CellOrganizer Documentation

Contents:

• Introduction
• Disclaimer
  • About this document
  • Downloads
• Installation
  • Installing CellOrganizer for Matlab
  • Installing CellOrganizer for Matlab on a HPC
• Tutorial: CellOrganizer in 45 Minutes
  • Introduction
  • Whom is this tutorial for?
  • Resources
  • Prerequisites
  • Requirements for inputs for building models
  • Setup
  • Training Models
  • Synthesizing an Image from a Model
  • Visualizing Model Results
• Demos
  • 2D/3D Demos
  • Demos Summary Table
  • Brief Descriptions
• Additional Information
  • Model classes and types
  • Reproducing Figures from Research Articles
  • OME-TIFF
  • SBML Spatial Level 3
  • T cell models
• API
  • im2blender
  • im2projection
  • im2reshape
  • img2slml
  • model2info
  • slml2img
  • syn2projection
  • syn2surfaceplot