/TigerFISH

Fork of FISH Image Analysis used at Princeton

Primary LanguageMATLABOtherNOASSERTION

TigerFISH Usage Guide

  1. Prepare a tab delimited file listing the experiments input files The columns of the file should be:

     Experiment, Region, Cy3_label, Cy3_file, Cy3.5_label, Cy3.5_file, Cy5_label, Cy5_file, DAPI_label, DAPI_file

    a. Use parse_experiemnt_direcotory when files for a given experiment are in a single directory:

         EXPERIMENT_SET/
         EXPERIMENT/
             EXPERIMENT_NUMBER-EXPERIMENT_NAME - Position #_CDYE.tiff
           
             DYE should be one of CY3, CY3.5, CY5, DAPI
             e.g. NS1-POL30_SUR4_OM45 - Position 1_CCY3.tiff

    b. Use generate_experiment_list if the files for each experiment are divided into subdirectories:

         EXPERIMENT_SET/
         EXPERIMENT/
             1/
                 EXPERIMENT_NUMBER-EXPERIMENT_NAME - Position #_CDYE.tiff
                 
                 DYE should be one of CY3, CY3.5, CY5, DAPI
                 e.g. NS1-POL30_SUR4_OM45 - Position 1_CCY3.tiff

     generate_experiment_list(path, 
                              [experiment_numbers=1:1000],
                              [output_filename='experiment_list.txt'], 
                              [filemask=*])

  2. Analyze experiment set:

     main( experiment_list_file, output_dir, [ini_file='my_parameters.ini'], [load_results=False] )

    The my_parameters.ini file is an ini-style configuration file specifying the parameters for the analysis. See default_parameters.ini for a list of parameters and documentation.

  3. Run generateFishView.py to generate HTML pages to view the output:

     python generateFishView.py path/to/results -n 'Experiment Set Name'

Examples

Example images and output are available at: http://genomics-pubs.princeton.edu/tigerfish-examples/