Metadata-Version: 2.1
Name: morphapi
Version: 0.1.1.1
Summary: A lightweight python package to download neuronal morphologies
Home-page: https://github.com/brainglobe/morphapi
Author: Federico Claudi
License: UNKNOWN
Description: # 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](https://celltypes.brain-map.org/)
          * [neuromorpho.org](http://neuromorpho.org/)
          * [Janelia Campus - Mouse Light project](https://www.janelia.org/project-team/mouselight)
        
        Neuromorph relies on the [`neurom`](https://zenodo.org/record/209498#.XraWUsZ7l24) package from
        the BlueBrain project ([github](https://github.com/BlueBrain/NeuroM)) to reconstruct morphology
        from `.swc` files and on [`vtkplotter`](https://github.com/marcomusy/vtkplotter) to create 3d
        rendering from morphological data.
        
        ![](media/exampleneuron.png)
        
        ## 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](examples/download).
        
        To see how to **visualise** neurons in 3d, have a look [here](examples/visualise).
        Keep in mind though that [brainrender](https://github.com/BrancoLab/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
Platform: UNKNOWN
Requires-Python: >=3.6, <3.8
Description-Content-Type: text/markdown
Provides-Extra: nb
Provides-Extra: dev
