morphapi 0.0.1

A lightweight python package to download neuronal morphologies

morphapi

Overview

Morphapi is a lightweight python package for downloading neurons morphological reconstructions from publicly available datasets.

Neuromorph api can be used to download data from the following sources:

• Allen brain atlas - Cell Types
• neuromorpho.org
• Janelia Campus - Mouse Light project

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

Installation

morphapi will be published on Pypi soon, meanwhile you can install with:

    pip install git+https://github.com/brainglobe/morphapi.git

References

• Juan Palacios, lidakanari, Eleftherios Zisis, MikeG, Liesbeth Vanherpe, Jean-Denis Courcol, & Oren Amsalem. (2016, December 19). BlueBrain/NeuroM: v1.2.0 (Version v1.2.0). Zenodo. http://doi.org/10.5281/zenodo.209498
• M. Musy et al. "vtkplotter, a python module for scientific visualization and analysis of 3D objects and point clouds based on VTK (Visualization Toolkit)", Zenodo, 10 February 2019, doi: 10.5281/zenodo.2561402.
• Winnubst, J. et al. (2019) Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain, Cell 179: 268-281