PROTO* Software Page

You can download from this page some of the computer programs developed by the Gelles lab for analysis of single-molecule light microscopy images. The programs listed here are old and rather user-hostile; new users should probably use Glimpse, which incorporates all of the functions of these programs.

All of the software available here is copyrighted. With one exception noted below, all is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should receive a copy of the GNU General Public License along with each program; if not, write to the Free Software Foundation, 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Except by special arrangement, we do not provide any technical support for these programs.

These programs are based on the work of a number of extremely talented programmers that we have employed over the years, notably Ivan Hristov and Bathsheeba Grossman. We also express our gratitude to the National Institute of General Medical Sciences, NIH, which partially funded the development of some of this software.

Executables -- Windows

These executables come with almost no documentation. As such, they are probably of limited use to people who have not already been trained in the operation of the programs. They are included here primarily as a service to collaborators and former lab members. They have not been tested on operating systems other than Windows NT 4.0 and Windows 2000.

PROTOF -- This program performs the curve-fitting analysis used for bandwidth-limited tethered particle motion (TPM) experiments performed with differential interference contrast light microscopy images. We have used it in our studies of RNA polymerase, lac repressor, and RecBCD. The algorithm is described in Biophys. J. (1994) 67:2468-78.
PROTOX -- This program does sub-pixel resolution particle tracking using a cross-correlation/thresholded centroid algorithm described in Nature (1988) 331:450-3. We have used it in our kinesin work.
PROTOC -- This program is similar to PROTOX except that it is faster (and usually somewhat less accurate) because it doesn't do the cross-correlation calculation.

These programs use a custom-designed video file format, SEQ. For those who do data acquisition in National Instruments' LabView, here are some VIs that can be used to write files in this format.

Source Code -- Win32 C/C++

This package contains the program code and makefiles (Microsoft Visual C++) for the indicated programs.

PROTO* -- The source code for PROTOC and PROTOX, and nearly all of the source code for PROTOF. The reason for that "nearly all": one module needed to build PROTOF, fit32.c, contains modified versions of four routines from Numerical Recipes in C that do the Levenberg-Marquardt calculations. Since this module is derived from a copyrighted work, we can't redistribute it without permission from the copyright holder. The copyright holder, Numerical Recipes Software, has consented to let us distribute a limited number of copies of this module on a by-request basis (to request one, send Jeff Gelles email) but we are not permitted to post it on the Web. For those who merely wish to peruse the code to learn how the program works, the Numerical Recipes routines are mrqmin, mrqcof, covsrt, and gaussj, and the modifications consist mainly of altering the types of some variables and generalizing the routines to handle a function of two independent variables.

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updated 1/13/06