LOAN AGREEMENT WITH M&I MARSHALL & ILSLEY BANK






Exhibit 10.38



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




Loan Agreement (“Agreement”)



TomoTherapy Incorporated (“Borrower”) agrees with M&I Marshall & Ilsley Bank (“Bank”) to all terms
and conditions set forth in this Agreement so long as any obligation is owed Bank (“Loans”), or
Bank has any obligation to lend to the Borrower under any note evidencing a loan from the Borrower
to the Bank (the “Note”), and all extensions, renewals or modifications of any note evidencing a
loan.





	1)	 	CONDITIONS FOR LOANS. Bank’s obligation to make any loan is subject to satisfaction of the
following conditions:






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






	2)	 	REPRESENTATIONS AND WARRANTIES. Borrower represents and warrants to Bank that on the date of
the Loans:






	 	a)	 	The Loans will be used solely for business purposes and are not and will not be used
for personal, family, household or agricultural purposes.
	 
	 	b)	 	Borrower will not use any part of the proceeds of the loans to purchase or carry any
margin stock within the meaning of Regulation U of the Board of Governors of the Federal
Reserve System.
	 
	 	c)	 	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.
	 
	 	d)	 	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.
	 
	 	e)	 	Borrower has paid all federal and state income taxes or other taxes of any kind 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.






	3)	 	COVENANTS. Borrower shall, so long as any amounts remain unpaid:






	 	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 balance sheet of Borrower as of the close of such fiscal year and related
statements of income and retained earnings for such year 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, and
	 
	 	ii)	 	Within forty-five (45) days after the end of each quarter a balance sheet of
Borrower as of the end of such quarter and related statements of income and retained
earnings 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 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)	 	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.
	 
	 	d)	 	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.
	 
	 	e)	 	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.
	 
	 	f)	 	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 [ * ].
	 
	 	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




Tangible Net Worth: shall mean 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.





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






	4)	 	ADDITIONAL SECURITY. Unless a lien would be prohibited by law or would render a nontaxable
account taxable, Borrower 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.




 









 












	5)	 	DEFAULT AND ACCELERATION. Any one or more of the following events shall constitute a default
hereunder and under the Notes:






	 	a)	 	Borrower fails to pay any amount when due under this Agreement or the Notes 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)	 	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;
	 
	 	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 Loan, Bank’s obligation to make 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 Loans under this Agreement shall automatically terminate and the total
unpaid balance of the Notes 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.





	6)	 	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 Notes 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 Notes shall at the option of the holder and without notice, mature and become immediately
due and payable.






	7)	 	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 Notes are 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.






	8)	 	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.
	 
	9)	 	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.
	 
	10)	 	ISDA. Obligations and Indebtedness 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.
	 
	11)	 	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
affect the validity of any other provisions of this Agreement.
	 
	12)	 	CONFLICT BETWEEN THIS AGREEMENT AND THE NOTES. In the case of any ambiguity or conflict
between this Agreement and the Notes, this Agreement will govern.
	 
	13)	 	PREVIOUS LOAN AGREEMENTS. This Agreement supersedes and replaces all previous loan
agreements between Bank and Borrower.





     Dated as of December 1, 2007



	 	 	 	 	 	 	 	 	 	 	 
	TomoTherapy Incorporated	 	 	 	M&I Marshall & Ilsley Bank	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Frederick A. Robertson, MD
 

	 	 	 	By:
	 	/s/ Kirt C. Soukup
 

	 	 
	Frederick A. Robertson, MD, Chief Executive Officer	 	 	 	Kirt C. Soukup, Vice President	 	 







	 	 	 	 	 	 	 	 	 	 	 
	Drafted By: br	 	 	 
	Loan [ * ]	 	 	 	By:
	 	/s/ Jeff Ticknor 

	 	 
	 	 	 	Jeff Ticknor, Senior Vice President