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:

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 )

System requirements

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

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Last Updated: 23 Jul 2012

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