Major New Release of CellOrganizer 2.0

Details

Published: Monday, 30 September 2013 14:06

Specific improvements or additions in the new release include:

Cell image synthesis

• Improved vesicular organelles model
  • Eliminate object/object and object/boundary overlap during generation
• Ability to combine models learned from images of different resolution, and synthesize images at desired resolution
• Ability to synthesis random walks in shape space from diffeomorphic models of cell and nuclear shape
  • Including directed random walks using Willmore energy and shape space density

Model training

• New capabilities for cell and nuclear shape model learning
  • Build nuclear models from images without nuclear marker
  • Build joint diffeomorphic models of cell and nuclear shape
• Per-cell representations for easy model building and comparison

Other

• Export to SBML-spatial and mesh formats for interfacing with tools such as CellBlender and VCell
• Parallelization of model learning pipeline
• Reporter tools
  • Assess learned models
  • Compare models
  • Compare per cell parameters within or across models