• Home
  • News
  • People
  • Publications
  • Downloads
    • Helper Utilities
    • CellOrganizer for Matlab
      • Version 2.10
      • Version 2.9.3
      • Version 2.9.2
      • Version 2.9.1
      • Version 2.8.1
      • Version 2.8.0
      • Version 2.7.2
      • Version 2.7.1
      • Version 2.7.0
      • Version 2.6.0
      • Version 2.5.2
      • Version 2.5.1
      • Version 2.5.0
      • Versions 2.0-2.4
      • Version 1.9
      • Version 1.8
      • Version 1.7
      • Version 1.6
    • CellOrganizer for Docker
    • CellOrganizer for Galaxy
    • CellOrganizer for Singularity
    • Trained Models Repository
  • Documentation
    • What can I do with CellOrganizer?
    • CellOrganizer for Matlab
    • CellOrganizer for Docker
    • CellOrganizer for Galaxy
  • CellOrganizer for Galaxy
  • Contact Us
CellOrganizer
  • Home
  • News
  • People
  • Publications
  • Downloads
    • Helper Utilities
    • CellOrganizer for Matlab
      • Version 2.10
      • Version 2.9.3
      • Version 2.9.2
      • Version 2.9.1
      • Version 2.8.1
      • Version 2.8.0
      • Version 2.7.2
      • Version 2.7.1
      • Version 2.7.0
      • Version 2.6.0
      • Version 2.5.2
      • Version 2.5.1
      • Version 2.5.0
      • Versions 2.0-2.4
      • Version 1.9
      • Version 1.8
      • Version 1.7
      • Version 1.6
    • CellOrganizer for Docker
    • CellOrganizer for Galaxy
    • CellOrganizer for Singularity
    • Trained Models Repository
  • Documentation
    • What can I do with CellOrganizer?
    • CellOrganizer for Matlab
    • CellOrganizer for Docker
    • CellOrganizer for Galaxy
  • CellOrganizer for Galaxy
  • Contact Us
1

CellOrganizer v2.10 Released

Jun 22, 2023

The latest release of CellOrganizer (v2.10) contains new and enhanced capabilities. CellOrganizer (http://cellorganizer.org) contains extensive functionality for converting images of cells and their components into generative models that capture many aspects of cell size, shape and intracellular organization. It contains tools for comparing models from different cell types or conditions in order to provide insight […]

2

New Release! CellOrganizer v2.9.3

Nov 17, 2021

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 […]

3

MMBioS 2021 Workshop

Jul 29, 2021

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]

4

New Release! CellOrganizer v2.9.2

Jul 13, 2021

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.

5

New Release! CellOrganizer v2.9.1

Jul 12, 2021

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 […]

6

CellOrganizer for Galaxy

Jun 4, 2019

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.

7

CellOrganizer for Docker and CellOrganizer for Singularity

May 31, 2019

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 […]

8

Slides from presentations on CellOrganizer at QCB Workshop on Visualizing and Modeling Cell Biology Posted

May 2, 2016

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

9

Seeking investigators for Collaborative or Service projects through the National Center for Multiscale Modeling of Biological Systems

Oct 5, 2014

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 […]

10

New Release! Version 2.1

Apr 29, 2014

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

  • 1
  • 2

Follow Us

  • Facebook
  • Twitter

Recent Posts

  • CellOrganizer v2.10 Released June 22, 2023
  • New Release! CellOrganizer v2.9.3 November 17, 2021
  • MMBioS 2021 Workshop July 29, 2021
  • New Release! CellOrganizer v2.9.2 July 13, 2021
  • New Release! CellOrganizer v2.9.1 July 12, 2021

Contact Us

If you have a question regarding any of the CellOrganizer products, then feel free to send us a message.

Send Message

Support for CellOrganizer has been provided by grants GM075205, GM090033 and GM103712 from the National Institute of General Medical Sciences, grants MCB1121919 and MCB1121793 from the U.S. National Science Foundation, by a Forschungspreis from the Alexander von Humboldt Foundation, and by the Freiburg Institute for Advanced Studies.

Copyright © 2007-2020 by the Murphy Lab, Carnegie Mellon University