pymaid
Python client for CATMAID, including the FAFB and other EM datasets VFB hosts.
pymaid talks to CATMAID servers and returns neurons as navis objects, so skeletons you pull
from CATMAID drop straight into the rest of the Python toolchain. VFB hosts the public CATMAID
instances for several connectomics datasets — see what is
available — and those are open for read-only access
without a token.
Install
pip3 install python-catmaid
Note the package name. There is an unrelated pymaid package on PyPI; installing that one will
not give you this library.
Quick start
VFB’s CATMAID servers are public, so connecting needs no API token:
import pymaid
import navis
# Connect to the VFB CATMAID server hosting the FAFB data
rm = pymaid.connect_catmaid(server="https://fafb.catmaid.virtualflybrain.org/",
api_token=None, max_threads=10)
print(f'Server is running CATMAID version {rm.catmaid_version}')
With a connection established, pymaid.get_neuron(16) fetches a skeleton by its ID, returning
a CatmaidNeuron that navis can plot, prune and compare like any other neuron.
Skeleton IDs are local to each CATMAID instance and are not unique between them, which is why VFB gives every image its own persistent identifier. VFB_connect can map between the two.
Where next
The pymaid tutorial works through retrieving neurons, filtering them by name and lineage, and plotting the results.
Full documentation: pymaid.readthedocs.io. Source: navis-org/pymaid. CATMAID itself: catmaid.readthedocs.io.