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

    Release date:

    • 13 July 2022

    First released:

    • 12 July 2022

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 2
    • Forks: 2
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

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

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