How to edit morphologies

Jaxley provides functionality to edit morphologies. In particular, it provides functions to delete parts of a morphology or to connect two cell morphologies into a single cell.

⚠️ IMPORTANT!
If you edit morphologies, please do so before you change the number of compartments per branch (via, e.g., cell.branch(0).set_ncomp(4)). In addition, you must delete all recordings, stimuli, trainable parameters, and channels before running morph_delete() or morph_connect().

Deleting parts of a morphology

Below, we will show how you can delete all apical branches of a morphology.

import jaxley as jx
from jaxley.morphology import morph_delete

cell = jx.read_swc("path_to_swc_file.swc", ncomp=1)

# Creates a new cell which has the apical dendrite deleted.
cell = morph_delete(cell.apical)

# Creates a new cell which has branches 10, 11, 12 deleted.
cell = morph_delete(cell.branch([10, 11, 12])

Attaching two morphologies

Jaxley also provides functionality to easily attach two morphologies. This is useful to, for example, replace the axon with a “stub”. Below, we show how one can attach two morphologies. We read one morphology from an SWC file and create the other one from scratch.

import jaxley as jx
from jaxley.morphology import morph_connect

# Read a cell from SWC.
cell = jx.read_swc("path_to_swc_file.swc", ncomp=1)

# Create a "stub" of 50um length.
stub = jx.Cell()
stub.set("length", 50.0)

new_cell = morph_connect(cell.branch(0).loc(0.0), stub.branch(0).loc(0.0))

Note that you have to use .loc() to specify the location at which to connect the cells. The location must be either 0.0 or 1.0.

Graph-backend for more flexibility

All of the above is achieved by using Jaxley’s “graph-backend”, which is based on networkX. As such, you can modify Jaxley morphologies with any feature of the networkX toolkit.

For more details on Jaxley’s graph-backend, see this tutorial, where we also provide an example of how to trim dendrites of a morphology.