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RELEASE_NOTES.txt
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CellOrganizer v2.8.1
====================
Fixes
-----
* Display shape space when dataset field is not present or empty.
* Generation of watertight SBML Spatial output has been corrected for translation errors.
Other
-----
* The following models have been rebuilt using this version of CellOrganizer. Updated models can be found in the model repository.
* 2D HeLa diffeomorphic framework
* 2D HeLa PCA framework
* 2D HeLa classic framework
* CellOrganizer for Galaxy now Galaxy server v19.05
CellOrganizer v2.8.0
====================
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.
Fixes
-----
* Fixed issues with options.train.flag. Valid options should be nuclear, cell, framework, and protein.
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.
* Enhanced SBML Spatial output
** SBML Spatial output can now include meshes for the whole framework
and CSG objects for vesicles.
** SBML Spatial output can now include watertight meshes generated
directly from SPHARM and ratio models.
** SBML Spatial output updated to comply with draft specification 0.93
from December 2018 and to be importable by an upcoming version of
CellBlender (available in CellBlender repository version since Apr 26,
2019).
Other
-----
* The following demos have been deprecated demo2D03, demo3D03, demo3D06, demo3D18, demo3D21, demo3D23, demo3D24 and demo3D27.
CellOrganizer v2.7.2
====================
Features
--------
* Added slml2slml to combine models into a single file.
Enhancements
------------
* Main methods slmlimg, slml2info, slml2report and img2slml have been optimized for the release of CellOrganizer for Galaxy tools.
CellOrganizer v2.7.1
====================
Features
--------
* Created method slml2info to replace model2info. The method creates a report with useful information from a model file. Method writes report with Matlab Publisher. When method is deployed, then it generates a report in Markdown.
* Created method slml2report. The method creates a report comparing two model files. Method writes report with Matlab Publisher. When method is deployed, then it generates a report in Markdown.
* Created demos demo2D08 and demo2D09 to show how to make a report from a PCA framework model.
Enhancements
------------
* Main methods slml2img, slml2info, slml2report and img2slml have been optimized for Matlab Compiler for release with CellOrganizer for Docker.
Fixes
-----
* Fixed problem with demo3D46. Unable to synthesize image from CSGO model when combined with a vesicle model.
CellOrganizer v2.7.0
====================
Features
--------
* Included new model class/type: constructive_geometry/half-ellipsoid.
* Included new model class/type: framework/pca.
* Included support for OME.TIFF with regions of interest.
* Included bash scripts to run demos from compiled versions of the main functions.
Enhancements
------------
* img2slml now checks the combination of model class and type for every submodel before attempting to extract parameters from image.
* Improved pipeline so that CellOrganizer will stop computation and report to user if no images are found in the path or if software fails to extract parameters.
* Added demo3D44 to show how to synthesize from a model class/type constructive_geomertry/half-ellipsoid.
* Added a battery of unit test for demos using Matlab testing framework.
* Added demo3D45 to show how to use OME.TIFF files with ROIs.
* Added demo2D05, demo2D06, demo2D07 to show how to train and synthesize from a classtype framework/pca model.
CellOrganizer v2.6.0
====================
Features
--------
* SBML Spatial 3 Level 1 draft 0.90 support. Included a new synthesis output option named 'SBMLSpatial3' 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 "soluble"/"standardized-map half-ellipsoid" which is used to model the protein distribution of T cell movies, given annotation of the synapse.
Enhancements
------------
* Included a new synthesis option named 'overwrite_synthetic_instances' that allows the user to 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 demo3Dtcell_train to show how to train a T cell model.
* Included demo3Dtcell_synth to show how to synthesize protein distribution from cell shape and t cell model.
CellOrganizer v2.5.2
====================
* Fixed issues with demo3D04 to demo3D07 due to nonexistent field.
* Centrosome model class and type has been update to reflect refactoring.
* Adjusted directory path for demo3D20.
* Updated 2D and 3D demos to match documentation.
* Fixed error in demo3D15 where synthetic images were empty.
CellOrganizer v2.5.1
====================
* Models have been retrained and reflect CellOrganizer?s updated model structure.
* Demos now have consistent documentation of both outputs and options.
* Demos have been been simplified to improve performance of public tests.
* Errors in diffeomorphic training and synthesis have been resolved by updating the model in the release.
* Failure in demo3D23 image extraction has been fixed.
* Fixed model name in demo3D30.
* The following demos have been refactored and verified: demo3D02, demo3D06, demo3D07, demo3D08, demo3D09, demo3D10, demo3D13, demo3D14, demo3D15, demo3D16, demo3D18, demo3D19, demo3D21, demo3D22, demo3D23, demo3D24, demo3D25, demo3D26 and demo3D27.
CellOrganizer v2.5
==================
* Refactored the process by which images are converted to parameterizations to improve performance and facilitate adding new models.
* Refactored and simplified demos to make it easier to use as templates for user scripts.
* Included methods to download Murphy Lab 2D/3D HeLa and 3D 3T3 image collections rather than downloading them each time demos run.
* Faster training and synthesis for 3D diffeomorphic models.
* Miscellaneous bug fixes and performance improvements.