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CATMAID tools

Overview of packages and scripts for the analysis of CATMAID data contributed by the FAFB community.

Contributing

  1. Add scripts/code to the repository or link to external resource
  2. Leave brief description in this README. If possible, include maintainer/contact

R

nat

An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons. nat is the core package of a wider suite of neuroanatomy tools introduced at http://jefferislab.github.io. Greg Jefferis, WT UK/Jefferis lab.

rcatmaid

R package providing API access to the CATMAID web image annotation tool. Provides interface with nat R package, enabling wide variety of analyses. Greg Jefferis, WT UK.

elmr

Provides tools to move between adult brain EM and light level data, emphasising the interaction between the CATMAID web application and the R Neuroanatomy Toolbox package. See also https://github.com/saalfeldlab/elm, from which this package borrows both a name and uses data. Greg Jefferis, WT UK.

catnat

R Package for use with rcatmaid and nat. catnat provides some higher level analysis function for, for example, clustering synapses within a neuron's tree structure, clustering together neurons by synapse position in 3D space and splitting a neuron into different compartments (e.g. axon-dendrite-primary neurite) and visualising these splits and clusters. Alexander Bates, Jefferis Lab.

tracerutils

R package with useful functions for EM tracers. Provides shortcuts for common tasks like plotting neurons from CATMAID, randomly sampling synapses, and checking for duplicate connectors. Fiona Love, WT UK.

Scripts

Python

pymaid

Python 3 package to fetch data from CATMAID server and analyse neuron anatomy and connectivity. Features include: fetch data from CATMAID, 2D and 3D plotting of neurons, virtual neuron surgery (cutting, stitching, pruning, rerooting, etc), R bindings (e.g. for libraries nat, nat.nblast and elmr), interface with Blender 3D, import/export from/to SWC, load and annotate image data. Philipp Schlegel, WT UK.

catbot

Slack chatbot that allows quick queries to a CATMAID server. Most notably it lets you NBLAST CATMAID neurons against e.g. the flycircuit database. Philipp Schlegel, WT UK.

Blender plugin

Plugin for Blender 3D that allows fetching data from CATMAID server for high-quality renderings. Philipp Schlegel, WT UK.

Scripts

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Overview of tools for the analysis of CATMAID data

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