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CellOrganizer
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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

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Recent Posts

  • New Release! CellOrganizer v2.9.3 November 17, 2021
  • MMBioS 2021 Workshop July 29, 2021
  • New Release! CellOrganizer v2.9.2 July 13, 2021
  • New Release! CellOrganizer v2.9.1 July 12, 2021
  • New Release! CellOrganizer v2.8.1 June 20, 2019

Contact Us

If you have a question regarding any of the CellOrganizer products, then feel free to send us a message.

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Support for CellOrganizer has been provided by grants GM075205, GM090033 and GM103712 from the National Institute of General Medical Sciences, grants MCB1121919 and MCB1121793 from the U.S. National Science Foundation, by a Forschungspreis from the Alexander von Humboldt Foundation, and by the Freiburg Institute for Advanced Studies.

Copyright © 2007-2020 by the Murphy Lab, Carnegie Mellon University