neuromorphopy 0.3.2

Lightweight standalone python CLI tool for downloading neuron morphologies from the NeuroMorpho archives.

neuromorphopy

neuromorphopy is a lightweight standalone python CLI tool for downloading neuron morphologies from the NeuroMorpho archives.

Features

• Simple and intuitive API for searching NeuroMorpho.org
• Efficient concurrent downloads of neuron morphologies
• Flexible query system with validation
• Automatic metadata handling
• Support for both synchronous and asynchronous operations

Installation

neuromorphopy is supported for python >= 3.11.

Using uv (Recommended):

The easiest way to install neuromorphopy as a standalone CLI tool is with uv:

# install the latest release
uv tool install neuromorphopy
# or install the latest development version from GitHub
uv tool install git+https://github.com/kpeez/neuromorphopy.git

Using pip:

Alternatively, you can install neuromorphopy into your project environment using pip:

# install the latest release
pip install neuromorphopy
# or install the latest development version directly from GitHub
pip install git+https://github.com/kpeez/neuromorphopy.git

Usage

Create a query file (YAML or JSON) to specify what neurons you want:

# query.yaml
filters:
  species: ["mouse"]
  brain_region: ["neocortex"]
  cell_type: ["pyramidal"]
sort: # sorting is optional
  field: "brain_region"
  ascending: true

To download all neurons, you can use an empty query:

# query.yaml
filters: {}

Use the command line interface to explore available fields, preview a query, or download neurons:

# Explore available query fields and values
neuromorpho fields
neuromorpho fields species

# Preview what a query would download
neuromorpho preview -q query.yaml

# Download neurons matching the query
neuromorpho download -q query.yaml -o ./data

For more detailed usage, see our documentation.