napari-bio-sample-data 0.0.4
a sample data plugin for bio-related demos
License: BSD-3-Clause
Requires Python: >=3.8

# napari-bio-sample-data

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a sample data plugin for bio-related demos

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This plugin contains 5 sample datasets with additional napari layer types:

(1) 3D EM dataset (image + points + vectors)  
Image credit: Alister Burt  
The [original data](https://github.com/alisterburt/napari-cryo-et-demo) is down-sampled to have smaller file size.  
<img width="300" alt="image" src="https://user-images.githubusercontent.com/89602983/178569428-7daa2eb8-a3ff-4c0e-8e5f-4f615a55684f.png">

(2) 2D skin RGB dataset (image + shape)  
Image credit: skimage.data.skin  
<img width="300" alt="image" src="https://user-images.githubusercontent.com/89602983/178569580-bf77e55c-71cc-4883-9fe5-ed94e05f2a29.png">
  
(3) 3D nuclei dataset (image + label + surface)  
Image credit: skimage.data.cells3d  
<img width="300" alt="image" src="https://user-images.githubusercontent.com/89602983/178569701-7c9b1cc3-c1c3-4e54-8ca0-fb2b530f858e.png">

(4) 2D timelapse dataset (image + points + tracks)  
Image credit: [Cell Tracking Challenge](http://celltrackingchallenge.net/2d-datasets/)  
The original data is cropped to have smaller file size.  
<img width="300" alt="image" src="https://user-images.githubusercontent.com/89602983/178569846-b995d1cb-c1ec-4363-ba1a-71243ffea4e0.png">

(5) large multi-resolution 3D EM dataset  
Image credit: [Janelia Open Organelle](https://openorganelle.janelia.org/datasets/jrc_hela-1)   
This plugin only accesses 2 lower resolution levels.  
<img width="300" alt="image" src="https://user-images.githubusercontent.com/89602983/178570136-6f59ba3c-d687-446c-9f5e-1df567a62948.png">

Datasets (1)-(4) are stored locally.   
Dataset (5) is downloaded and temporarily stored on RAM when accessed.    

This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.

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## Installation

You can install `napari-bio-sample-data` via [pip]:

    pip install napari-bio-sample-data

To install latest development version :

    pip install git+https://github.com/chili-chiu/napari-bio-sample-data.git


## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

## License

Distributed under the terms of the [BSD-3] license,
"napari-bio-sample-data" is free and open source software

## Issues

If you encounter any problems, please [file an issue] along with a detailed description.

[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin

[file an issue]: https://github.com/chili-chiu/napari-bio-sample-data/issues

[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/