SEC Form 4

FORM 4		UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934 or Section 30(h) of the Investment Company Act of 1940	OMB APPROVAL OMB Number: 3235-0287 Estimated average burden hours per response: 0.5
	Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

1. Name and Address of Reporting Person* NEIS JOHN (Last) (First) (Middle) 1240 DEMING WAY (Street) MADISON WI 53717 (City) (State) (Zip)	2. Issuer Name and Ticker or Trading Symbol TomoTherapy Inc [ TOMO ]	5. Relationship of Reporting Person(s) to Issuer (Check all applicable) X Director 10% Owner Officer (give title below) Other (specify below)
	3. Date of Earliest Transaction (Month/Day/Year) 02/26/2008
	4. If Amendment, Date of Original Filed (Month/Day/Year)	6. Individual or Joint/Group Filing (Check Applicable Line) Form filed by One Reporting Person X Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1. Title of Security (Instr. 3)	2. Transaction Date (Month/Day/Year)	2A. Deemed Execution Date, if any (Month/Day/Year)	3. Transaction Code (Instr. 8)		4. Securities Acquired (A) or Disposed Of (D) (Instr. 3, 4 and 5)			5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4)	6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	7. Nature of Indirect Beneficial Ownership (Instr. 4)
			Code	V	Amount	(A) or (D)	Price
Common Stock	02/26/2008		J		281,797	D	$0.00	863,400(1)	I	Held by Venture Investors Early Stage Fund II Limited Partnership(2)(3)
Common Stock	02/26/2008		J		476,270	D	$0.00	1,459,248(1)	I	Held by Venture Investors Early Stage Fund III Limited Partnership(2)(4)
Common Stock	02/26/2008		S		34,554	D	$14.5265	948,640	I	Held by Advantage Capital Wisconsin Partners I, Limited Partnership(2)(5)
Common Stock								62,760(6)	D

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned (e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security (Instr. 3)	2. Conversion or Exercise Price of Derivative Security	3. Transaction Date (Month/Day/Year)	3A. Deemed Execution Date, if any (Month/Day/Year)	4. Transaction Code (Instr. 8)		5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5)		6. Date Exercisable and Expiration Date (Month/Day/Year)		7. Title and Amount of Securities Underlying Derivative Security (Instr. 3 and 4)		8. Price of Derivative Security (Instr. 5)	9. Number of derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4)	10. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	11. Nature of Indirect Beneficial Ownership (Instr. 4)
				Code	V	(A)	(D)	Date Exercisable	Expiration Date	Title	Amount or Number of Shares

1. Name and Address of Reporting Person* NEIS JOHN (Last) (First) (Middle) 1240 DEMING WAY (Street) MADISON WI 53717 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer X Director 10% Owner Officer (give title below) Other (specify below)

1. Name and Address of Reporting Person* Venture Investors LLC (Last) (First) (Middle) 505 SOUTH ROSA ROAD, #201 (Street) MADISON WI 53719 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) Other (specify below)

Explanation of Responses:

1. Pro rata distribution to partners.

2. Mr. Neis is one of six managers and the managing director of Venture Investors LLC. Mr. Neis disclaims beneficial ownership of these securities except to the extent of his pecuniary interest therein, and the inclusion of these securities in this report shall not be deemed an admission of beneficial ownership by him of all the reported shares for purposes of Section 16 or for any other purposes.

3. Venture Investors LLC is the general partner of Venture Investors Founders Limited Partnership, which is the general partner of Venture Investors Early Stage Fund II Limited Partnership.

4. Venture Investors LLC is the general partner of Venture Investors Early Stage Fund III Limited Partnership.

5. Venture Investors LLC is the sub-managing agent of Advantage Capital Wisconsin Partners I, Limited Partnership.

6. Mr. Neis received 19,131 shares from Venture Investors Early Stage Fund II Limited Partnership in connection with its pro rata distribution to its partners and 43,629 shares from Venture Investors Early Stage Fund III Limited Partnership in connection with its pro rata distribution to its partners. These acquisitions are exempt pursuant to Rule 16a-13 as a mere change in the form of beneficial ownership.

Remarks:

	/s/ Shawn D. Guse, as attorney in fact	02/28/2008
	/s/ Shawn D. Guse, as attorney in fact	02/27/2008
	** Signature of Reporting Person	Date
Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.
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