June 26, 2017 New Release! 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. Included a new model class/type called standardized_voxels/standardized-map half-ellipsoid which is used to model the protein distribution of T cell movies, given annotations of the synapse.

September 12, 2016 New Release! 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 New Release! 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 New Release! 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 rather than downloading them each time demos run.
  • Faster training and synthesis for 3D diffeomorphic models.
  • Miscellaneous bug fixes and performance improvements.

May 2, 2016 Slides from presentations on CellOrganizer at QCB Workshop on Visualizing & Modeling Cell Biology posted.

September 16, 2015 New Release! 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 as well as cell and nuclear shape space relationships.
  • Included new diffeomorphic model of H1299 cells and a corresponding demo.
  • Included new independent cell and nuclear diffeomorphic models from HeLa cells.

May 19, 2015 New Release! Version 2.3

New Release Highlights!

  • Microtubule model training.

April 27, 2015 New Release! Version 2.2

New Release Highlights!

  • Optimized shape space calculation.
  • Image size is no longer set to a default value and it will automatically determine the image size based on the model instance.
  • Enhanced training demos to allow users to generate images from the trained models.
  • Updated SBML-spatial support in keeping with v0.89 of the specification.

October 5, 2014 Seeking investigators for Collaborative or Service projects through the National Center for Multiscale Modeling of Biological Systems

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 generative models of cell size, shape and subcellular organization (or to help with further development). We can provide extensive training to external personnel, consultation on appropriate methods and design of studies, help with local installation of any desired software, and access to computational resources at the Center for image analysis, modeling and simulation. CellOrganizer learns modular models of things such as cell shape, nuclear shape, vesicular organelle distribution and microtubule distribution directly from 2D or 3D images and can produce specific instances of cell geometries without the need to create them by hand or to segment microscope images (see Buck et al, 2012 for an overview). Through Center funding, pipelines have been created whereby these geometries can be combined with biochemical models to perform spatially realistic cell simulations with a minimum of effort (Center resources can be provided to run these using the cell simulation engine MCell. The biochemical models can be encoded in SBML (i.e., investigator created or downloaded from models databases) or can be generated by BioNetGen (a powerful rule-based modeling package). This combination of CellOrganizer and MCell allows investigators to explore the effect of different cell geometries on their models (e.g., to independently explore different modes of variation in the generative models, such as variation in organelle number vs. shape). Existing generative models of 3T3 cells, HeLa cells, and C2C12 cells can be used so that making extensive image collections can be avoided.

If interested, please contact murphy@cmu.edu or fill out the form at the MMBioS web site. We would be happy to further explain the capabilities of the current system and discuss development of new capabilities.

The CellOrganizer project provides tools for

  • learning generative models of cell organization directly from images
  • storing and retrieving those models in XML files
  • synthesizing cell images (or other representations) from one or more models
Model learning captures variation among cells in a collection of images. Images used for model learning and instances synthesized from models can be two- or three-dimensional static images or movies.

CellOrganizer can learn models of

  • cell shape
  • nuclear shape
  • chromatin texture
  • vesicular organelle size, shape and position
  • microtubule distribution.
These models can be cossnditional upon each other. For example, for a given synthesized cell instance, organelle position is dependent upon the cell and nuclear shape of that instance.

Cell types for which generative models for at least some organelles have been built include human HeLa cells, mouse NIH 3T3 cells, and Arabidopsis protoplasts. Planned projects include mouse T lymphocytes and rat PC12 cells.

Synthesized Cell Images
(click to view)

2D HeLa (endosomes)

3D HeLa (mitochondria)

3D protoplast (chloroplasts)

3D HeLa (microtubules)

3D HeLa movie

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 © 2007-2015 by the Murphy Lab, Carnegie Mellon University