NeuroMorphopy

Lightweight python package for downloading neuron morphologies from the NeuroMorpho archives.

• Github repository: https://github.com/kpeez/neuromorphopy/
• Documentation https://kpeez.github.io/neuromorphopy/

Installation

If using poetry, simply clone the repo and install

git clone https://github.com/kpeez/neuromorphopy.git
cd neuromorphopy
make install

Usage

First, import and create a NeuroMorpho object:

import neuromorphopy as nm

neuromorph = nm.NeuroMorpho()

To see a list of valid search fields you can access the valid_field_names attribute:

neuromorph.valid_field_names

Getting neuron metadata from NeuroMorpho

To search the NeuroMorpho archives, construct a search query and run search_archives(query).

The query can be explicitly written, or loaded from a json file using nm.load_json_query(path_to_query_file)

For example, to get all of the mouse interneurons and pyramidal cells from hippocampus and neocortex, you would use the following:

query = {
    "species": ["mouse"],
    "brain_region": ["neocortex", "hippocampus"],
    "cell_type": ["interneuron", "pyramidal"],
    "experiment_condition": ["Control"]
}

# alternatively
query = nm.load_json_query(path_to_query_file)

neuromorph.search_archives(query)

Note: this may take some time if you are request a large set of neurons. For example, the above query takes ~3 mins to get info for ~26,000 neurons.

The results of the search can be viewed by accessing the neuron_metadata attribute:

metadata = neuromorph.neuron_metadata

If you already have a search query, you can pass in the query dictionary at initialization to automatically get the metadata:

neuromorph = nm.NeuroMorpho(query)

Downloading morphology data

Morphology data for a single neuron (in .swc format) can be obtained by passing in the neuron_name:

neuromorph.get_neuron_swc(neuron_name)

In order to get morphological reconstructions for every neuron in the query, use get_neuron_swc:

neuromorph.download_query_swc()

Note: this takes a long time for large groups of neurons. The above query takes ~7 hours to complete.

Once completed you can access a dictionary of {neuron_name: swc_data}:

neuromorph.swc_data

Exporting data

The metadata from your query can be exported to a .csv file by providing an export path and a file name:

neuromorph.export_metadata(export_path, query_filename)

After downloading swc data you can export that as a .pkl file the same way:

neuromorph.export_swc_data(export_path, swc_filename)