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.
- 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: firstname.lastname@example.org
- The plugin is still under development. We appreciate all reports of issues / errors which occur during use.
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
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.
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
- 18 October 2023
- 24 January 2022
- Stars: 6
- Forks: 1
- Issues + PRs: 0