Version 2.6



version 2.6.0

Release Notes


  • SBML Spatial 3 Level 1 draft 0.90 support. Included a new synthesis output option named 'SBMLSpatial' that saves a synthetic image as an SBML instance.
  • OME-TIFF support. Included a new synthesis output options named 'OMETIFF' that saves a synthetic image as an OME-TIFF Bioformats.
  • T cell models. Included a new model class/type called standardized_voxels/standardized-map half-ellipsoid which is used to model the protein distribution of T cell movies, given annotations of the synapse.


  • Included a new synthesis option named 'overwrite_synthetic_instances' that allows the user to stop and resume synthesis of large image collection without overwriting existing images.
  • Included demo3D34 to show how to use new synthesis output options 'SBMLSpatial3' and 'OMETIFF'.
  • Included demo3D42 to show how to train a T cell model.
  • Included demo3D43 to show how to synthesize protein distribution from cell shape and t cell model.
  • Cleaned up and optimized demos to improve performance in personal computers.



  • To read the documentation online, click here.


  • Matlab 2016b or newer
  • Bioinformatics Toolbox
  • Computer Vision System Toolbox
  • Control System Toolbox
  • Curve Fitting Toolbox
  • Image Processing Toolbox
  • Mapping Toolbox
  • Optimization Toolbox
  • Robust Control Toolbox
  • Signal Processing Toolbox
  • Simulink
  • Simulink Design Optimization
  • Statistics and Machine Learning Toolbox
  • System Identification Toolbox
  • Wavelet 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


CellOrganizer releases for the 2.0 family have been tested on
  • Matlab 2016b/Ubuntu 12.04
  • Matlab 2016b/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.