Welcome to Vizgen Post-processing Tool documentation!

Contents:

• Installation
• Command Line Interface
  • Commands
  • Options
  • Sub-commands
• Segmentation Options
  • Overview
  • Segmentation Algorithm JSON File Structure
  • Segmentation Task Definition
  • Task Fusion Definition
  • Watershed Options
  • Cellpose Options
  • Cellpose2 Options
  • CellposeSAM Options
  • InstanSeg Options
  • Segmentation Benchmarks
• Output Data Formats
  • Biological Entities and Segmentation
  • Geometry File Format
  • Entity-By-Gene Matrix File Format
  • Detected Transcripts File Format
  • Entity Metadata File Format
  • VZG File Format
• Analysis Vignettes
  • Example: Segmenting a Small Dataset Saved on a Local Hard Drive
  • Example: Re-segmenting a MERSCOPE Heart Dataset with a Machine Learning Model Customized with Manual Annotations
  • Example: Segmenting the U2OS Small Dataset with Newer Plugins
• Experimental Features
  • Building a Third-Party Plugin
  • Multiple Entities