Readme for FAST, a tool for Force Algorithm Semi-automated Tracker. Created by Max Shokhirev. (C) 2013-2014. 

To run, simply double-click the jar file. Or run from command line using java -jar FAST.jar.

The included cheat-sheet will get you started tracking B/T cells in a stack of PNG/JPEG brightfield images. You may need to change some of the tracking parameters to reflect the size and geometry of your cells and the lighting conditions (see the program for descriptions). 

See the paper for more details:

Maxim N. Shokhirev, Jonathan Almaden, Jeremy Davis-Turak, Harry A. Birnbaum, Theresa M. Russell, Jesse A.D. Vargas, Alexander Hoffmann. A multi-scale approach reveals that NFkB cRel enforces a B-cell decision to divide.
This program is provided under the following license:

Copyright (c)  2014   The Regents of the University of California
All Rights Reserved
 
Permission to copy, modify and distribute any part of this FAST for educational, research and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.

Those desiring to incorporate this FAST program into commercial products or use for commercial purposes should contact the Technology Transfer Office, University of California, San Diego, 9500 Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, Ph: (858) 534-5815, FAX: (858) 534-7345, E-MAIL:invent@ucsd.edu.

IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS FlowMax, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

THE FAST program PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.  

THE UNIVERSITY OF CALIFORNIA MAKES NO REPRESENTATIONS AND EXTENDS
NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, 
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE FAST program WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS.