Metadata-Version: 2.1
Name: navis
Version: 1.6.0
Summary: Neuron Analysis and Visualization library
Home-page: http://navis.readthedocs.io
Author: Philipp Schlegel
Author-email: pms70@cam.ac.uk
License: GNU GPL V3
Project-URL: Documentation, http://navis.readthedocs.io
Project-URL: Source, https://github.com/navis-org/navis
Project-URL: Changelog, https://navis.readthedocs.io/en/latest/source/whats_new.html
Keywords: Neuron Analysis Visualization Morphometrics Morphology Anatomy Connectivity Transform Neuroscience NBLAST Skeletons SWC neuPrint
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
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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) [![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/logo_new.png" height="150">

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**: work and convert between neuron skeletons, meshes, dotprops and images
* **visualize**: 2D (matplotlib) and 3D (vispy, plotly or k3d)
* **process**: skeletonization, meshing, smoothing, repair, downsampling, etc.
* **morphometrics**: Strahler analysis, cable length, volume, tortuosity and more
* **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
* **model** neurons and networks using the *NEURON* simulator
* **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 [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:

```sh
pip3 install 'navis[all]'
```

which includes all optional extras providing features and/or performance improvements.
Currently, this is
`igraph`,
`pathos`,
`shapely`,
`kdtree`,
`hash`,
`flybrains`,
`cloudvolume`,
`meshes`,
and `vispy-default`.

3D plotting from a python REPL is provided by `vispy`, which has a choice of backends.
Different backends work best on different combinations of hardware, OS, python distribution, and REPL, so there may be some trial and error involved.
`vispy`'s backends are [listed here](https://vispy.org/installation.html#backend-requirements), and each can be installed as a navis extra, e.g. `pip3 install 'navis[vispy-pyqt6]'`.

![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
[here](https://navis.readthedocs.io/en/latest/source/whats_new.html).

## NAVis & friends
<p align="center">
<img src="https://github.com/navis-org/navis/blob/master/docs/_static/navis_ecosystem.png?raw=true" width="700">
</p>

NAVis comes with batteries included but is also highly extensible. Some
libraries built on top of NAVis:
* [flybrains](https://github.com/navis-org/navis-flybrains) provides templates and transforms for *Drosophila* brains to use with navis
* [pymaid](https://pymaid.readthedocs.io/en/latest/) pulls and pushes data from/to CATMAID servers
* [fafbseg](https://fafbseg-py.readthedocs.io/en/latest/index.html) contains tools to work with auto-segmented data for the FAFB EM dataset including FlyWire

## Who uses NAVis?
NAVis has been used in a range of neurobiological publications. See [here](publications.md) for a list.

We have implemented various published algorithms and methods:

1. NBLAST: Comparison of neurons based on morphology [(Costa et al., 2016)](https://www.cell.com/neuron/fulltext/S0896-6273(16)30265-3?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627316302653%3Fshowall%3Dtrue)
2. Vertex Similarity: Comparison of neurons based on connectivity [(Jarrell et al., 2012)](http://science.sciencemag.org/content/337/6093/437.long)
3. Comparison of neurons based on synapse distribution
[(Schlegel et al., 2016)](https://elifesciences.org/content/5/e16799)
4. Synapse flow centrality for axon-dendrite splits [(Schneider-Mizell et al., 2016)](https://elifesciences.org/articles/12059)

Working on your own cool new method? Consider adding it to NAVis!

## Citing NAVis
We'd love to know if you found NAVis useful for your research! You can help us
spread the word by citing the DOI provided by Zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8191725.svg)](https://zenodo.org/doi/10.5281/zenodo.4699382)

## License
This code is under [GNU GPL V3](LICENSE).

## Acknowledgments
NAVis is inspired by and inherits much of its design from the excellent
[natverse](http://natverse.org) R packages by
[Greg Jefferis](https://github.com/jefferis), [Alex Bates](https://github.com/alexanderbates),
[James Manton](https://github.com/ajdm) and others.

## 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.

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`
4. Install the package in editable mode with `pip install -e ".[all]"`
5. Create, `git add`, `git commit`, `git push`, and pull request your changes.

Run the tests locally with `pytest -v`.

Docstrings should use the [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html) format,
and make sure you include any relevant links and citations.
Unit tests should be [doctests](https://docs.python.org/3/library/doctest.html)
and/or use [pytest](https://docs.pytest.org/en/stable/) in the `./tests` directory.

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.
