napari-ome-zarr-navigator

A plugin to browse OME-Zarr plates by conditions and load images, labels and features from ROIs

Usage

The ImageBrowser recognizes OME-Zarr plates that were loaded via napari-ome-zarr and allows the selection of wells in the multiwell plate.

The ImageBrowser allows to zoom to a given well ("Go to well") & puts a white bounding box around the selected well.

Using prototype condition tables (to be defined better, see sample data provided by the plugin orthe example in the test data below), the ImageBrowser allows for selecting subsets of the well list based on conditions defined in the condition table. The operetta-compose Fractal task package provides a task to create such condition tables.

The ROI loader (formerly available separately as a napari plugin) can be used standalone or integrated with the ImageBrowser. If a well is selected from the ImageBrowser, all the images in that well can be loaded via the ROI loader. This supports:

• Loading images from different multiplexing acquisitions
• Loading any ROI based on Fractal ROI tables
• Loading label images
• Loading feature measurements (based on Fractal feature tables in the AnnData format)

This approach of loading label images and feature data has been optimized for and tested with the napari feature classifier.

This plugin is meant to work well for OME-Zarr files generated by Fractal.

Test data

Test data is available at https://zenodo.org/records/11262587

Installation

You can install napari-ome-zarr-navigator via pip:

pip install napari-ome-zarr-navigator

To install latest development version :

pip install git+https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator.git

Contributing

Contributions are very welcome. 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-ome-zarr-navigator" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.