EX-10.1






Exhibit 10.1




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.



M&I Marshall & Ilsley Bank

AMENDED AND RESTATED LOAN AGREEMENT (this “Agreement”)




TomoTherapy Incorporated (“Borrower”) agrees with M&I Marshall & Ilsley Bank (“Bank”) agree as
follows:



1. AMENDING AND RESTATING. This Agreement amends, restates and replaces that certain Loan
Agreement by and between Borrower and Bank, dated as of December 1, 2007.



2. CERTAIN DEFINITIONS. As used in this Agreement, the following terms have the meanings set
forth below:




“Adjusted Credit Limit” means the amount set forth in the Adjusted Credit Limit Table,
below, that corresponds at a given point in time with the amount of TNW and the amount of
EBITDA.




“EBITDA” means, with respect to Borrower, for the trailing twelve (12) month period, (i) net
income during such period, plus (ii) interest expense for such period to the extent deducted
in the computation of net income, plus (iii) amortization expense for such period to the
extent deducted in the computation of net income, plus (iv) depreciation expense for such
period to the extent deducted in the computation of net income, all determined in accordance
with generally accepted principles of accounting applied on a consistent basis.




“Tangible Net Worth” means the excess of the total of all assets of the Borrower and all
consolidated subsidiaries and affiliates, of every kind and character, other than goodwill,
corporate franchises and other intangibles, less the aggregate of all liabilities (excluding
tax asset value) and reserves of every kind and character of the Borrower and all
consolidated subsidiaries and affiliates, all determined in accordance with generally
accepted principles of accounting.




“TNW” means Tangible Net Worth.




“<” means the item to the right of this symbol is greater than the item to the left of
this symbol.




“=” means the item to the right of this symbol is greater than or equal to the item to the
left of this symbol.



ADJUSTED CREDIT LIMIT TABLE




	 	 	 	 	 	 	 	 	 
	 	 	$[ * ] = TNW < $[ * ]
	 	$[ * ] = TNW < $[ * ]
	 	       $[ * ] = TNW
	 	


	 	 	        $20,000,000
	 	        $25,000,000
	 	        $30,000,000
	 	EBITDA < $[ * ]

	Adjusted Credit

Limit
	 	

        $25,000,000
	 	

        $30,000,000
	 	

        $35,000,000
	 	

$[ * ] = EBITDA < $[ * ]

	 	 	        $30,000,000
	 	        $35,000,000
	 	        $40,000,000
	 	$[ * ] = EBITDA

	 	 	 
	 	 
	 	 
	 	








3. REVOLVING LOANS. Borrower requests that Bank lend to Borrower from time to time such
amounts as Borrower may request in accordance with this Agreement (the “Revolving Loans”), and,
subject to the terms of this Agreement, Bank agrees to lend such amounts up to the aggregate
principal amount of forty million and no/100 Dollars ($40,000,000.00) at any time outstanding (the
“Credit Limit”). Upon the first calendar quarter end to occur during the term of this Agreement,
Bank will adjust the Credit Limit to the Adjusted Credit Limit, and the Adjusted Credit Limit will
be further adjusted quarterly, as follows:




	 	(a)	 	Following the end of each calendar quarter, Bank will determine
the Adjusted Credit Limit as set forth in the Adjusted Credit Limit Table,
above, based on Borrower’s Tangible Net Worth and EBITDA as of such calendar
quarter end, which Adjusted Credit Limit shall become effective sixty (60) days
after the end of such calendar quarter end.






	 	(b)	 	The Adjusted Credit Limit shall become effective without notice
to Borrower, but Bank will give Borrower notice of the Adjusted Credit Limit.





The Credit Limit and the Adjusted Credit Limit, as applicable, are evidenced by an Amended and
Restated Promissory Note dated November 30, 2010, and any renewals, extensions or modifications
(the “Promissory Note”). Within the Credit Limit or the Adjusted Credit Limit, as applicable,
Borrower may borrow, repay and reborrow under this Agreement. Bank is not obligated to, but may
make Revolving Loans in excess of the Credit Limit or the Adjusted Credit Limit, as applicable, and
in any event, Borrower is liable for and agrees to pay all Revolving Loans.



4. LETTERS OF CREDIT. Borrower may request that Bank issue letters of credit from time to
time during the term of this Agreement in amounts, in aggregate, up to the unused portion of the
Credit Limit or the Adjusted Credit Limit, as applicable, and Bank agrees to issue such letters of
credit. Bank shall charge an issuance fee for each such letter of credit equal to a rate of 1.60%
per annum multiplied by the amount of each letter of credit, which shall be payable upon issuance.
The availability to Borrower of the Credit Limit, or the Adjusted Credit Limit, as applicable, for
cash borrowing hereunder shall be reduced by the amounts, in aggregate, of such letters of credit
from time to time outstanding.



5. CONDITIONS FOR LOANS. Bank’s obligation to make the initial Revolving Loan is subject to
satisfaction of the following conditions:




	 	(a)	 	Bank shall have received copies, certified by the Secretary of
Borrower, of the Articles of Incorporation and Bylaws of Borrower, resolutions
of the Board of Directors of Borrower, authorizing the issuance, execution and
delivery of this Agreement, the Promissory Note, and a certification of the
names and titles of the representatives of Borrower authorized to sign this
Agreement and the Promissory Note and to request Revolving Loans under this
Agreement, together with true signatures of such representatives. Borrower
shall also provide Bank with evidence that Borrower is current in regard to all
annual report filing with the Secretary of State of the state of its
incorporation and any other state in which it does business.






	 	(b)	 	Borrower shall not be in default under this Agreement or any
other obligation to Bank or to any other creditor of Borrower.






	 	(c)	 	Borrower shall provide Bank with current financial statements,
balance sheets, profit and loss statements of Borrower in a form and content
satisfactory to Bank, and Borrower’s financial condition, as reflected on said
financial statements, shall be satisfactory to Bank.






	 	(d)	 	Borrower shall provide Bank with such other documents as Bank
or its counsel may reasonably require for the proper closing and documentation
of this Agreement and the Revolving Loans contemplated hereunder.





6. LOAN PROCEDURES. Borrower may only obtain Revolving Loans under this Agreement as follows:




Borrower shall give Bank notice of any Revolving Loan requested under this Agreement,
specifying the date of the Revolving Loan request and the amount of the Revolving Loan
request. All such requests shall be in writing unless Bank agrees to accept telephonic
requests as provided in the Promissory Note. Written requests shall be on forms approved by
Bank. If notice of a Revolving Loan request is made telephonically and accepted in such
form by Bank, such request shall be confirmed in writing by Borrower within five (5) banking
business days of such request on the same forms as are required to be used by Borrower when
making the request in writing. If Borrower’s then-outstanding Revolving Loans balances,
plus the amount of the request, are within the Adjusted Credit Limit then applicable and
Borrower is not in default under this Loan Agreement, the Promissory Note delivered pursuant
hereto, or any other loan agreement with Bank or promissory note held by Bank, then within
two banking business days of receipt of the request, Bank will make the Revolving Loan
available to Borrower by crediting the amount of the Revolving Loans to Borrower’s account
(Account No. [ * ]) with Bank. Each Revolving Loan which does not utilize the full amount
available to Borrower under this Agreement shall be in an amount not less than two thousand
dollars ($2,000.00).



7. REPRESENTATIONS AND WARRANTIES. Borrower represents and warrants to Bank that on the date
of each Revolving Loan:




	 	(a)	 	Neither the making of this Agreement nor the execution of the
Promissory Note or other documents provided for hereunder will violate any
provision of any other agreement, indenture, note, Article of Incorporation or
Bylaw or other instrument which is binding upon the Borrower, nor give cause
for acceleration of any indebtedness of the Borrower.






	 	(b)	 	All Revolving Loans are and will be used solely for business
purposes and are not and will not be used for personal, family, household or
agricultural purposes.






	 	(c)	 	No portion of the proceeds of the Revolving Loans shall be used
directly or indirectly in violation of any provision of any statute,
regulation, order or restriction applicable to the Bank or the Borrower,
including, without limitation, Regulation U of the Board of Governors of the
Federal Reserve System.






	 	(d)	 	The execution and delivery of this Agreement, and the
performance by Borrower of its obligations under this Agreement, are within its
power, have been duly authorized by proper action on the part of Borrower, are
not in violation of any existing law, rule or regulation, any order or decision
of any court, the Articles of Incorporation, Bylaws, or other governing
documents of Borrower, as applicable, or the terms of any agreement or
restriction to which Borrower is a party or by which it is bound and do not
require the approval or consent of any person or entity. This Agreement and
the Promissory Note, when executed and delivered, will constitute the valid and
binding obligations of Borrower enforceable in accordance with their terms.






	 	(e)	 	Borrower is a corporation validly existing under the laws of
the State of Wisconsin and is duly qualified to do business and is current with
its annual report filing in every jurisdiction in which the nature of its
business or the ownership of its properties requires such qualification.






	 	(f)	 	All financial statements, balance sheets and profit and loss
statements of Borrower furnished to Bank were prepared in accordance with
generally accepted accounting principles consistently applied throughout the
periods involved and are correct and complete as of their dates.






	 	(g)	 	There is no litigation or administrative proceeding pending or,
to the knowledge of Borrower, threatened against Borrower, which might result
in any material adverse change in the business or financial condition of
Borrower.






	 	(h)	 	Borrower has no notice or knowledge of any substance which has
been, is, or will be present, used, stored, deposited, treated, or disposed of
on, under or about any real estate now or at any time owned or occupied by the
Borrower which would require clean up, removal or some other remedial action
under any federal, state or local laws, regulations, ordinances, codes or
rules. In the event any such substance is present on such real estate,
Borrower shall indemnify and • hold harmless Bank, its directors, officers,
employees and agents from all loss, costs (including reasonable attorneys fees
and expenses), and liability of every kind and nature resulting from or arising
out of or based upon such substance. Borrower shall immediately notify bank in
writing of any governmental or regulatory action or third party claim
instituted or threatened in connection with any such substance.






	 	(i)	 	Borrower has paid all federal and state income taxes or other
taxes of any kind or material owed by it for all past years and no claim is
being asserted against it with respect to any federal or state income taxes for
any past years or with respect to any other federal, state, or other taxes of
any kind or nature for any past years.





8. INTEREST RATE. Borrower agrees to pay interest to Bank on the unpaid principal balance
outstanding from time to time under this Agreement in accordance with the Promissory Note.



9. PAYMENT SCHEDULE. Borrower agrees to pay Bank the unpaid principal balance and interest in
accordance with the Promissory Note. In addition, Borrower shall immediately pay Bank any amount
by which the Revolving Loans exceed the Credit Limit or the Adjusted Credit Limit, as applicable,
and any prior unpaid payments. Payments must be made to the Bank at its address indicated on the
signature page hereto and are not credited until received in Bank’s office and funds are deemed by
Bank to be collected. Bank is authorized to make book entries evidencing Revolving Loans and
payments under this Agreement and the aggregate unpaid amount of all Revolving Loans as evidenced
by those entries is presumptive evidence that those amounts are outstanding and unpaid to Bank.



10. COVENANTS. Borrower shall, so long as any amounts remain unpaid, or Bank has any
commitment to make Revolving Loans under this Agreement:




	 	(a)	 	Furnish to Bank, as soon as available, such financial
information respecting Borrower as Bank from time to time requests, and without
request furnish to Bank:






	 	(i)	 	Within one hundred twenty (120) days after the
end of each fiscal year of Borrower, a consolidated financial report of
Borrower and its subsidiaries, including a consolidated statement of
financial position, balance sheet, statement of income and retaining
earnings, and the related consolidated statements of operations, for
the fiscal year then ended, all in reasonable detail and satisfactory
in scope to Bank, audited by a certified public accounting firm
acceptable to Bank in accordance with generally accepted accounting
principles applied on a consistent basis, certified by the chief
financial representative of Borrower, and






	 	(ii)	 	Within forty-five (45) days after the end of
each fiscal quarter of the Borrower, the Borrower’s statement of
financial position, balance sheet, statement of income and retaining
earnings, and the related statement of operations as of the end of each
such fiscal quarter; for the period from the beginning of the fiscal
year to the end of such quarter, prepared in accordance with generally
accepted accounting principles applied on a consistent basis,
certified, subject to normal year-end adjustments, by the chief
financial representative of Borrower.






	 	(b)	 	Keep complete and accurate business books and records. Permit
any representative of the Bank to visit and inspect any of the Borrower’s
tangible or intangible properties as often as desired by Bank.






	 	(c)	 	Pay and discharge all lawful taxes, assessments and
governmental charges upon Borrower or against its properties prior to the date
on which penalties attach, unless and to the extent only that such taxes,
assessments or charges are contested in good faith and by appropriate process
by Borrower.






	 	(d)	 	Do all things necessary to maintain its existence, to preserve
and keep in full force and effect its agreements, rights and franchises
necessary to continue its business and comply with all applicable laws,
regulations and ordinances.






	 	(e)	 	Borrower shall keep all of its financial records located at its
principal place of business as indicated on the signature page of this
Agreement or at such other place as agreed to in writing with Bank.






	 	(f)	 	Comply with all the terms and provisions of all other loan
agreements and promissory notes relating to loans by Bank to Borrower.






	 	(g)	 	Permit Bank, at any reasonable time during business hours,
access to all of the financial records of Borrower to enable Bank to copy
and/or audit Borrower’s financial records using persons designated by Bank.
Borrower shall pay Bank, upon demand, for the reasonable cost of such audits.






	 	(h)	 	Not take any action or permit any event to occur which
materially impairs Borrower’s ability to make payments under this Agreement
when due. Such events include, without limitation, the fact that Borrower, or
any surety or Guarantor for Borrower’s obligations under this Agreement ceases
to exist, dies, or becomes insolvent or the subject of bankruptcy or insolvency
proceedings.






	 	(i)	 	Maintain, preserve and keep its machinery, equipment and all
other property in good repair and condition and duly pay and discharge all
taxes and other charges imposed upon said properties.






	 	(j)	 	Timely perform and observe all of the following financial
covenants, all calculated in accordance with generally accepted principles of
accounting applied on a consistent basis:






	 	(i)	 	Maintain at all times a Tangible Net Worth (as
defined below) of equal to or greater than [ * ] dollars ($) [ * ];






	 	(ii)	 	Maintain at all times a ratio of Total
Liabilities to Tangible Net Worth equal to or less than [ * ] to [ *
]. Calculated as: total liabilities / Tangible Net Worth; and






	 	(iii)	 	Maintain at all times cash and short-term
investments in value, in aggregate, of equal to or greater than [ * ]
dollars ($) [ * ].






	 	(k)	 	Not create or permit to exist any lien or encumbrance with
respect to Borrower’s property, except liens in favor of Bank, liens associated
with existing loans provided to Borrower by Wisconsin Department of Commerce
and Madison Development Corporation, liens for taxes if they are being
contested in good faith by appropriate proceedings and for which appropriate
reserves are maintained and liens or encumbrances permitted under any of the
Security Documents.






	 	(l)	 	Borrower shall have a sixty (60) day right to cure period if
any of the covenants are not complied with.





11. ADDITIONAL SECURITY. Except as hereinafter provided, this Agreement is unsecured. This
Agreement shall be secured by any and all future security agreements, collateral pledge agreements,
assignments and mortgages from Borrower to Bank, from any guarantor of this Agreement to Bank, and
from any other person to Bank, providing collateral security for Borrower’s obligations and payment
of the amounts due under this Agreement and the Promissory Note. Unless a lien would be prohibited
by law or would render a nontaxable account taxable, Borrower also grants to Bank a security
interest and lien in any deposit account Borrower may at any time have with Bank to secure all
debts, obligations and liabilities of Borrower under this Agreement. Bank may at any time after
the occurrence of an event of default set-off any amount under this Agreement against any deposit
balances or other money now or hereafter owed to Borrower by Bank.



12. DEFAULT AND ACCELERATION. Any one or more of the following events shall constitute a
default hereunder and under the Promissory Note:




	 	(a)	 	Borrower fails to pay any amount when due under this Agreement
or the Promissory Note delivered by Borrower pursuant to this Agreement;






	 	(b)	 	Any representation or warranty made under this Agreement or
information provided by Borrower in connection with this Agreement is or was
false or fraudulent in any material respect;






	 	(c)	 	A material adverse change occurs in Borrower’s financial
condition;






	 	(d)	 	Borrower fails to timely observe or perform any of the
covenants or duties contained in this Agreement;






	 	(e)	 	Any guaranty of Borrower’s obligation under this Agreement is
revoked or becomes unenforceable for any reason;






	 	(f)	 	Any event of default occurs under any security agreement;






	 	(g)	 	A default by Borrower with respect to any terms or provisions
of documents evidencing any other indebtedness of Borrower to Bank;






	 	(h)	 	The Borrower shall admit in writing the inability to pay any of
its debts or shall have made a general assignment for the benefit of creditors,
or shall have applied for or otherwise have a receiver, trustee, or custodian
appointed for any of its property or assets; or






	 	(i)	 	The occurrence of any other event which causes the Bank, in
good faith, to deem itself insecure.






Then, at Bank’s option, and upon verbal or written notice to Borrower, given at any
time including after receipt from Borrower of a request for a Revolving Loan, Bank’s
obligation to make Revolving Loans under this Agreement shall terminate and the total unpaid
balance shall become immediately due and payable without presentment, demand, protest or
further notice of any kind, all of which are hereby expressly waived by Borrower.




Bank’s obligation to make Revolving Loans under this Agreement shall automatically
terminate and the total unpaid balance of the Promissory Note shall automatically become due
and payable in the event Borrower becomes the subject of bankruptcy or other insolvency
proceedings. Bank may waive any default without waiving any other subsequent or prior
default. Borrower agrees to pay Bank’s cost of administration of this Agreement, including
reasonable attorneys’ fees. Borrower also agrees to pay all of Bank’s costs of collection,
before and after judgment, including reasonable attorneys’ fees (including those incurred in
successful defense or settlement of any counterclaim brought by Borrower or incident to any
action or proceeding involving Borrower brought pursuant to the Federal Bankruptcy Code).



13. CROSS DEFAULT OF ALL OTHER OBLIGATIONS OF BORROWER WITH BANK. As an inducement to Bank to
extend the credit referenced herein, Borrower agrees that in the event it is in default with
respect to this Agreement or the Promissory Note delivered pursuant hereto, it shall also be in
default with respect to all other agreements, notes, or other documents evidencing Borrower’s other
indebtedness to Bank. Conversely, if any payment is not made when due under any other note,
agreement, assignment or mortgage in favor of the Bank, or if any event of default should occur as
defined in any such note, agreement, assignment or mortgage, the unpaid balance of the Promissory
Note shall at the option of the holder and without notice, mature and become immediately due and
payable.



14. INDEMNIFICATION. Borrower agrees to defend, indemnify and hold harmless Bank, its
directors, officers, employees and agents, from and against any and all loss, cost, expense, damage
or liability (including reasonable attorneys’ fees) incurred in connection with any claim,
counterclaim or proceeding brought as a result of, arising out of or relating to any transaction
financed or to be financed, in whole or in part, directly or indirectly, with the proceeds of any
Revolving Loan or the entering into and performance of this Agreement or any document or instrument
relating to the Agreement by Bank. This indemnity will survive termination of this Agreement and
the repayment of all Revolving Loans.



15. VENUE. To the extent not prohibited by law, venue for any legal proceeding relating to
enforcement of this Agreement shall be, at Bank’s option, the county in which Bank has its
principal office in this state, the county in which Borrower resides, or the county in which this
Agreement was executed by Borrower.



16. TERMINATION. Unless sooner terminated by Borrower’s default, Borrower’s right to obtain
loans and Bank’s obligation to extend the credit under this Agreement shall terminate on the date
the Promissory Note is due by maturity or default (the “Termination Date”). The Borrower may
terminate Borrower’s right to obtain loans under this Agreement at any time and for any reason by
written notice to Bank. Such notice of termination signed by Borrower shall be binding on each
Borrower who signs this Agreement. Termination, for whatever reason, does not affect Bank’s
rights, powers and privileges, nor Borrower’s duties and liabilities, with regard to the
then-existing balance under this Agreement.



17. AMENDMENT. No amendment, modification, termination or waiver of any provision of this
Agreement, nor consent to any departure by Borrower from any provision of this Agreement shall in
any event be effective unless it is in writing and signed by Bank. Any such waiver or consent
shall be effective only in the specific instance and for the specific purpose for which given.



18. ENTIRE AGREEMENT. This Agreement is intended by Borrower and Bank as a final expression
of this Agreement and as a complete and exclusive statement of its terms, there being no conditions
to the full effectiveness of this Agreement except as set forth in this Agreement.



19. NO WAIVER; REMEDIES. No failure on the part of Bank to exercise, and no delay in
exercising, any right, power or remedy under this Agreement shall operate as a waiver of such
right, power or remedy; nor shall any single or partial exercise of any right under this Agreement
preclude any other or further exercise of the right or the exercise of any other right. The
remedies provided in this Agreement are cumulative and not exclusive of any remedies provided by
law.



20. HEDGING INSTRUMENTS. Borrower’s obligations and Indebtedness hereunder includes, without
limitation all obligations, indebtedness and liabilities arising pursuant to or in connection with
any interest rate swap transaction, basis swap, forward rate transaction, interest rate option,
price risk hedging transaction or any similar transaction between the Borrower and Bank.



21. UNUSED COMMITMENT FEE. Borrower shall pay a commitment fee in an amount equal to a rate
of .05% per annum multiplied by the average daily unused portion of the Credit Limit or Adjusted
Credit Limit, as applicable, from the date of the Promissory Note until the Maturity Date (as
defined in the Promissory Note), which shall be payable on the last day of each calendar quarter.



22. NOTICE. Except as otherwise provided in this Agreement, all notices required or provided
for under this Agreement shall be in writing and mailed, sent or delivered, if to Borrower, at
Borrower’s address indicated on the signature page hereto, and if to Bank, at its address indicated
on the signature page hereto, or, as to each party, at such other address as shall be designated by
such party in a written notice to the other party. All such notices shall be deemed duly given
when delivered by hand, three (3) business days after being deposited in the mail, sent by
certified mail, postage paid, or upon confirmation of delivery by overnight courier if sent by a
nationally-recognized overnight courier; provided that notice to Bank pursuant to Section 16
(Termination) hereof shall not be effective until received by Bank.



23. WAIVER OF JURY TRIAL. The Borrower and the Bank hereby jointly and severally waive any
and all right to trial by jury in any action or proceeding relating to this Agreement, any note, or
any other document delivered hereunder or in connection herewith, or any transaction arising from
or connected to any of the foregoing. The Borrower and the Bank each represent that this waiver is
knowingly, willingly and voluntarily given.



24. DUE ON SALE. In the event that Borrower or substantially all its assets are sold, the
Note shall be considered due payable.



25. BORROWER’S ADDRESS. Borrower shall immediately notify Bank in writing of any change of
address.



26. SUCCESSORS AND ASSIGNS. This Agreement shall be binding upon and inure to the benefit of
Bank and Borrower and their respective heirs, personal representatives, successors and assigns,
except that Borrower may not assign or transfer any of Borrower’s rights under this Agreement
without the prior written consent of Bank.



27. INTERPRETATION. The validity, construction and enforcement of this Agreement are governed
by the internal laws of Wisconsin. Invalidity of any provision of this Agreement shall not effect
the validity of any other provisions of this Agreement.



28. PREPARATION FEES. Borrower shall reimburse Bank for all costs and expenses incurred in
connection herewith including the following: Uniform Commercial Code searches, recording fees,
express mail charges, appraisals, credit reports, real estate searches, title insurance, attorneys’
fees, and similar costs and expenses.



29. CONFLICT BETWEEN THIS AGREEMENT AND THE PROMISSORY NOTE. In the case of any ambiguity or
conflict between this Agreement and the Promissory Note, this Agreement will govern.



30. PREVIOUS LOAN AGREEMENTS. This Agreement supersedes and replaces all previous loan
agreements between Bank and Borrower with respect to the Revolving Loans.



IN WITNESS WHEREOF, the parties have duly executed this Agreement as of the date below.



Dated as of November 30, 2010.



BORROWER:



TomoTherapy Incorporated



By: /s/ Thomas E. Powell

Thomas E. Powell, Chief Financial Officer




Borrower’s Address:      1240 Deming Way



                          Madison, WI 53717



BANK:



M&I Marshall & Ilsley Bank



By: /s/ Jason D. Lavicky

Jason D. Lavicky, Vice President




By: /s/ Jeffrey T. Ticknor

Jeffrey T. Ticknor, Senior Vice President




Bank’s Address:             One West Main Street



                          Madison, WI 53705