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
  • Training tracers
  • Annotations
  • Widgets
  • Using the CATMAID API
  • API Reference
  • Volumes
  • Workflows
  • 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
  • Setting Up Nginx for CATMAID
  • Example configurations
  • Database backups
  • Node providers
  • Permissions and access control
  • Installation of the Celery task queue
  • WebSockets and ASGI
  • Tracing data caching
  • History and provenance tracking
  • Data replication
  • Postgres administration
  • Docker
  • User accounts
  • Additional back-ends
  • R setup for NBLAST and related tools
  • Configuring NBLAST
  • External sign-in using OAuth2
  • Frequently Asked Questions
  • Installing Catmaid with an RDS database backend
• Developer Documentation
  • Developer setup with Vagrant
  • 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
  • CATMAID Releases