Note: If you are looking for a Python interface to the CATMAID API, please visit https://github.com/catmaid/catpy

cat

Connectome Analysis Toolbox

---

Create a connection to a CATMAID instance in Python.

from cat.connection import Connection
c = Connection( CATMAID_URL, USERNAME, PASSWORD, CATMAID_PROJECT_ID )
c.login()

Retrieve a skeleton morphology, its neuron name and information about synapses

from cat import morphology
skeleton = morphology.get_skeleton(c, SKELETON_ID )

Update the skeleton graph edges with distance between to skeleton nodes and compute the total cable length of the skeleton

from cat import labeling, features
labeling.update_skeleton_edge_with_distance( skeleton )
print features.get_total_cable_length( skeleton )