CellOrganizer v2.8.0
3D HeLa (mitochondria)
Release Highlights
Features
- Added improved model for generating protein distributions during T cell synapse formation that only requires annotation of cell couples at a single time point model and improves synapse alignment. Includes training, synthesis and info demos.
- Added SPHARM-RPDM model for 3D cell and nuclear shapes (see https://doi.org/10.1093/bioinformatics/bty983). Includes training, synthesis and info demos.
Enhancements
- Modularized and cleaned up img2slml.
- Documented mandatory and nonmandatory options for training and synthesis of all models
- Modified PCA, SPHARM-RPDM, and T cell model options structure.
Fixes
- Fixed issues with options.train.flag. Valid options should be nuclear, cell, framework, and protein.
Other
- The following demos have been deprecated demo2D03, demo3D03, demo3D06, demo3D18, demo3D21, demo3D23, demo3D24 and demo3D27.
Downloads
- CellOrganizer v2.8.0 Compressed Source Code [784 MB]
- CellOrganizer v2.8.0 Compressed Source Code + Image Collection [9.2 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