1. Lance Parsons
  2. WormCount

Overview

WormCount
=========
Evaluates images of a plate of worms and estimates the number of worms present.
Calcualtes the chemotaxis index of experiments.

Source available at https://bitbucket.org/lance_parsons/wormcount


Usage
=====
Ensure that the count_worms_vX.X directory is in your MATLAB PATH.


Count worms for an entire experiment (directory)
------------------------------------------------

Square Grid Plates (BETA)
~~~~~~~~~~~~~~~~~~~~~~~~~
count_data = count_worms_directory_grid() allows gui
   selection of the directory to analyze.  The directory must contain
   sets of whole plate images for each strain, time point, and
   replicate. File names must conform for the following specification:

       [strain]_T[time]_[replicate].png

Round Plates
~~~~~~~~~~~~
count_data = count_worms_directory() allows gui
   selection of the directory to analyze.  The directory must contain
   sets of whole plate images for each strain, time point, and
   replicate. File names must conform for the following specification:

       [strain]_T[time]_[replicate].png


Calculate cheomotaxis index
----------------------------   
chemotaxis_data = chemotaxis_index(count_data)

    count_data is a struct with four fields:
        total, ori, but, eth

    CHEMOTAXIS_INDEX = (but-eth)/(total-ori)


License
=======
This software was developed by Lance Parsons at the Lewis-Sigler Institute
of Integrative Genomics at Princeton University, Princeton, NJ, USA
Licensed under the BSD 2-Clause License http://www.opensource.org/licenses/BSD-2-Clause

Other Software
--------------
The cellwrite.m function was derived from source available at 
http://francisbarnhart.com/blog/2005/01/19/matlab_pain/

The imoverlay.m function is covered by the BSD License 
(see lib/imoverlay/license.txt).  It was written by Steve Eddins and obtained 
from MATLAB Central File Exchange 
http://www.mathworks.com/matlabcentral/fileexchange/10502

The intersections.m is Copyright (c) 2008, Douglas M. Schwarz
See lib/intersections/LICENSE.txt

The nesteredSortStruct functions are Copyright (c) 2010, Jake Hughey
See lib/nestedSortStruct/LICENSE.txt