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

v0.1.3:

Added all available summary fMOST datasets

v0.2.0:

Added support for SWC neuron tracings

v0.3.0:

Added support for multiscale OME zarr data

v0.4.0:

Add scale controls for layers

v0.4.2:

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

v0.5.0:

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

v0.5.1:

Add metadata link to curated datasets

v0.6.0:

Add widget to visualize histology RGB tiffs

Version:

  • 0.6.0

Last updated:

  • 28 February 2024

First released:

  • 24 January 2022

License:

Supported data:

  • Information not submitted

Plugin type:

Open extension:

GitHub activity:

  • Stars: 6
  • 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
  • neurom ==3.2.2
  • napari-ome-zarr ==0.5.2

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