Pythonic interface to neuroglancer for displaying neuronal data like neurons, synapses, meshes (surfaces, volumes), annotations (points) in the precomputed format.
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
https://SridharJagannathan.github.io/pyroglancer
- 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 |
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 (c) 2021, Sridhar Jagannathan. 3-clause BSD License.