- Added new 3D model type (class “vesicle” and type “spharm_obj”) for organelles; it models organelle size and shape as well as subcellular position. “Vesicle” is the CellOrganizer class that includes all organelles that consist of discrete objects. The previous models in the “vesicle” class used ellipsoids to model individual objects. The new model is learned by first segmenting all objects in a protein image using adaptive thresholding, and the position of each object relative to the cell and nuclear membranes is recorded. A size and shape model is then constructed from all objects using the SPHARM-RPDM method, and a logistic regression model is learned to capture the probability density of an object occurring at any position in a standardized cell. Synthesis from the learned models is not yet supported, but strong support is provided (through slml2report) for comparing models between datasets. New demos demo3D61 and demo3D62 illustrate training this new model type.
- Added new functionality to slml2report to provide comparison of SPHARM models.
- Added support for exporting synthetic cell instances as VCML files for use in Virtual Cell.
- Support for exporting instances as SBML Spatial files has been updated to the latest version of the standard. Demo demo3D64 illustrates the creation of SBML spatial files.
- CellOrganizer v2.8.1 Compressed Source Code [784 MB]
- CellOrganizer v2.8.1 Compressed Source Code + Image Collection [9.2 GB]
- To read the documentation online, click here.
- Matlab 2019b 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 2.8+ family have been tested on
- Matlab 2019b/Ubuntu 12.04
- Matlab 2019b/MacOSX El Capitan