nonexclusive, nontransferable, irrevocable, paid-up license to practice or have
practiced the invention of such Licensed Patents for governmental purposes. Any license granted to
TomoTherapy in this Agreement shall be subject to such right.

     Section 14. Confidentiality.

     Both parties agree to keep all information marked confidential or otherwise subject to an
obligation of confidentiality under the terms of this Agreement confidential except to the extent
that:

     a. The receiving party can show by written record within sixty (60) days after disclosure
of the Information that it possessed such Information prior to its receipt from the other party;

     b. The information was already available to the public or became so through no fault of
the receiving party;

     c. The information is subsequently disclosed to the receiving party by a third party that
has the right to disclose it to the receiving party free of any obligations of confidentiality;

     d. Five years have elapsed from the later of the date of this Agreement or the disclosure
of the information to the receiving party by the other; or

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     e. Information the receiving party independently develops without reference to the confidential
information.

     Section 15. Miscellaneous.

     This Agreement shall be governed by and construed in all respects in accordance with the laws of
the State of Wisconsin. If any provisions of this Agreement are or shall come into conflict with
the laws or regulations of any jurisdiction or any governmental entity having jurisdiction over the
parties or this Agreement, those provisions shall be deemed automatically deleted, if such deletion
is allowed by relevant law, and the remaining terms and conditions of this Agreement shall remain
in full force and effect. If such a deletion is not so allowed or if such a deletion leaves terms
thereby made clearly illogical or inappropriate in effect, the parties agree to substitute new
terms as similar in effect to the present terms of this Agreement as may be allowed under the
applicable laws and regulations. The parties hereto are independent contractors and not joint
venturers or partners.

     Section 16. Notices.

     Any notice required to be given pursuant to the provisions of this Agreement shall be in writing
and shall be deemed to have been given at the earlier of the time when actually received as a
consequence of any effective method of delivery, including but not limited to hand delivery,
transmission by telecopier, or delivery by a professional courier service or the time when sent by
certified or registered mail addressed to the party for whom intended at the address below or at
such changed address as the party shall have specified by written notice, provided that any notice
of change of address shall be effective only upon actual receipt.

	 	(a)	 	Wisconsin Alumni Research Foundation

Attn: Managing Director

614 Walnut Street

Madison, Wisconsin 53705
	 
	 	(b)	 	TomoTherapy Incorporated

Attn: President

P.O. Box 8024

Madison, Wisconsin 53708-8024

     With a copy of such notice to:

Michael E. Skindrud, Esq.

LaFollette & Sinykin

P.O. Box 2719

One East Main Street

Madison, Wisconsin 53701-2719

     Section 16. Integration.

     This Agreement constitutes the full understanding between the parties with reference to the subject
matter hereof, and no statements or agreements by or between the parties, whether orally or in
writing, made prior to or at the signing hereof, shall vary or modify the written terms of this
Agreement. Neither party shall claim any amendment, modification, or release from any provisions of
this Agreement by mutual agreement, acknowledgment, or otherwise, unless such mutual agreement is
in writing, signed

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by the other party, and specifically states that it is an amendment to this Agreement. This
Agreement supersedes the Prior License Agreement in its entirety.

     Section 17. Authority.

          A. No agreement between the parties shall exist unless the duly authorized representative of
TomoTherapy and the managing director of WARF have signed this document within forty-five (45) days
of the effective date written on the first page of this Agreement.

          B. The persons signing on behalf of WARF and TomoTherapy hereby warrant and represent that
they have authority to execute this Agreement on behalf of the party for whom they have signed.

     IN
WITNESS WHEREOF, the parties hereto have duly executed this Agreement on the dates
indicated below.

	 	 	 	 	 	 	 
	  WISCONSIN ALUMNI RESEARCH FOUNDATION	 	 
	 
	 	 	 	 	 	 
	By:

	 	/s/ Richard H. Leazer
	 	 	 	Date: 2/24, 1999
	 

	 	 	 	 	 	 
	 

	 	Richard H. Leazer, Managing Director	 	 	 	 
	 
	 	 	 	 	 	 
	  TOMOTHERAPY INCORPORATED	 	 
	 
	 	 	 	 	 	 
	By:

	 	/s/ Paul J. Reckwerdt
	 	 	 	Date: 2/24, 1999
	 

	 	 	 	 	 	 
	 

	 	Paul J. Reckwerdt, Vice-President	 	 	 	 
	 
	 	 	 	 	 	 
	Reviewed by WARF’s Attorney:	 	 	 	 
	 
	 	 	 	 	 	 
	/s/ Elizabeth L.R. Donley	 	 	 	2/27, 1999
	 	 	 	 	 
	Elizabeth L.R. Donley, Esq.	 	 	 	 

(WARF’s attorney shall not be deemed a signatory to this Agreement.)

WARF Ref: Swerdloff-P91009US

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APPENDIX A

     A. “Licensed Patents” shall refer to and mean those patents and patent applications listed on
Appendix B hereto and any subsequent patent application owned by WARF but only to the extent it
claims an invention claimed in a patent application listed on Appendix B.

     B. “Products” shall refer to and mean any and all products that employ or are in any way
produced by the practice of an invention claimed in the Licensed Patents or that would otherwise
constitute infringement of any claims of the Licensed Patents.

     A. “Affiliates” shall mean and include affiliated companies or other legal entities at least
fifty percent (50%) of whose outstanding stock entitled to vote for election of directors is now
or hereafter owned or controlled by TomoTherapy either directly or through one or more affiliated
companies or both, but such company or other legal entity shall be deemed to be an affiliated
company only so long as such ownership or control exists.

     D. “Development Report” shall mean a written account of TomoTherapy’s progress under the
development plan having at least the information specified on Appendix D to this Agreement, and
shall be sent to the address specified on Appendix D.

     E. “Licensed Field” shall be limited to the field of medical applications of all types,
including without limitation, both human and animal diagnostics and therapeutic applications and
all research uses designed to lead to such applications. However, WARF retains the right to use and
to designate other research institutions, including but not limited to the University of
Wisconsin-Madison and the UW Hospitals and Clinics, to use the Licensed Patents for noncommercial
research purposes.

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APPENDIX B

LICENSED PATENTS

	 	 	 	 	 	 	 	 	 
	REFERENCE	 	 	 	PATENT	 	ISSUE	 	APPLICATION
	NUMBER	 	COUNTRY	 	NUMBER	 	DATE	 	SERIAL NUMBER
	 
	 	 	 	 	 	 	 	 	 
	METHOD AND APPARATUS FOR RADIATION THERAPY (Swerdloff, Mackie, Holmes)
	 	 	 	 	 	 	 	 	 
	P91009US	 	UNITED STATES
	 	5,317,616.	 	5/31/94.	 	—
	P91009AU	 	AUSTRALIA
	 	661,640	 	12/12/95	 	 
	P91009BE	 	BELGIUM
	 	 	 	 	 	93301672.7
	P91009CA	 	CANADA
	 	 	 	 	 	2091275
	P91009DE	 	GERMANY
	 	 	 	 	 	 
	P91009FR	 	FRANCE
	 	 	 	 	 	93301672.7
	P91009GB	 	UNITED KINGDOM
	 	 	 	 	 	93301672.7
	P91009IL	 	ISRAEL
	 	104896	 	5/19/97	 	 
	P91009JP	 	JAPAN
	 	 	 	 	 	5-58983
	P91009KR	 	SOUTH KOREA
	 	 	 	 	 	4146/1993
	P91009MX	 	MEXICO
	 	 	 	 	 	931495
	P91009NL	 	NETHERLANDS
	 	 	 	 	 	93301672.7
	P91009NZ	 	NEW ZEALAND
	 	247042	 	6/4/96	 	 

P. O. BOX 7365     •     MADISON, WISCONSIN 53707-7365     •     TEL (608) 263-2500     •     FAX (608) 263-1064

Page 11 of 18

 

	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	APPLICATION
	REFERENCE	 	 	 	PATENT	 	ISSUE	 	SERIAL
	NUMBER	 	COUNTRY	 	NUMBER	 	DATE	 	NUMBER
	 
	 	 	 	 	 	 	 	 	 
	RADIATION THERAPY SYSTEM WITH CONSTRAINED ROTATIONAL FREEDOM (Swerdloff, Mackie, Holmes)
	 	 	 
	 	 	 	 	 	 
	P92135DE	 	GERMANY
	 	—	 	—	 	94920124.8
	P92135FR	 	FRANCE
	 	 	 	 	 	94920124.8
	P92135GB	 	UNITED KINGDOM
	 	 	 	 	 	94920124.8
	P92135IL	 	ISRAEL
	 	 	 	 	 	109960
	P92135JP	 	JAPAN
	 	8-511452	 	12/03/96	 	 
	P92135NL	 	NETHERLANDS
	 	 	 	 	 	94920124.8
	 	 	 
	 	 	 	 	 	 
	RADIATION THERAPY SYSTEM (Swerdloff, Mackie, Holmes)
	 	 	 
	 	 	 	 	 	 
	P92136EP	 	EPO
	 	—	 	—	 	97113658.5
	 	 	 
	 	 	 	 	 	 
	DYNAMIC BEAM FLATTENING APPARATUS FOR RADIATION THERAPY (Swerdloff, Mackie, Holmes)
	 	 	 
	 	 	 	 	 	 
	P92137DE	 	GERMANY
	 	—	 	—	 	94920125.5
	P92137FR	 	FRANCE
	 	 	 	 	 	94920125.5
	P92137GB	 	UNITED KINGDOM
	 	 	 	 	 	94920125.5
	P92137IL	 	ISRAEL
	 	 	 	 	 	109961
	P92137JP	 	JAPAN
	 	8-511453	 	12/03/96	 	 
	P92137NL	 	NETHERLANDS
	 	 	 	 	 	94920125.5

P. O. BOX 7365     •     MADISON, WISCONSIN 53707-7365     •     TEL (608) 263-2500     •     FAX (608) 263-1064

Page 12 of 18

 

	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	APPLICATION
	REFERENCE	 	 	 	PATENT	 	ISSUE	 	SERIAL
	NUMBER	 	COUNTRY	 	NUMBER	 	DATE	 	NUMBER
	 
	 	 	 	 	 	 	 	 	 
	RADIATION THERAPY SYSTEM (Swerdloff, Mackie, Holmes)
	 	 	 
	 	 	 	 	 	 
	P92138EP	 	EPO
	 	—	 	—	 	97113657.7
	 	 	 
	 	 	 	 	 	 
	DYNAMIC COLLIMATOR FOR RADIATION THERAPY (Swerdloff, Mackie, Holmes, Reckwerdt)
	 	 	 
	 	 	 	 	 	 
	P92138US	 	UNITED STATES
	 	5,442,675.	 	8/15/95.	 	—	 
	 	 	 
	 	 	 	 	 	 
	VERIFICATION SYSTEM FOR RADIATION THERAPY (Swerdloff, Mackie, Holmes)
	 	 	 
	 	 	 	 	 	 
	P92140US	 	UNITED STATES
	 	5,394,452.	 	2/28/95.	 	—
	P92140IL	 	ISRAEL
	 	 	 	 	 	109962
	 	 	 
	 	 	 	 	 	 
	MULTI-LEAF RADIATION ATTENUATOR FOR RADIATION THERAPY (Swerdloff, Mackie, Holmes)
	 	 	 
	 	 	 	 	 	 
	P92142US	 	UNITED STATES
	 	5,351,280.	 	9/27/94.	 	—
	P92142DE	 	GERMANY
	 	 	 	 	 	94920712.0
	P92142FR	 	FRANCE
	 	 	 	 	 	94920712.0
	P92142GB	 	UNITED KINGDOM
	 	 	 	 	 	94920712.0
	P92142IL	 	ISRAEL
	 	 	 	 	 	109962
	P92142JP	 	JAPAN
	 	8-511451	 	12/03/96	 	 
	P92142NL	 	NETHERLANDS
	 	 	 	 	 	94920712.0

P. O. BOX 7365     •     MADISON, WISCONSIN 53707-7365     •     TEL (608) 263-2500     •     FAX (608) 263-1064

Page 13 of 18

 

	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	APPLICATION
	REFERENCE	 	 	 	PATENT	 	ISSUE	 	SERIAL
	NUMBER	 	COUNTRY	 	NUMBER	 	DATE	 	NUMBER
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	MULTI-LEAF RADIATION ATTENUATOR FOR RADIATION THERAPY WITH VERIFICATION SYSTEM (Swerdloff, Mackie, Holmes)
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	P92143EP

	 	EPO
	 	 	—	 	 	—	 	 	97100108.6	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	MULTI-LEAF RADIATION ATTENUATOR FOR RADIATION THERAPY (Swerdloff, Mackie, Holmes)
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	P92144EP

	 	EPO	 	 	—	 	 	—	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	METHOD AND APPARATUS FOR RADIATION THERAPY (Swerdloff, Mackie, Holmes)
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	P94001US

	 	UNITED STATES
	 	 	5,528,650.	 	 	6/18/96.	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	RADIATION TREATMENT PLANNING METHOD AND APPARATUS (Holmes)
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	P95083US

	 	UNITED STATES
	 	 	5,647,663.	 	 	7/15/97.	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	METHOD OF REGISTERING A RADIATION TREATMENT PLAN TO A PATIENT (Reckwerdt, Mackie)
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	P95107US

	 	UNITED STATES
	 	 	5,673,300	 	 	9/30/97	 	 	 	 
	P95107CA

	 	CANADA
	 	 	—	 	 	—	 	 	2,207,539	 
	P95107EP

	 	EPO
	 	 	 	 	 	 	 	 	97303909.2	 
	P95107JP

	 	JAPAN
	 	 	 	 	 	 	 	 	09-167979	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	RADIATION THERAPY SYSTEM WITH CONSTRAINED ROTATIONAL FREEDOM (Swerdloff, Mackie, Holmes)
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	P95141US

	 	UNITED STATES
	 	 	5,548,627.	 	 	8/20/96.	 	 	 	 

P.O.BOX 7365  •  MADISON, WISCONSIN 53707-7365  •  TEL (608) 263-2500  •  FAX (608) 263-1064

Page 14 of 18

 

	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	APPLICATION
	REFERENCE	 	 	 	PATENT	 	ISSUE	 	SERIAL
	NUMBER	 	COUNTRY	 	NUMBER	 	DATE	 	NUMBER
	DYNAMIC BEAM FLATTENING APPARATUS FOR RADIATION THERAPY (Swerdloff, Mackie, Holmes)
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	P95201US

	 	UNITED STATES
	 	 	5,625,663.	 	 	04/29/97.	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	INTERFACE FOR RADIATION THERAPY MACHINE(SwerdIoff, Mackie, Holmes)
	P95202US

	 	UNITED STATES
	 	 	5,661,773	 	 	08/26/97	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	RADIATION THERAPY SYSTEM WITH CONSTRAINED ROTATIONAL FREEDOM (Swerdloff, Mackie, Holmes)
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	P95254US

	 	UNITED STATES
	 	 	5,724,400.	 	 	03/03/98.	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	METHOD AND
APPARATUS FOR CALIBRATION OF RADIATION THERAPY EQUIPMENT AND VERIFICATION OF RADIATION TREATMENT (Mackie, Reckwerdt, McNutt)
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	P98069US

	 	UNITED STATES	 	 	—	 	 	—	 	 	—	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	RADIATION THERAPY SYSTEM WITH CONSTRAINED ROTATIONAL FREEDOM AND DYNAMIC COLLIMATOR (Swerdloff, Mackie, Holmes)
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	P98167IL

	 	ISRAEL	 	 	 	 	 	—	 	 	 	 

P.O.BOX 7365  •  MADISON, WISCONSIN 53707-7365  •  TEL (608) 263-2500  •  FAX (608) 263-1064

Page 15 of 18

 

APPENDIX C

WARF ROYALTY REPORT

	 	 	 	 	 	 	 	 	 
	Licensee:

	 	 	 	 	 	Agreement No:	 	 
	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Inventor:

	 	 	 	 	 	P#:
	 	P
	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Period Covered:

	 	From:
	 	                    /                    /
	 	Through:
	 	                    /                    /
	 

	 	 	 	 
	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Prepared By:

	 	 	 	 	 	Date:	 	 
	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Approved By:

	 	 	 	 	 	Date:	 	 
	 	 	 	 	 	 	 

If license covers several major product lines, please prepare a separate report

for each line. Then combine all product lines into a summary report.

	 	 	 	 	 
	Report Type:

	 	o
	 	Single Product Line Report:                                         
	 
	 	 	 	 
	 

	 	o
	 	Multiproduct Summary Report. Page 1 of                      Pages
	 
	 	 	 	 
	 

	 	o
	 	Product Line Detail. Line:                      Tradename:                      Page:                     
	 
	 	 	 	 
	Report Currency:

	 	o
	 	U.S. Dollars   o    Other                                                             

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Gross	 	 	Less	 	 	Net	 	 	Royalty	 	 	Period Royalty Amount	 
	Country	 	Sales	 	 	Allowances	 	 	Sales	 	 	Rate	 	 	This Year	 	 	Last Year	 
	 
	U.S.A.
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Canada
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Europe:
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 
	Japan
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Other:
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 
	 
	TOTAL:
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 

Total
Royalty:                      Conversion Rate:                      Royalty in U.S. Dollars: $                     

The following royalty forecast is non-binding and for WARF’s internal planning purposes only:

     Royalty Forecast Under This Agreement: Next Quarter:                      Q2:                      Q3:              
        Q4:                     

* On a separate page, please indicate the reasons for returns or other adjustments if significant.

Also note any unusual occurrences that affected royalty amounts during this period.

To assist WARF’s forecasting, please comment on any significant expected trends in sales volume.

P.O.BOX 7365  •  MADISON, WISCONSIN 53707-7365  •  TEL (608) 263-2500  •  FAX (608) 263-1064

Page 16 of 18

 

APPENDIX D

DEVELOPMENT REPORT

	A.	 	Date development plan initiated and time period covered by this report.
	 
	B.	 	Development Report (4-8 paragraphs).

	 	1.	 	Activities completed since last report including the object and parameters of
the
development, when initiated, when completed and the results.
	 
	 	2.	 	Activities currently under investigation, i.e., ongoing activities including
object and parameters of such activities, when initiated, and projected date of completion.

	C.	 	Future Development Activities (4-8 paragraphs).

	 	1.	 	Activities to be undertaken before next report including, but not limited to,
the type and object of any studies conducted and their projected starting and completion dates.
	 
	 	2.	 	Estimated total development time remaining before a product will be commercialized.

	D.	 	Changes to initial development plan (2-4 paragraphs).

	 	1.	 	Reasons for change.
	 
	 	2.	 	Variables that may cause additional changes.

	E.	 	Items to be provided if applicable:

	 	1.	 	Information relating to Product that has become publicly available, e.g.,
published articles, competing products, patents, etc.
	 
	 	2.	 	Development work being performed by third parties other than TomoTherapy to
include name of third party, reasons for use of third party, planned future uses of third
parties including reasons why and type of work.
	 
	 	3.	 	Update of competitive information trends in industry, government compliance
(if applicable) and market plan.

PLEASE SEND DEVELOPMENT REPORTS TO:

Wisconsin Alumni Research Foundation

Attn.: Contract Coordinator

614 Walnut Street

P.O. Box 7365

Madison, WI 53707-7365

P.O.BOX 7365  •  MADISON, WISCONSIN 53707-7365  •  TEL (608) 263-2500  •  FAX (608) 263-1064

 Page  17 of 18 

 

APPENDIX E

DEVELOPMENT PLAN

     WARF hereby accepts the Business Plan submitted by TomoTherapy to WARF prior to the
execution of this Agreement as the development plan required hereunder.

P.O.BOX 7365  •  MADISON, WISCONSIN 53707-7365  •  TEL (608) 263-2500  •  FAX (608) 263-1064

 Page  18 of 18exv10w5

 

Exhibit 10.5

Agreement
No. 98-0227

EQUITY AGREEMENT

     This Agreement is made effective the 22nd day of February, 1999, by and between
Wisconsin Alumni Research Foundation (hereinafter called “WARF”), a nonstock, nonprofit
Wisconsin corporation, and TomoTherapy Incorporated (hereinafter called “TomoTherapy”), a
corporation organized and existing under the laws of Wisconsin;

     WHEREAS, WARF and TomoTherapy have entered into a License Agreement, as defined below,
with respect to certain inventions owned by WARF;

     WHEREAS, as an accommodation to TomoTherapy, WARF is willing to accept Shares in lieu of
the cash payment of license fees and patent reimbursement due under the License Agreement
(defined below);

     NOW, THEREFORE, in consideration of the mutual covenants and agreements set forth below,
the parties covenant and agree as follows:

     Section 1. Definitions.

     For the purpose of this Agreement, the Appendix A definitions shall
apply.

     Section 2. Issuance of Shares to WARF. 

          A. Issuance of Shares.

               (i) TomoTherapy shall issue to WARF 1,281 Shares equivalent to five percent (5%) of the
outstanding Equity Securities of TomoTherapy plus the five percent (5%) of Shares described in
Section 2A(ii) below within thirty (30) days after the execution of this Agreement. Within
such period, TomoTherapy shall deliver, or cause to be delivered, to WARF a stock certificate,
duly signed by appropriate officers of TomoTherapy and issued in WARF’s name, representing all
of the Shares required to be issued to WARF during that period.

               (ii) All Shares shall be fully-paid and non-assessable upon their issuance to WARF and
shall have the same rights and preferences granted other holders of Shares. TomoTherapy agrees
that WARF’s percentage interest in Equity Securities shall be maintained through the first
round of equity financing and until the cash investment in or net worth of TomoTherapy is
greater than $3,000,000 (the “End Date”). Thereafter, WARF’s percentage interest shall be
subject to dilution in the same manner as the most favored of the other holders of
TomoTherapy’s Shares. For purposes of calculating WARF’s percentage interest pursuant to this
paragraph, WARF shall be entitle to five percent (5%) of the Equity Securities of TomoTherapy
outstanding from time to time through the End Date plus five percent (5%) of the Shares that
TomoTherapy becomes obligated to issue pursuant to Section 8.4 of the Loan Agreement (see
Appendix C) and five percent (5%) of all Shares subject to stock option agreements granted by
TomoTherapy to employees, officers and directors through the End Date.

               (iii) WARF’s execution of this Agreement and agreement to waive the cash payment of the
License Agreement license fees and patent reimbursement as provided in Section 2C of this
Agreement shall be deemed full consideration for the issuance of the Shares, and no additional

P.O.BOX7365      •      MADISON, WISCONSIN 53707-7365      •      TEL(608) 263-2500      •      FAX(608) 263-1064

 Page 1 of 15 

 

consideration for such Shares shall be due from WARF. No Shares shall be subject to any
restrictions on their transfer other than the restrictions specified in herein,

          B. Certain Adjustments.

     If TomoTherapy pays a stock dividend or undertakes a split of its common stock, a
reverse split, a recapitalization, reorganization, or other similar action with respect to
its common stock between the date of this Agreement and the date that Shares are issued to
WARF pursuant to this Agreement, then appropriate adjustments shall be made to the number of
Shares to be issued to WARF pursuant to Section 2A so that WARF receives an equivalent
percentage of TomoTherapy’s issued and outstanding Shares.

          C. Effect on License Agreement.

     If TomoTherapy meets its obligations under Sections 2A and 2B of this Agreement and the
representations and warranties made by TomoTherapy in Section 6 of this Agreement are then
true, then, upon WARF’s receipt of a stock certificate representing all of the Shares to be
issued to WARF under Section 2A(i) (as adjusted), WARF shall waive the payment in cash of the
initial license fee specified in Section 3B and patent reimbursement specified in Section 3C
of the License Agreement.

     Section
3. Put Option.

          A. Grant of Put Option.

     TomoTherapy hereby agrees to repurchase the Shares issued to WARF pursuant to this
Agreement, at the option of WARF, on the terms contained in this Section 3.

          B. Period for Exercise.

     WARF shall have the right to exercise part or all of its put option under this Section 3
after the earlier of: (i) December 31, 2004; or (ii) one year after an initial public offering
but in no event earlier that the first date any other put option is permitted to be exercised
as held by a venture capital investor or founder. TomoTherapy shall notify WARF of the events
specified in clause (ii) of this Section 3B within ten (10) days after such event occurs. Such
right shall expire on the final day of the twenty-fourth calendar month following the first
day such right may be exercised hereunder.

          C. Price Per Share.

     TomoTherapy shall pay WARF consideration for each Share put to it hereunder in cash in
an amount equal to the Fair Market Value of the Shares being put as of the date WARF
exercises its put option, or in the event of an initial public offering, the average daily
closing price of a share of common stock of TomoTherapy as reported on the NASDAQ or such
other consolidated reporting system for the twenty (20) trading day period immediately
preceding the exercise of such put.

          D. Exercise of Option.

     WARF may exercise its put option only by its delivery of a written notice to TomoTherapy
that WARF is exercising its rights under this Section 3. In WARF’s sole discretion, WARF may
exercise its rights to either some or all of the Shares with respect to which it has a put
option under this Section 3 at any time after any of the events specified in Section 3B of
this Agreement and prior to its expiration date as set forth in Section 3B.

P.O.BOX7365      •      MADISON, WISCONSIN 53707-7365      •      TEL(608) 263-2500      •      FAX(608) 263-1064

 Page 2 of 15 

 

          E. Stock Splits, etc.

     If TomoTherapy pays a stock dividend or undertakes a split of its common stock, a reverse
split, a recapitalization, reorganization, or other similar action with respect to its common
stock, this put option shall apply to any new shares issued to WARF pursuant to such corporate
action and appropriate adjustments shall be made to the number of shares subject to this put
option (including any new shares) and the price per share under this option so that the value
of this option to WARF is not diminished by such corporate action.

          F. Inability of TomoTherapy to Purchase.

     If TomoTherapy is unable to lawfully purchase all of the Shares which it is required or
permitted to purchase pursuant to this Agreement because such purchase would cause TomoTherapy
to be insolvent, then until such time as TomoTherapy is legally able to purchase the Shares
pursuant to this Agreement at the original purchase price provided herein, or, if applicable,
the value redetermined as hereinafter set forth, the purchase thereof shall be considered to
be deferred, and the rights of TomoTherapy to purchase or demand purchase hereunder shall not
be considered to commence until that time. Notwithstanding the forgoing, if WARF shall so
request, TomoTherapy shall purchase as many Shares as it is legally able to purchase as
requested by WARF on the date originally required by this Section 3 (the “Original Closing
Date”) and at such times as WARF may thereafter reasonably request. Any deferral of the
purchase of Shares hereunder shall not change, defer or otherwise affect the date as of which
the value of each Share to be purchased is to be determined as provided herein (the “Original
Valuation Date”) with respect to deferred purchases occurring during the one (1) year period
following the Original Closing Date. Thereafter, the value per share of any Shares, the
purchase of which has been deferred hereunder (the “Deferred Shares”) shall be redetermined on
each successive one (1) year anniversary (“Redetermination Date”) of the Original Closing Date
and the value of each Deferred Share remaining to be purchased at any time shall be the
greater of (a) the value thereof determined on the Original Valuation Date, or (b) the value
thereof determined on the Redetermination Date last preceding the purchase of such Shares.

          Section 4. General Restriction on Sale or Transfer of Shares.

     Except as expressly permitted by this Agreement, WARF shall not transfer in any manner or
permit to be transferred in any manner, any Shares, which are now owned or which hereafter may
be acquired by WARF. For purposes of this Agreement, reference to a “transfer” of Shares means
any disposition of Shares or any interest therein, including, without limitation, any sale,
gift, assignment, pledge or encumbrance, whether such disposition occurs voluntarily, by
operation of law or otherwise. Except as otherwise expressly provided in this Agreement, any
Shares transferred (whether or not in compliance with the terms of this Agreement) shall
continue to be subject to the restrictions on transfer contained in this Agreement, and any
transferee of such Shares shall be deemed to have accepted and consented to be bound by the
restrictions hereof as if such transferee had originally executed this Agreement as a party
hereto, and such transferee shall be a Stockholder for purposes of the restriction on sale of
Shares in this Agreement.

          A. Voluntary Sale. If WARF receives a bona fide written offer (“Third Party
Offer”) from a purchaser to purchase some or all of the Shares held by WARF (the “Offered
Shares”), WARF may sell such Shares to such purchaser in accordance with this Section 4A.

               (i) Offer to Corporation. WARF shall first give written notice (“Sale Notice”) to
TomoTherapy of the Third Party Offer, specifying the purchaser, the price for the Offered
Shares (the “Third Party Price”) and the payment terms of the proposed sale (the “Third Party
Payment Terms”). The

P.O.BOX7365      •      MADISON, WISCONSIN 53707-7365      •      TEL(608) 263-2500      •      FAX(608) 263-1064

 Page 3 of 15 

 

Sale
Notice shall constitute an offer by WARF to sell the Shares to TomoTherapy at the Third Party Price and on the Third Party Payment
Terms. TomoTherapy shall have the exclusive right and option for a period of thirty (30) days
after the date the Sale Notice is given to accept such offer with respect to any or all of the
Offered Shares. If TomoTherapy accepts such offer, it shall notify WARF in writing of such
acceptance within the thirty-day option period, specifying the number of Shares as to which the
offer is accepted.

               (ii) Offer to Other Stockholders. If the option to purchase the Offered Shares
is not exercised by TomoTherapy pursuant to Section 4A(i) as to some or all of the Offered
Shares within the option period, then the other stockholders shall have the exclusive right
and option for a period of thirty (30) days after the expiration of the first option period,
in their own behalf and exercisable in the same manner as TomoTherapy, to accept the offer
as to all of the remaining Offered Shares. Such option shall be exercised by the other
stockholders in proportion to the Shares then registered in their respective names, or in
such other proportion as they may agree on in writing, by written notice of such exercise to
WARF within the second option period. If such option is not exercised by all of the other
stockholders as to all of the remaining Offered Shares within the second option period, then
the other stockholders who have elected to exercise their option as set forth in the
immediately preceding sentence (the “Electing Stockholders”) shall have the further
exclusive right and option for a period of thirty (30) days following the expiration of the
second option period, in their own behalf and exercisable in the same manner as TomoTherapy,
to accept the offer as to all of the remaining Offered Shares. Such option shall be
exercised by the Electing Stockholders in proportion to the Shares then registered in their
respective names, or in such other proportion as they may agree on in writing, by written
notice of such exercise to WARF within the third option period.

               (iii) Right to Sell. If the offers referred to in Sections 4A(i) and (ii) are
not accepted as to all of the shares in the aggregate by TomoTherapy or the other
stockholders as to any of the Offered Shares within the applicable option periods, then such
Offered Shares may be sold by WARF to the proposed purchaser specified in the Sale Notice at
any time within thirty (30) days after the expiration of the last of such option periods, but
only at or above the Third Parry Price and on the Third Party Payment Terms. The Offered
Shares that are sold to the proposed purchaser shall remain subject to the restrictions on
such Shares set forth in this Agreement for WARF and the proposed purchaser shall execute a
copy of a Stockholder Agreement containing similar restrictions simultaneously to becoming a
registered stockholder. If the Offered Shares are not sold by WARF to the proposed purchaser
in accordance with this Section 4A(iii), or if there is a change in any of the terms of the
Third Party Offer, the Offered Shares may not be sold to the proposed purchaser unless WARF
again fully complies with the provisions of Sections 4A(i) and (ii).

     Section 5. Obligations at Closing.

     Any
closing shall occur at WARF’s offices in Madison, Wisconsin at such time and place that is mutually acceptable to both parties; however, in no event shall the closing occur
later than ninety (90) days after TomoTherapy receives notice of WARF’s exercise of its
option under Section 3 or 4. At such closing:

          A. TomoTherapy (the Other Stockholders) shall deliver to WARF either a certified check
or suitable proof of a wire transfer of immediately available funds to WARF’s account in the
amount of the aggregate purchase price for the Shares being transferred by WARF to
TomoTherapy (or the Other Stockholders); and

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          B. WARF shall deliver to TomoTherapy one or more certificates representing the number
of Shares being transferred by WARF to TomoTherapy (or the Other Stockholders), properly endorsed
for transfer or accompanied by executed stock powers.

     Section 6. Representations and Warranties.

          A. Representations and Warranties by TomoTherapy.

     TomoTherapy represents and warrants to WARF that:

               (i) TomoTherapy was duly organized and is a validly existing corporation under the laws
of the State of Wisconsin with adequate power and authority to conduct the business in which
it is now engaged, and TomoTherapy is duly qualified to do business as a foreign corporation
and is in good standing in such other states or jurisdictions as is necessary to enable it
to carry on its business.

               (ii) There are no actions, suits, or proceedings pending or threatened against
TomoTherapy, its properties, or its patents in any court or before any governmental or
administrative agency, which can have any material or adverse effect on the business as now
conducted or on the properties, the financial condition, or income of TomoTherapy, and
TomoTherapy is not in default under any order or judgment of any court or governmental or
administrative agency.

               (iii) TomoTherapy is not a party to any agreement or instrument, or subject to any
charter, bylaw, or other corporate restrictions materially adversely affecting its business
and operations, present or prospective, or its property, assets, or condition, financial or
otherwise.

               (iv) TomoTherapy is not in default in the performance, observance, or fulfillment of any
of the obligations, covenants, or conditions contained in any bond, debenture, note, or other
evidence of indebtedness or any contract or other agreement of TomoTherapy.

               (v) This Agreement has been duly authorized, executed and delivered on behalf of
TomoTherapy and constitutes the valid and binding agreement of TomoTherapy, enforceable in
accordance with its terms, and TomoTherapy has full power and lawful authority to issue,
sell, and repurchase the Shares on the terms and conditions herein set forth.

               (vi) Consummation of the transactions contemplated by this Agreement in compliance with
provisions of this agreement will not result in any breach of any of the terms, conditions, or
provisions of, or constitute a default under, or result in the creation of any lien, charge,
or encumbrance on, any property or assets of TomoTherapy pursuant to any indenture, mortgage,
deed of trust, agreement, corporate charter, contract, or other instrument to which
TomoTherapy is a party or by which TomoTherapy may be bound.

               (vii) TomoTherapy is in compliance with all federal, state and local environmental laws
and there are no conditions currently existing or contemplated which are likely to subject
TomoTherapy to damages, penalties, injunctive relief, removal costs, remedial costs or
cleanup costs under any such laws or assertions thereof.

               (viii) Attached hereto as Appendix B and hereby made a part hereof are the Articles of
Incorporation (including any amendments thereto) and the Bylaws (including any amendments
thereto) of TomoTherapy.

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               (ix)Pursuant to its Articles of Incorporation, TomoTherapy is authorized to issue
51,717 Shares, 16,652 Shares of which are validly issued and outstanding, fully paid and
nonassessable, and not subject to any other parties’ preemptive rights. There are no other
authorized or outstanding Equity Securities of any class, kind, or character, and there are no
outstanding subscriptions, options, warrants, or other agreements, or commitments obligating
TomoTherapy to issue any additional shares of its capital stock of any class, or any options or
rights with respect thereto, or any securities convertible into any shares of stock of any class
except under the terms of Section 8.4 of the Loan Agreement and under the terms of the Incentive
Stock Option Plan.

               (x) Attached hereto as Appendix C and hereby made a part hereof is a list of all
restrictions on the transfer of any Shares or other securities of TomoTherapy and all
agreements between any shareholders or convertible debtholders of TomoTherapy regarding the
valuation or transfer of any Shares or other securities of TomoTherapy.

               (xi) Attached hereto as Appendix D and hereby made a part hereof are the Financial
Statements of TomoTherapy which are provided to WARF as of the date of this Agreement.

               (xii) Since the date of the most recent Financial Statements provided to WARF under this
Agreement, there has been no: (a) material adverse change in the condition, financial or
otherwise, of TomoTherapy other than changes in the ordinary course of business; (b) damage
or loss, whether or not covered by insurance, materially and adversely affecting
TomoTherapy’s properties or business taken as a whole; and (c) declaration or setting aside,
or payment of any dividend or other distribution in respect of the stock of TomoTherapy or
any direct or indirect redemption, purchase or other acquisition of such shares.

               (xiii) All Financial Statements provided or to be provided to WARF under this Agreement
are true and complete and have been prepared in accordance with generally accepted accounting
principles. As of the date of the most recent Financial Statements provided to WARF under
this Agreement, TomoTherapy had no material liabilities, absolute or contingent, that are not
reflected in such Financial Statements except obligations incurred in the ordinary course of
business.

               (xiv) TomoTherapy has filed all tax returns and reports required to be filed by it.
TomoTherapy has paid all taxes, interest and penalties required to be paid pursuant to said
returns or otherwise required to be paid by it.

          B. Representations and Warranties by WARF. 

     WARF represents and warrants to TomoTherapy that:

               (i) WARF is acquiring the Shares for investment for its own account and not with a view
to resale or distribution within the meaning of the Securities Act, and WARF does not intend
to divide its participation with others or to resell or otherwise dispose of all or any part
of the Shares without registration under the Securities Act, except to TomoTherapy or unless
and until it determines at some future date that changed circumstances, not now in its
contemplation, make such disposition advisable.

               (ii) This Agreement has been duly authorized, executed, and delivered on behalf of WARF
and constitutes the valid and binding Agreement of WARF, enforceable in accordance with its
terms, and WARF has full power and lawful authority to purchase and sell the Shares on the
terms and conditions herein set forth.

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          C. Survival and Timing of Warranties.

     The warranties and representations made in this Section 6 shall survive the closing of any
issuance of shares to WARF. The warranties and representations made in this Section 6 shall be
true and correct as of the date of this Agreement and as of the date the Shares are issued to
WARF.

     Section 7. Miscellaneous Covenants.

          A. Financial Statements and Other Information.

     As long as WARF owns any Shares, TomoTherapy shall promptly provide to WARF such Financial
Statements, amendments to or restatements of its Articles of Incorporation or Bylaws, stock
transfer restrictions and agreements between shareholders with respect to the valuation or
transfer of shares and amendments thereto, and such other information respecting the business,
affairs, and financial condition of TomoTherapy as WARF may reasonably request and WARF’s
representatives may visit and inspect any of the properties, books and information of
TomoTherapy.

          B. Preemptive Rights.

     In addition to its other rights under this Agreement, WARF shall have a preemptive right
during the term of this Agreement to acquire such Equity Securities as may be issued from time to
time in accordance with the terms of this Agreement. Such preemptive right shall apply with
respect to all Equity Securities issued by TomoTherapy after the effective date of this Agreement,
whether such additional Equity Securities constitute a part of the Equity Securities presently or
subsequently authorized or constitute Equity Securities held in the treasury of TomoTherapy but
its preemptive right shall not apply to the grant of stock options or Equity Securities to
employees, directors and officers in connection with services rendered to TomoTherapy by such
persons or to those Equity Securities for which WARF receives additional Shares under the
anti-dilution provisions set forth in Section 2A(ii). WARF shall have the right to acquire Equity
Securities of the type being issued in an amount equal to WARF’s Share percentage immediately
before the issuance multiplied by the number of Equity Securities of that type that are to be
issued to all persons or entities pursuant to that issuance. The
terms and conditions of WARF’s
exercise of its preemptive rights, including the consideration to be paid for such Equity
Securities, shall be no less favorable to WARF than the most favorable terms and conditions
offered to any other shareholder or prospective shareholder with respect to the Equity Securities
then being issued. WARF may, at its option, exercise such preemptive rights to some or all of the
Shares or other Equity Securities to which it has preemptive rights under this Section 7B.

          C. Issuance of Shares to Affiliates.

     Except under the terms of Section 8.4 of the Loan Agreement and under the terms of the
Incentive Stock Option Plan, TomoTherapy shall not issue any Equity Securities (including Shares)
to any Affiliate for less than the fair market value of that security. TomoTherapy shall have the
burden of proving that it received consideration for any such issuance equal to the fair market
value of the Equity Securities issued.

          D. Piggyback Registration Rights.

               (i) If at any time TomoTherapy shall determine to Register any Shares, TomoTherapy
shall:

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                    (1) promptly
give WARF written notice thereof (which shall include
a list of the jurisdictions in which TomoTherapy intends to attempt to qualify such Shares under
the applicable Blue Sky or other state securities laws); and

                    (2) will use its best efforts to include in such Registration (and
any related qualification under Blue Sky laws or other compliance), and in any underwriting involved
therein, all of the Shares specified in a written request by WARF received by TomoTherapy within
twenty (20) days after the giving of such written notice by TomoTherapy. If TomoTherapy is unable
to include WARF in such Registration despite its best efforts, TomoTherapy agrees to share equally
in the expense incurred by WARF in connection with registering its Shares in a separate offering.

               (ii) All Registration Expenses incurred in connection with any registration pursuant to
Section 7D(i) shall be borne by TomoTherapy.

          E. Notice of Fundamental Corporate Transactions.

     During the term of this Agreement, TomoTherapy shall provide WARF with written notice of any
of the following fundamental transactions: (i) merger with another entity, consolidation,
reorganization (including without limitation by any reverse stock split), liquidation, or
dissolution of TomoTherapy; (ii) sale, lease, exchange or other disposal of all or substantially
all of the property or assets of TomoTherapy; or (iii) adoption of any plan or agreement to do
any of the foregoing.

          F. Board Meetings.

     TomoTherapy agrees that WARF shall be allowed to attend all meetings of the Board of
Directors as a non-voting observer. WARF shall be provided advance notice of all meetings and
shall be provided the same materials provided to members of the Board.

     Section 8. Termination.

          A. Unless terminated sooner by either party as provided below, this Agreement shall
terminate on the date that WARF, after having been issued Shares hereunder, no longer owns any
Equity Securities. If this Agreement terminates automatically as provided in this Section 8A, the
License Agreement shall remain in effect according to the terms specified therein.

          B. If TomoTherapy fails to issue Shares to WARF on a timely basis, fails to timely
repurchase Shares from WARF, or otherwise commits a material breach of this Agreement, or if
any of the representations or warranties made by TomoTherapy are untrue as of any date on which they
are required to be true and correct, and TomoTherapy fails to remedy any such breach or default
within thirty (30) days after written notice thereof by WARF, WARF may, at its option, terminate this
Agreement.

          C. If WARF at any time commits a material breach of this Agreement or any of the
representations or warranties made by WARF are untrue as of any date on which they are
required to be true and correct, and WARF fails to remedy any such breach or default within thirty (30) days
after written notice thereof by TomoTherapy, TomoTherapy may, at its option, terminate either this
Agreement, the License Agreement, or both.

     Section 9. Assignability.

          Neither party may assign its rights or obligations under this Agreement.

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          Section 10. Miscellaneous.

     This Agreement shall be governed by and construed in all respects in accordance with the laws
of the State of Wisconsin. If any provisions of this Agreement are or shall come into conflict
with the laws or regulations of any jurisdiction or any governmental entity having jurisdiction
over the parties or this Agreement, those provisions shall be deemed automatically deleted, if
such deletion is allowed by relevant law, and the remaining terms and conditions of this Agreement
shall remain in full force and effect. If such a deletion is not so allowed or if such a deletion
leaves terms thereby made clearly illogical or inappropriate in effect, the parties agree to
substitute new terms as similar in effect to the present terms of this Agreement as may be allowed
under the applicable laws and regulations.

          Section 11. Notices.

     Any
notice required to be given pursuant to the provisions of this Agreement shall be in
writing and shall be deemed to have been given at the earlier of the time when actually
received as a consequence of any effective method of delivery, including but not limited to
hand delivery, transmission by telecopier, or delivery by a professional courier service or
the time when sent by certified or registered mail addressed to the party for whom intended at
the address below or at such changed address as the party shall have specified by written
notice, provided that any notice of change of address shall be effective only upon actual
receipt.

	 	(a)	 	Wisconsin Alumni Research
Foundation

Attn: Managing Director

614 Walnut Street 

Madison, Wisconsin 53705
	 
	 	(b)	 	TomoTherapy
Incorporated

Attn: President

P.O. Box 8024

Madison, Wisconsin 53708-8024

     With a copy of such notice to:

     Michael E. Skindrud, Esq.

     LaFollette & Sinykin 

     P.O. Box
     2719 

     One East Main Street

     Madison, Wisconsin 53701-2719

          Section 12.
Integration.

     This Agreement constitutes the full understanding between the parties with reference to
the subject matter hereof, and no statements or agreements by or between the parties, whether
orally or in writing, made prior to or at the signing hereof, shall vary or modify the written
terms of this Agreement. Neither party shall claim any amendment, modification, or release
from any provisions of this Agreement by mutual agreement, acknowledgement, or otherwise,
unless such mutual agreement is in writing, signed by the other party, and specifically states
that it is an amendment to this Agreement.

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     IN
WITNESS WHEREOF, the parties hereto have duly executed this Agreement on the dates
indicated below.

WISCONSIN ALUMNI RESEARCH FOUNDATION

	 	 	 	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard H. Leazer
	 	Date:
	 	2/24
	 	 	,1999	 	 	 
	 

	 	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	Richard H. Leazer, Managing Director	 	 	 	 	 	 	 	 	 	 

TOMOTHERAPY INCORPORATED

	 	 	 	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Paul J. Reckwerdt
	 	Date:
	 	2/24
	 	 	,1999	 	 	 
	 

	 	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	Paul J. Reckwerdt, Vice -President	 	 	 	 	 	 	 	 	 	 

Reviewed by WARF’s Attorney:

	 	 	 	 	 	 	 	 	 	 	 	 	 
	 

	 	/s/ Elizabeth L.R. Donley	 	 
	 	2/28
	 	 	,99	 	 	 
	 

	 	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	Elizabeth L.R. Donley, Esq.	 	 	 	 	 	 	 	 	 	 

(WARF’s attorney shall not be deemed a signatory to this Agreement.)

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APPENDIX
A

     A. “Shares” shall mean shares of TomoTherapy’s common stock, $.01 par value per
share.

     B. “License Agreement” shall mean the license agreement entered into by WARF and
TomoTherapy of even date herewith.

     C. “Affiliate” shall mean any person who is related by blood or marriage to any person or
entity who owns more than twenty percent of the issued and outstanding shares of TomoTherapy
or to any officer or director of TomoTherapy or any entity in which any such person has a direct or
indirect beneficial ownership interest or for which any such person serves as a director or officer.

     D. “Financial Statements” shall mean a balance sheet, statement of earnings, stockholders’
equity and cash flow as of the end of the last fiscal year that has been completed when the
statements are to be provided to WARF and a balance sheet and income statement as of the end of the last
fiscal quarter that has been completed when the statements are to be provided to WARF. If TomoTherapy’s
Financial Statements have been audited, then TomoTherapy shall provide WARF with such audited
statements.

     E. “Equity Securities” shall mean the Shares, any other shares of TomoTherapy (including
preferred shares), and any securities of TomoTherapy that are convertible into shares of
TomoTherapy or that carry a right to subscribe to or acquire shares of TomoTherapy.

     F. “WARF’s Share Percentage” shall mean the percentage derived by dividing the sum of
the number of Shares then owned by WARF by the total number of issued and outstanding Shares
at such time.

     G. “Fair Market Value” shall mean the value of the Shares as determined, if possible, by the
mutual consent of the parties. If the parties cannot agree on such value, the fair market
value of the Shares shall be determined by an independent appraiser who shall be jointly appointed by the
parties, but whose fees and expenses shall be paid by each party in equal shares. The independent appraiser
shall make his appraisal based on a hypothetical sale of all of the Equity Securities of TomoTherapy
on a fully diluted basis to a willing third party buyer who intends to continue TomoTherapy as a going
concern, and such appraisal shall not contain any minority interest discount, any discount for lack of
marketability or any other discount that would not apply uniformly to all shares of TomoTherapy Equity
Securities with respect to such a hypothetical sale.

     H. “Register,” “Registered,” and “Registration” shall refer to a registration effected
by preparing and filing a Registration Statement in compliance with the Securities Act, and
the declaration or ordering of the effectiveness of such Registration Statement.

     I. “Securities Act” shall mean the Securities Act of 1933, as amended, or any similar
federal statute, and the rules and regulations of the Securities and Exchange Commission
issued under such act, as they each may, from time to time, be in effect.

     J. “Registration
Statement” shall mean a registration statement on Form S-1 or Form S-3
filed by TomoTherapy with the Securities and Exchange Commission for a public offering and
sale of securities of TomoTherapy.

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      K. Registration
Expenses” shall mean all expenses incurred by TomoTherapy in
complying with Section
7D(i) of this Agreement, including, without limitation, all registration and filing fees printing
expenses, and fees and disbursements of counsel for TomoTherapy.

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APPENDIX B

TomoTherapy Articles of Incorporation and Bylaws 

 (Attached)

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APPENDIX C

Stock
Transfer Restrictions,

Shareholder Agreements, and Convertible Debt

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APPENDIX D

TomoTherapy
Financial Statements 

(Attached)

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