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Murphy Lab - Software - Cytometry Part A 2011 Generative Models from Raw Image Data


The software and data used for the following paper can be downloaded below:

T. Peng and R.F. Murphy (2011) Image-derived, Three-dimensional Generative Models of Cellular Organization. Cytometry Part A 79A:383-391.

The data and code are contained in .tgz files:

Source Code 35Mb
Intermediate Results 806Mb
Data 7.6Gb

Recreating Results from Raw Image Data

  • To recreate the results from the article from raw image data, i.e. the 8 figures and 1 table, download the source and data from the above links.
  • Expand the data and source code to the desired destination.
  • In Matlab set the location of the data and use it as an input argument to the main method run, e.g.
    >> imagepath = '/path/to/images/Hela/3D';
    >> run( imagepath )

Recreating Results from Intermediate Results

  • To recreate the results from the article from intermediate results, i.e. the 8 figures and 1 table, download the source code and intermediate results from the above links.
  • Expand the intermediate results and source code to the desired destination and move the intermediate results folder into the source code folder.
    tar -xf source_v1.0.tgz
    tar -xf inter_results_v1.0.tgz
    mv inter_results source
    cd source
  • In Matlab set the location of the data and use it as an input argument to the main method run, e.g.
    >> imagepath = '/path/to/images/Hela/3D';
    >> run( imagepath )
This code has been tested on Matlab 2010a for Linux x64.

System requirements

  • Matlab
    • Image Processing Toolbox for Matlab
    • Spline Toolbox for Matlab
    • Statistics Toolbox for Matlab



Last Updated: 23 Jul 2012




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