- 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
- 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.
- CellOrganizer v2.6 Compressed Source Code [484 MB]
- CellOrganizer v2.6 Compressed Source Code + Image Collection [3.2 GB]
- 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 Design Optimization
- Statistics and Machine Learning Toolbox
- System Identification Toolbox
- Wavelet Toolbox
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
- 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