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napari bio sample data

napari-bio-sample-data

a sample data plugin for bio-related demos

License PyPI Python Version napari hub

a sample data plugin for bio-related demos


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.
image

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

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

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

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

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.

Version:

  • 0.0.4

Last updated:

  • 13 July 2022

First released:

  • 12 July 2022

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 4
  • Forks: 3
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • numpy
  • fsspec
  • zarr (>=2.12.0)
  • dask
  • s3fs

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