Highlights When exporting a synthetic instance as an SBML instance, the positioning of the mesh has been corrected for translation errors. CellOrganizer for Galaxy has been tested on the latest stable release, version 19.05. In the shape space plot, there is a field to label images in the field to label the images, if that […]

  Today we release CellOrganizer v2.8.0! The main highlights for this release include 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 […]

CellOrganizer for Galaxy! CellOrganizer for Galaxy is the new member of the CellOrganizer family! It brings CellOrganizer to Galaxy, an open source, web-based platform for data intensive biomedical research. A public server has been made available for academic use. CellOrganizer version 2.7.2 and CellOrganizer for Docker The latest release of CellOrganizer and CellOrganizer for Docker now includes a method […]

CellOrganizer Version 2.7.1 The latest release of CellOrganizer now includes methods to generate reports from generative models. slml2info replaces model2info, and creates a report with useful information from a single generative model file. slml2report creates a report comparing two generative model files. Both methods write reports with Matlab Publisher, and when deployed as binaries, they […]

March 7, 2018 CellOrganizer Version 2.7.0 Release Highlights Features Included new model class/type constructive_geometry/half-ellipsoid Included new model class/type:framework/pca Included support for constructing models with OME.TIFF containing regions of interest   Enhancements img2slml now checks the combination of model class and type for every submodel before attempting to extract parameters from images Added demo3D44 to show […]

June 26, 2017 CellOrganizer Version 2.6.0 Release Highlights 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. […]

September 12, 2016 CellOrganizer Version 2.5.2 Release Highlights 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.

August 1, 2016 CellOrganizer Version 2.5.1 Release Highlights Models have been retrained and reflect CellOrganizer updated model structure. Demos have been updated to have consistent documentation. Issues in 3D diffeomorphic training have been resolved. Outputs corrected in demos. Some demos were refactored.

June 1, 2016 CellOrganizer Version 2.5 New Release Highlights! 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 […]

September 16, 2015 CellOrganizer Version 2.4 New Release Highlights! Demo recreating results found in G. R. Johnson, T.E. Buck, D. P. Sullivan, G. R. Rohde, and R. F. Murphy (2015) Joint Modeling of Cell and Nuclear Shape Variation. Molecular Biology of the Cell, in press (Special Issue on Quantitative Biology). Enhanced reporting of time series […]