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The software we use and develop

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. To try out this tool, see this CATMAID instance maintained by the Virtual Fly Brain project, that collects the FAFB published neuronal morphologies.

In addition, project members and their collaborators have developed a variety of tools to interact with CATMAID via its API and to interact with other types of neuronal data, to enable analysis and visualisation of traced neurons. These tools are either R or Python packages. Most of the relevant R packages are part of the natverse environment

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


One of the datasets we use, a full adult female brain (FAFB, Zheng et al. 2018) is available here. It includes instructions to download and set up a CATMAID instance.

The other dataset we work on is the hemibrain (Xu et al., 2020), produced by HHMI Janelia Research Campus. Data can be accessed via neuPrint platform or via the neuprintr R package (part of natverse).


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

  • All natverse packages
  • 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
  • neuprintr R package
    • enables neurons to be fetched from neuPrint
    • queries by connectivity, location, neuron type
  • 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