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Since October 1, 2024, this version is no longer actively maintained and will not be updated. New plugins and plugin updates will continue to be listed.

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