Python module for accessing NeuroMorpho.org

The NeuroMorpho.org database is centrally curated inventory of reconstructions of neurons which are associated with peer-reviewed publications. The provided Python wrapper makes the interaction with the website through the NeuroMorpho.org v7 REST API available for procedural processing, e.g. batch processing. The database can be queried, and neurons can be downloaded in the SWC file format. See get_swc.py or the examples below. Additionally consistency of the geometry can be checked with the --validate switch. This checks for self-intersections of the cylindrical geometry in three-dimensional space.

Depends only on standard modules, no 3rd party dependencies. Python >=2.5 is required however.

A first example can be found here and the API documentation there.

Build status

Linux	Windows	OSX

Features

Get neurons matching a search term and additional filters (Usage Example 1 and 2)
Get a neuron by global index in database (Example 3)
Get a neuron by known name in database (Example 4)
Get a certain number of neurons by brain region (Example 5)
Get a certain number of neurons by archive name (Example 6)

Usage:

Example 0

Omitting any arguments and just typing python get_SWC.py in a a terminal will output the following usage string:

usage: get_swc.py [-h] [--region R] [--neurons C] [--name N] [--index I]
                  [--archive A] [--filters [FILTER]] [--search S]

Access NeuroMorpho.org v7 w/ REST API and download SWC files

optional arguments:
  -h, --help          show this help message and exit
  --region R          Brain region
  --neurons C         Count of neurons (-1 means all)
  --name N            Name of neuron
  --index I           Index of neuron
  --archive A         Archive name
  --filters [FILTER]  One or multiple filters (OPTIONAL)
  --search S          Search term

Example 1

Most useful usage is probably the following to specify a search term and additional filters:

python get_swc.py --filter "cell_type=pyramidal" --neurons 10 --search "brain_region:neocortex" --filter "archive=Allen Cell Types"

This will search for the brain region neocortex and then filter the result by the cell type pyramidal and archive Allen Cell Types. The first 10 neurons stored in NeuroMorpho.org database will then be downloaded and stored as SWC files.

Example 2

Get a neuron of this search term by index of total neurons matching the search criteria (The below will pick neuron with index 7):

python get_swc.py --filter "cell_type=pyramidal" --index 7 --search "brain_region:neocortex" --filter "archive=Allen Cell Types"

Example 3

Get a neuron (Here: The first neuron in the database) by the global index (1) from the database:

python get_swc.py --index 1

Example 4

Get a neuron by it's known name and download as SWC file:

python get_swc.py --name cnic_001

Example 5

The following will download all SWC files from the region Neocortex to the current working directory

python get_swc.py --region neocortex

and the following command will just download the first ten neurons from the Neocortex region.

python get_swc.py --region neocortex --neurons 10

Example 6

To download a whole Smith archive in SWC format from the database, use the following commmand:

python get_swc.py --archive Smith

marwan-abdellah / neuromorpho