From d77436c7ad650b8b7e611519964f32fcb439a4a3 Mon Sep 17 00:00:00 2001 From: Philipp Schlegel Date: Fri, 27 Oct 2023 11:17:12 +0100 Subject: [PATCH] update README --- README.md | 36 ++++++++++++++++++++++++++++-------- 1 file changed, 28 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index c68db8df..03cda4f9 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -[![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) - + NAVis is a Python 3 library for **N**euron **A**nalysis and **Vis**ualization. @@ -8,20 +8,20 @@ NAVis is a Python 3 library for **N**euron **A**nalysis and **Vis**ualization. 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: @@ -48,6 +48,10 @@ Different backends work best on different combinations of hardware, OS, python d ![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 @@ -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` @@ -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.