README.txt

JAABA: The Janelia Automatic Animal Behavior Annotator
Copyright 2012, Kristin Branson, HHMI Janelia Farm Resarch Campus
http://jaaba.sourceforge.net/
bransonk@janelia.hhmi.org

***

JAABA is a machine learning-based system that enables researchers to
automatically compute interpretable, quantitative statistics
describing video of behaving animals. Through our system, users encode
their intuition about the structure of behavior by labeling the
behavior of the animal, e.g. walking, grooming, or following, in a
small set of video frames. JAABA uses machine learning techniques to
convert these manual labels into behavior detectors that can then be
used to automatically classify the behaviors of animals in large data
sets with high throughput. JAABA combines an intuitive graphical user
interface, a fast and powerful machine learning algorithm, and
visualizations of the classifier into an interactive, usable system
for creating automatic behavior detectors.  

***

Documentation and up-to-date versions of the software are available on
our project homepage:

                    http://jaaba.sourceforge.net/

***

JAABA was developed by 
Mayank Kabra, Alice Robie, Marta Rivera-Alba, Steven Branson, 
and Kristin Branson.
All work was funded by the Howard Hughes Medical Institute and 
the Janelia Farm Research Campus. 

This program 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 3 of the License, or
(at your option) any later version.

This program 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 (version 3 pasted below) for more
details.

***

JAABA contains code from the following sources:

* Ctrax by Kristin Branson et al.: 
  http://ctrax.sourceforge.net/
* Piotr's Image & Video MATLAB Toolbox by Piotr Dollar et al.: 
  http://vision.ucsd.edu/~pdollar/toolbox/doc/
* Netlab by Christopher Bishop et al.: 
  http://www1.aston.ac.uk/eas/research/groups/ncrg/resources/netlab/
* ellipsedraw.m by Lei Wang: 
  http://www.mathworks.com/matlabcentral/fileexchange/3224-ellipsedraw1-0/content/ellipsedraw.m
* savefig_pa.m and eps2pdf.m by Peder Axensten: 
  http://www.mathworks.com/matlabcentral/fileexchange/10889-savefig
* MATLAB and Octave Functions for Computer Vision and Image Processing by Peter Kovesi:
  http://www.csse.uwa.edu.au/~pk/research/matlabfns/
* rotateticklabel.m by Andrew Bliss:
  http://www.mathworks.com/matlabcentral/fileexchange/8722-rotate-tick-label
* findjobj.m by Yair Altman:
  http://www.mathworks.com/matlabcentral/fileexchange/14317-findjobj-find-java-handles-of-matlab-graphic-objects
* hatchfill.m by Neil Tandon
  http://www.mathworks.us/matlabcentral/fileexchange/30733-hatchfill
* JavaSysMon by Jez Humble
  https://github.com/jezhumble/javasysmon
* Optical Flow computation code from Deqing Sun for "Secrets of Optical Flow Estimation and Their Principles", CVPR 2010 
 http://cs.brown.edu/~dqsun/research/software.html 
* Implementation of the Deep Matching algorithm, published at ICCV 2013 in
"DeepFlow: Large displacement optical flow with deep matching".
 http://lear.inrialpes.fr/src/deepflow/

***

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