napari-bil-data-viewer

napari-bil-data-viewer

Napari plugin for viewing Brain Image Library datasets


    View datasets archived at the Brain Image Library.

    **NOTE: This plugin is under early development. Currently, only a subset of single-channel, fMOST datasets which include projections are available to view. An example can be found here.

    Plugin Demo GIF

    Features

    • Multiscale Rendering
      • In datasets that include multiple resolution representations of the data, each resolution can be combined to improve the speed of browsing and user experience. An example of a dataset with multiple resolution projections can be found here.
      • All datasets included in the current release of napari-bil-data-viewer use multi-resolution datasets.
    • 3D rendering of whole datasets. The lowest resolution is used for rendering. Currently, this is a limitation imposed by napari.
    • The plugin does NOT require a BIL account as datasets are already accessible via https.

    Known Issues / limitations

    • Currently the only datasets that are available are those which have been manually selected by the developers. If you would like a specific dataset to be included please consider adding the dataset(s) to the dataset_info.py file and submitting a pull request.
    • To inquire about this plugin please contact Brain Image Library support: bil-support@psc.edu
    • The plugin is still under development. We appreciate all reports of issues / errors which occur during use.

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

    Installation

    Option #1: Install plugin via the napari plugin menu

    1. Menu: Plugins >> Install/Uninstall Plugins
    2. Search: napari-bil-data-viewer
    3. Select install

    Option #2: Install a fresh python virtual environment

    # Example of venv creation using conda
    conda create -y -n bil-viewer python=3.8
    conda activate bil-viewer
    
    # Install napari-bil-data-viewer
    pip install napari-bil-data-viewer
    
    # Run Napari
    napari

    Contributing

    Please consider contributing to this project! 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-bil-data-viewer" is free and open source software

    Issues

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

    Change Log:

    v0.1.0:

    Initial release.

    v0.1.1 & v0.1.2:

    Changes to documentation

    Version:

    • 0.1.2

    Release date:

    • 25 January 2022

    First released:

    • 24 January 2022

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 3
    • Forks: 1
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • napari[all]
    • napari-plugin-engine (>=0.1.4)
    • scikit-image
    • fsspec
    • requests
    • aiohttp
    • imagecodecs
    • beautifulsoup4
    • dask

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