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