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


  • 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 file and submitting a pull request.
  • To inquire about this plugin please contact Brain Image Library support:
  • 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.


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


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.


Distributed under the terms of the BSD-3 license, "napari-bil-data-viewer" is free and open source software


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

Change Log:


Initial release.

v0.1.1 & v0.1.2:

Changes to documentation


Added all available summary fMOST datasets


Added support for SWC neuron tracings


Added support for multiscale OME zarr data


Add scale controls for layers


Add URL input to visualize image stacks (tif, tiff, jp2)


Split the plugin into 5 widgets:

  • Load Curated Datasets
  • Load Image Stack From URL
  • Load Multiscale Data From URL
  • Load Neuron Morphology From URL
  • Layer Scale Controls


Add metadata link to curated datasets


Add widget to visualize histology RGB tiffs


  • 0.6.0

Last updated:

  • 28 February 2024

First released:

  • 24 January 2022


Supported data:

  • Information not submitted

Plugin type:

Open extension:

GitHub activity:

  • Stars: 6
  • Forks: 1
  • Issues + PRs: 0

Python versions supported:

Operating system:


  • napari[all]
  • napari-plugin-engine >=0.1.4
  • scikit-image
  • fsspec
  • requests
  • aiohttp
  • imagecodecs
  • beautifulsoup4
  • dask
  • neurom ==3.2.2
  • napari-ome-zarr ==0.5.2

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