napari bio sample data

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 is down-sampled to have smaller file size.

(2) 2D skin RGB dataset (image + shape)
Image credit: skimage.data.skin

(3) 3D nuclei dataset (image + label + surface)
Image credit: skimage.data.cells3d

(4) 2D timelapse dataset (image + points + tracks)
Image credit: Cell Tracking Challenge
The original data is cropped to have smaller file size.

(5) large multi-resolution 3D EM dataset
Image credit: Janelia Open Organelle
This plugin only accesses 2 lower resolution levels.

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.

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.