morphapi 0.0.5

A lightweight python package to download neuronal morphologies

morphapi

Please not that this package is currently under development. Expect frequent changes and some bugs.

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

To install the latest stable build simply use:

  pip install morphapi

To upgrade:

  pip install -U morphapi

If you want to get the latest code from the github you can use:

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

Usage

To see how to use morphapi to download neuronal morphological data, head over to the examples here.

To see how to visualise neurons in 3d, have a look here. Keep in mind though that brainrender is the reccomended way to visualise neural morphologies.

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