pyroglancer

Pythonic interface to neuroglancer for displaying neuronal data like neurons, synapses, meshes (surfaces, volumes), annotations (points) in the precomputed format.

Installation

The easiest way to install the package is via pip:

$ pip3 install pyroglancer

The easiest way to install the latest developments from GitHub is:

$ pip3 install git+git://github.com/SridharJagannathan/pyroglancer@master

Documentation

https://SridharJagannathan.github.io/pyroglancer

Features

• Fetch and display neurons/neuropil meshes from electron microscopy (EM) datasets like hemibrain, FAFB etc and light microscopy (LM) neurons in mesh format.
• Display locally modified neurons or neuropil meshes.
• Display synapse annotations etc

Elements	Format	Source	Datasets
neuron	skeletons (swc) or volumetric meshes	CATMAID, neuprint, vritualflybrain or other locally modified data	EM datasets like FAFB, hemibrain or any other LM dataset like lineage clones etc
neuropils	volumetric meshes	CATMAID, neuprint or other locally modified data	FAFB, hemibrain
synapses	point annotations or precomputed format	neuroglancer layers or other locally modified data	FAFB, hemibrain

Acknowledgements

Thanks to Jeremy Maitin-Shepard from google for inventing the precomputed format and answering many of my queries. The pyroglancer logo was inspired from PyPy. The pyroglancer critically depends on packages like NAVis for interfacing with neuron data.

Copyright & License

Copyright (c) 2021, Sridhar Jagannathan. 3-clause BSD License.