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schlegelp committed Oct 27, 2023
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[![Documentation Status](https://readthedocs.org/projects/navis/badge/?version=latest)](http://navis.readthedocs.io/en/latest/?badge=latest) [![Tests](https://github.com/navis-org/navis/actions/workflows/test-package.yml/badge.svg)](https://github.com/navis-org/navis/actions/workflows/test-package.yml) [![Run notebooks](https://github.com/navis-org/navis/actions/workflows/notebooktest-package.yml/badge.svg)](https://github.com/navis-org/navis/actions/workflows/notebooktest-package.yml) [![Coverage Status](https://coveralls.io/repos/github/navis-org/navis/badge.svg?branch=master)](https://coveralls.io/github/navis-org/navis?branch=master) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/navis-org/navis/blob/master/examples/colab.ipynb) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8191725.svg)](https://zenodo.org/doi/10.5281/zenodo.4699382) [![Downloads](https://pepy.tech/badge/navis)](https://pepy.tech/project/navis)
[![Documentation Status](https://readthedocs.org/projects/navis/badge/?version=latest)](http://navis.readthedocs.io/en/latest/?badge=latest) [![Tests](https://github.com/navis-org/navis/actions/workflows/test-package.yml/badge.svg)](https://github.com/navis-org/navis/actions/workflows/test-package.yml) [![Run notebooks](https://github.com/navis-org/navis/actions/workflows/notebooktest-package.yml/badge.svg)](https://github.com/navis-org/navis/actions/workflows/notebooktest-package.yml) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/navis-org/navis/blob/master/examples/colab.ipynb) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8191725.svg)](https://zenodo.org/doi/10.5281/zenodo.4699382) [![Downloads](https://pepy.tech/badge/navis)](https://pepy.tech/project/navis)

<img src="https://github.com/navis-org/navis/raw/master/docs/_static/favicon.png" height="60">
<img src="https://github.com/navis-org/navis/raw/master/docs/_static/logo_new.png" height="120">

NAVis is a Python 3 library for **N**euron **A**nalysis and **Vis**ualization.

## Documentation
NAVis is on [ReadTheDocs](http://navis.readthedocs.io/ "NAVis ReadTheDocs").

## Features
* **polyglot**: ``navis`` works with skeletons,meshes dotprops and image data
* **polyglot**: ``navis`` works with skeletons, meshes, dotprops and image data
* **visualize**: 2D (matplotlib) and 3D (vispy, plotly or k3d)
* **process**: skeletonization, smoothing, repair, downsampling, etc.
* **surgery**: e.g. cutting, stitching, pruning, rerooting or intersections
* **process**: skeletonization, meshing, smoothing, repairing, downsampling, etc.
* **edit**: e.g. cutting, stitching, pruning, rerooting or intersecting
* **morphometrics**: Strahler analysis, cable length, volume, tortuosity and more
* **similarity**: compare & cluster by morphology (e.g. NBLAST, persistence, form factor) or connectivity metrics
* **similarity**: compare & cluster by morphology (e.g. NBLAST, persistence or form factor) or connectivity metrics
* **transform**: move data between template brains (built-in support for HDF5, CMTK, Elastix and landmark-based transforms)
* **interface**: load neurons directly from [neuPrint](https://neuprint.janelia.org), [neuromorpho.org](http://neuromorpho.org) and other data sources
* **simulate** neurons and networks using the *NEURON* simulator
* **render**: use **Blender 3D** for high quality [visualizations](https://youtu.be/wl3sFG7WQJc)
* **render**: use Blender 3D for high quality [visualizations](https://youtu.be/wl3sFG7WQJc)
* **R** neuron libraries: interfaces with [nat](https://github.com/jefferis/nat), [rcatmaid](https://github.com/jefferis/rcatmaid), [elmr](https://github.com/jefferis/elmr) and more
* **import-export**: read/write SWCs, neuroglancer's ["*precomputed*"](https://github.com/google/neuroglancer/tree/master/src/neuroglancer/datasource/precomputed) format, NMX/NML, NRRD, mesh-files and more
* **scalable**: out-of-the-box support for multiprocessing
* **extensible**: build your own package on top of navis - see for example [pymaid](https://pymaid.readthedocs.io/en/latest/)
* **extensible**: build your own package on top of navis - see [pymaid](https://pymaid.readthedocs.io/en/latest/) for example

## Getting started
See the [documentation](http://navis.readthedocs.io/ "NAVis ReadTheDocs") for detailed installation instructions, tutorials and examples. For the impatient:
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![movie](https://user-images.githubusercontent.com/7161148/114312307-28a72700-9aea-11eb-89a6-ee1d72bfa730.mov)

## Questions?
Questions on how to use `navis` are best placed in [discussions](https://github.com/navis-org/navis/discussions). Same goes for cool projects or analyses you made using `navis` -
we'd love to hear from you!

## Changelog

A summary of changes can be found
Expand Down Expand Up @@ -115,6 +119,19 @@ Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li, Feng L, Zwart M …

## Contributing

Want to contribute? Great, here is how!

### Report bugs or request features
Open an [issue](https://github.com/navis-org/navis/issues). For bug reports
please make sure to include some code/data with a minimum example for us to
reproduce the bug.

### Contribute code
We're always happy for people to contribute code - be it a small bug fix, a
new feature or improved documentation/tutorials.

Here's how you'd do it in a nutshell:

1. Fork this repository
2. `git clone` it to your local machine
3. Install the full development dependencies with `pip install -r requirements.txt`
Expand All @@ -130,3 +147,6 @@ and/or use [pytest](https://docs.pytest.org/en/stable/) in the `./tests` directo

Doctests have access to the `tmp_dir: pathlib.Path` variable,
which should be used if any files need to be written.

Feel free to get in touch either through an [issue](https://github.com/navis-org/navis/issues) or [discussion](https://github.com/navis-org/navis/discussions) if you need
pointers or input on how to implement an idea.

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