napari-bil-data-viewer

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.

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.

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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

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