Significant additions have been made to the function (slml2report.m) for comparing two CellOrganizer spharm-obj models of organelle shape and spatial distribution. The report now includes  improved plots of the spatial distributions of objects, and a statistical comparison between the positions of objects (relative to cell and nuclear boundaries) in the two models.  This is done […]

The MMBioS 2021 Cell Modeling Workshop was run virtually on July 12 – 16th. Updated materials from the CellOrganizer sessions, including installation instructions for Docker/Jupyter Notebook version of CellOrganizer [link] and introductory and advance tutorials can be found here [link]

Bug Fixes Fixes to functions img2slml in param2model_3D in which the correct pathway for spharm obj models weren’t properly handled. Other minor pathway and integrity fixes to slml2info.

New features 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 […]

Today we are releasing CellOrganizer for Galaxy v2.8.0! CellOrganizer for Galaxy is a collection of tools so that Galaxy users can run CellOrganizer on this platform. The tools released with this version have been updated to be compatible with release 2.8.0. To request access to our public server, please use this form.

Today we are releasing a new product and an update in the CellOrganizer family. For more information, click the logos below. The latest release of CellOrganizer for Docker now includes Jupyter Notebook to facilitate the exploration and analysis of generative models and all of its derivatives. CellOrganizer for Singularity is the latest product in the […]

Presentations at QCB Workshop on Visualizing & Modeling Cell Biology, Salt Lake City, May 2, 2016 Tutorial given by Greg Johnson Talk given by Bob Murphy

October 5, 2014 The image analysis and modeling team at the NIH-supported National Center for Multiscale Modeling of Biological Systems would like to bring to your attention an opportunity to engage in a collaborative or service project with researchers at the Center. We are seeking investigators who wish to use CellOrganizer for learning and using […]

April 29, 2014 CellOrganizer Version 2.1.0 The latest version of CellOrganizer has been released.

September 30, 2013 CellOrganizer Version 2.0.0 The latest version of CellOrganizer has been released.