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Software for the Analysis of Focal Adhesion Images
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Introduction: Congratulations, you have downloaded the focal adhesion analysis suite. You should see three folders: -data: used to hold the raw imaging data, along with config files controlling the options used for processing are stored here -src: all the source code that processes the images and conducts the statistical analysis is in this folder Prerequisites: In addition to the programs in the src folder, I also expect that you have working installations of MATLAB and R. You will also need to download and put in your MATLAB path a set of freely available scripts used to find curve extremas: -http://www.mathworks.com/matlabcentral/fileexchange/12275-extrema-m-extrema2-m There are also several needed perl libraries, all of which can be installed from CPAN: -Benchmark -Config::General -Cwd -Data::Dumper -File::Basename -File::Copy -File::Find -File::Find::Rule -File::Path -File::Spec::Functions -File::Temp -Getopt::Long -IO::File -IO::Handle -Image::ExifTool -Math::Matlab::Local -Math::Matrix -Math::Trig -POSIX -Statistics::Descriptive -Statistics::Distributions -Storable -Text::CSV::Simple Sample Experiment and Results: There is a master control script that should be used to process your images, located at 'src/scripts/build_all_images.pl'. It expects a single command line parameter, a config file. In order to get started a sample data set has been provided. This zip file should be unzipped into the data directory. Working from the 'src/scripts' directory, exclude the command: ./build_all_results.pl -cfg ../../data/config/FA_default.cfg Now wait for several hours (~5.5 hrs on a 2.67 Ghz 8-core i7 with 12 gigs RAM). You should see several status messages print to the terminal window. The longest running part of the script is 'collect_fa_image_set'. To put new data into the system, I would suggest modeling your data folder after the sample data set provided, although that can be modified through the config files. After the programs run, you should see a new directory called results at the top level of the directory structure. The subfolders within this directory hold all the image processing results. There are a wide range of temporary files created during the image processing and analysis steps, some of the output files you might be interested in are: -'visualizations/tracking_seq/edge_track': holds a set of images showing each detected adhesion (highlighted in a different color throughout its lifetime) and an overlay showing where each of the cell edges were detected -'visualizations/single_ad': holds sets of small mulitple images showing the adhesion of interest in green, other adhesions in blue and the cell edge in red, the name of each file corresponds to the lineage number assigned during image processing -'adhesion_props/assemb_disassem_rates_filtered.csv': This CSV formated file contains information about each of the adhesion assembly and disassembly rates filtered to only include the significant and positive rates, you can see the unfiltered rates in the with a similar name in the same folder. If you are interested in seeing a specific adhesion from the experiment, cross reference the "lineage_num" column with the images in 'visulizations/single_ad'