popidd-io

A simple plugin to read digital pathology images and annotations. Made by Ferran Cardoso at the Integrated Pathology Unit (ICR/RMH).

This is still an experimental and in-development project, so expect considerable additions and changes to existing methods. Documentation and tests will be added in the coming weeks.

This napari plugin was generated with copier using the napari-plugin-template.

Installation

Setup conda environment

mamba create -n popidd_io python=3.12 pip pyqt

Activate conda environment

mamba activate popidd_io

End users

You can install popidd-io via pip:

pip install popidd-io

Development

Install test version from project base directory

pip install -e ".[testing]"

Run dev environment with

python developing.py

Before contributing, please install and use pre-commit hooks:

pip install pre-commit
pre-commit install

Also test the project using pytest from the project's root directory:

pytest

Description

This plugin brings support for brightfield and fluorescence images to Napari, as well as adding support for polygonal annotations in geoJSON files saved by QuPath.

Brightfield images are loaded as a single layer, incorporating also resolution information if found on the metadata. Fluorescence images are separated into channels annotated using the information present in the image metadata. Support for this latter modality is still ongoing and will improve in the coming weeks.

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

Made by Ferran Cardoso Rodriguez with the help of colleagues at the Integrated Pathology Unit.

Distributed under the terms of the GNU GPL v3.0 license, "popidd-io" is free and open source software

Issues

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