napari-bil-data-viewer 0.1.1

Napari plugin for viewing Brain Image Library datasets

Description

This plugin enables viewing of datasets archived in the Brain Image Library.

https://www.brainimagelibrary.org/

**NOTE: This plugin is under early development. Currently, only a subset of single color, fMOST datasets which include projections are available to view. An example can be found here: https://download.brainimagelibrary.org/2b/da/2bdaf9e66a246844/mouseID_405429-182725/

Features

• Multiscale Rendering
  • Datasets which include multiple resolution representations of the data can be used for https://download.brainimagelibrary.org/2b/da/2bdaf9e66a246844/mouseID_405429-182725/
• 3D rendering of whole datasets. The lowest resolution will be used for rendering.
• 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: https://github.com/brain-image-library/napari-bil-data-viewer/blob/main/napari_bil_data_viewer/dataset_info.py
• The plugin is still under development. We appreciate all reports of errors which occur during use. https://github.com/brain-image-library/napari-bil-data-viewer/issues

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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

Change Log:

v0.1.0:

Initial release.

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.