morphapi

morphapi is a lightweight python package for downloading neuronal morphological reconstructions from publicly available datasets. It provides a number of APIs that facilitate the download of selected neurons and functionality to create 3d meshes with the neuronal reconstruction for visualization with packages like brainrender.

morphapi relies on the neurom package from the BlueBrain project (github) to reconstruct morphology from .swc files and on vedo to create 3d rendering from morphological data.

Currently supported datasets

• Allen brain atlas - Cell Types

• neuromorpho.org

• Janelia Campus - Mouse Light project

• Kunst et al 2019 - Zebrafish neurons

Installation

To install morphapi in a python environment with python >= 3.6 simply:

pip install morphapi

Usage

• Downloading data
• Rendering data