SNT script for bulk export of soma coordinates of MouseLight Neurons to a CSV file

download_ML_soma_locations.py

from sc.fiji.snt.analysis import SNTTable
from sc.fiji.snt.io import MouseLightQuerier, MouseLightLoader

"""
Jython script for bulk export of soma coordinates of MouseLight Neurons to a CSV file.
To Run this script:
- Download Fiji and install SNT (by subscribing to Fiji's Neuroanatomy update site)
- Edit the 'destination' variable and run this script from Fiji's Script Editor
  (using Python as language)
- For instructions on how to run SNT from a native python environment have a look at
  https://github.com/morphonets/SNT
- For details on SNT, have a look at https://imagej.net/plugins/snt
"""

destination = '/path/to/CSV/file.csv'
table = SNTTable()
ids = MouseLightQuerier.getAllIDs()
for id in ids:
    print("Parsing %s..." % id)
    loader = MouseLightLoader(id)
    try:
        # If soma is a well-defined neuronal compartment  use it (MouseLight uses
        # single-node soma definitions), otherwise retrive it as the root of the
        # full neuronal arbor
        tree = loader.getTree("soma")
        if not tree:
            tree = loader.getTree()
        root = tree.getRoot()
    except:
        # internet connection lost!?
        table.save(destination)
        print("Exception occured. See Console for details...")
    table.insertRow(id)
    table.appendToLastRow("X", root.getX())
    table.appendToLastRow("Y", root.getY())
    table.appendToLastRow("Z", root.getZ())
    table.appendToLastRow("Comp", root.getAnnotation())
    parsed.append(id)
table.save(destination)
print('done')