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CellOrganizer DocumentationΒΆ

Contents:

  • Introduction
  • Disclaimer
  • About this document
  • Installation
    • Installing CellOrganizer
    • Installing CellOrganizer on a HPC
    • Installing CellOrganizer for Docker
  • Running CellOrganizer for Docker
    • Access cellorganizer-docker container interactively
    • Run a demo that invokes img2slml
    • Run a demo that invokes slml2img
    • Exit the container
    • Export generated data out of the container
  • 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
  • Main Functions
    • img2slml
    • slml2info
    • slml2img
    • slml2report

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