neuPrint clients

neuPrint is Janelia’s connectome database, hosting the hemibrain, MANC, optic-lobe and male-CNS datasets. Both language ecosystems have a client for it: neuprint-python and, on the R side, neuprintr.

Either needs an authentication token, which you get by logging in to neuPrint and copying it from your account page. The datasets themselves are public; the token identifies you to the server.

neuprint-python

pip3 install neuprint-python

import neuprint as neu

client = neu.Client('https://neuprint.janelia.org',
                    dataset='hemibrain:v1.1',
                    token={your_token})

Most functions accept neu.NeuronCriteria, a filter over body IDs, types, instance names and regions of interest, which is how you select the neurons a query applies to.

neuprintr

neuprintr is part of the natverse and is installed with it:

install.packages('natmanager')
natmanager::install('natverse')

Which neurons am I looking at

Body IDs are local to a neuPrint dataset. VFB assigns its own persistent identifiers to the same neurons and records the cross-references, so VFB_connect can map between a neuPrint body ID and everything else VFB holds for that neuron — including imagery and its classification in the anatomy ontology.

Where next

The neuPrint tutorial covers fetching neurons, synaptic partners and paths through the connectome, and plotting the resulting graphs. VFB’s own connectivity data is described under Data.

Full documentation: neuprint-python and neuprintr.