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Details of software in use and developed by the team

The project's principal tool for EM reconstruction is the CATMAID web application, an open source tool for collaborative tracing optimised for serial section TEM volumes.

In addition, project members and their collaborators have developed a variety of tools to interact with CATMAID via its API and to enable analysis and visualisation of traced neurons. 


The tools listed below, and others are also available from our GitHub page here.

  • catmaid R package
    • enables neurons to be fetched from CATMAID via its API
    • queries by connectivity, names, annotations
    • bulk annotation
    • scripts for quality control etc
    • bridge to NeuroAnatomy Toolbox (nat) a rich toolset for analysing neuron structure/circuit organisation.
  • elmr R package
    • bridging EM and light datasets to move data such as neurons or neuropil models bidirectionally between different coordinate spaces
    • querying databases of light level single neuron or Gal4 images
  • CATMAID Blender plugin
    • generate 3D movies of tracings
    • generate meshes (manual tracing, alpha shapes) based on image data or tracings
  • PyMaid - CATMAID Python package
    • fetching data from CATMAID via its API
    • morphological and connectivity analysis
    • 2D and 3D plotting
    • Python interface with R tools (see above)

Project members have also developed tools for light microscopy analysis that we are now using with EM data. The relevant publications are below.