Version 2.5

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version 2.5.2

Release Notes

  • Fixed issues with demo3D04 to demo3D07 due to nonexistent field.
  • Centrosome model class and type has been update to reflect refactoring.
  • Adjusted directory path for demo3D20.
  • Updated 2D and 3D demos to match documentation.
  • Fixed error in demo3D15 where synthetic images were empty.

Downloads

Documentation

  • To read the documentation online, click here.

Requirements

  • Matlab 2014b or newer
  • Image Processing Toolbox for Matlab
  • Statistics and Machine Learning Toolbox/Statistics Toolbox
  • SymBiology Toolbox
  • Curve Fitting Toolbox

Validating Suite

CellOrganizer releases for the 2.0 family are continuously tested using a set of
  • public tests using the Matlab Unit Testing Framework
  • private tests for compatibility with old releases of Matlab

Compatibility

CellOrganizer releases for the 2.0 family have been tested on
  • Matlab 2015a/Ubuntu 12.04
  • Matlab 2014a/Ubuntu 12.04
  • Matlab 2016a/MacOSX El Capitan

version 2.5.1

Release Notes

  • Models have been retrained and reflect CellOrganizer updated model structure.
  • Demos have been updated to have consistent documentation.
  • Issues in 3D diffeomorphic training have been resolved.
  • Outputs corrected in demos.
  • Some demos were refactored.

Downloads

Documentation

  • To read the documentation online, click here.

Requirements

  • Matlab 2014b or newer
  • Image Processing Toolbox for Matlab
  • Statistics and Machine Learning Toolbox/Statistics Toolbox
  • SymBiology Toolbox
  • Curve Fitting Toolbox

Validating Suite

CellOrganizer releases for the 2.0 family are continuously tested using a set of
  • public tests using the Matlab Unit Testing Framework
  • private tests for compatibility with old releases of Matlab

Compatibility

CellOrganizer releases for the 2.0 family have been tested on
  • Matlab 2015a/Ubuntu 12.04
  • Matlab 2014a/Ubuntu 12.04
  • Matlab 2016a/MacOSX El Capitan

version 2.5

Release Notes

  • Refactored the process by which images are converted to parameterizations to improve performance and facilitate adding new models.
  • Refactored and simplified demos to make it easier to use as templates for user scripts.
  • Included methods to download Murphy Lab 2D/3D HeLa and 3D 3T3 image collections rather than downloading them each time demos run.
  • Faster training and synthesis for 3D diffeomorphic models.
  • Miscellaneous bug fixes and performance improvements.

Downloads

Documentation

  • To read the documentation online, click here.

Requirements

  • Matlab 2014b or newer
  • Image Processing Toolbox for Matlab
  • Statistics and Machine Learning Toolbox/Statistics Toolbox
  • SymBiology Toolbox
  • Curve Fitting Toolbox

Validating Suite

CellOrganizer releases for the 2.0 family are continuously tested using a set of
  • public tests using the Matlab Unit Testing Framework
  • private tests for compatibility with old releases of Matlab

Compatibility

CellOrganizer releases for the 2.0 family have been tested on
  • Matlab 2015a/Ubuntu 12.04
  • Matlab 2014a/Ubuntu 12.04
  • Matlab 2016a/MacOSX El Capitan

Support for CellOrganizer has been provided by grants GM075205 and GM090033 from the National Institute of General Medical Sciences, by a Forschungspreis from the Alexander von Humboldt Foundation, and by the School of Life Sciences of the Freiburg Institute for Advanced Studies.