CellOrganizer v2.6.0

Release Notes

Features

• 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.

Enhancements

• 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.

Downloads

• CellOrganizer v2.6 Compressed Source Code [484 MB]
• CellOrganizer v2.6 Compressed Source Code + Image Collection [3.2 GB]

Documentation

• To read the documentation online, click here.

Requirements

• 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

Compatibility

CellOrganizer releases for the 2.0 family have been tested on

• Matlab 2016b/Ubuntu 12.04
• Matlab 2016b/MacOSX El Capitan