Napari plugin for viewing Brain Image Library datasets
Project description
Description
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.
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
- Menu: Plugins >> Install/Uninstall Plugins
- Search: napari-bil-data-viewer
- 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
Project details
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