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
  • 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
  • History and provenance tracking
  • Trying CATMAID with Docker
  • User Profiles
  • Additional back-ends
  • Installing R and required dependencies on Ubuntu 16.04
  • Frequently Asked Questions
• Developer Documentation
  • Creating New Data View Types
  • Contributing to CATMAID
  • Tile Source Conventions
  • Deep Link URL Format
  • Database Migrations
  • Django Unit Tests for CATMAID
  • Models, State and Commands
  • Creating a CATMAID Instance on EC2
  • Creating CATMAID extensions