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Welcome to CATMAID¶

The Collaborative Annotation Toolkit for Massive Amounts of Image Data

Features:

  • Fast terabyte-scale image data browsing
  • Collaborative microcircuit reconstruction and annotation
  • Flexible hierarchical semantic annotation
  • Multiple linked image stack display
  • Neuron Catalog
  • SVG and WebGL-based neuronal morphology viewer
  • Open source software (GPLv3)

User interface

Documentation¶

  • User Documentation
    • Introduction
    • Screenshots and videos
    • Tools
    • Instructions for Tracing Neurons
    • Widgets
    • Using the CATMAID API
    • API Reference
    • Volumes
    • Frequently Asked (User) Questions
    • Exporting and Importing Data
    • Using Data Views
    • Similar Software Tools
  • Administrator Documentation
    • Basic Installation Instructions
    • Configuration options
    • Administering a CATMAID Instance
    • Production setup
    • Permissions and access control
    • Installation of the Celery task queue
    • WebSockets and ASGI
    • Tracing data caching
    • History and provenance tracking
    • Trying CATMAID with Docker
    • User Profiles
    • Additional back-ends
    • R setup for NBLAST and related tools
    • Configuring NBLAST
    • Frequently Asked Questions
    • Installing Catmaid with an RDS database backend
  • Developer Documentation
    • Contributing to CATMAID
    • Tile Source Conventions
    • Creating widgets
    • Creating New Data View Types
    • Deep Link URL Format
    • Database Migrations
    • Django Unit Tests for CATMAID
    • Models, State and Commands
    • Creating a CATMAID Instance on EC2
    • Creating CATMAID extensions

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