Metadata-Version: 2.1
Name: napari-wsi
Version: 0.1.4
Summary: A plugin to read whole slide images within napari.
Home-page: https://github.com/AstraZeneca/napari-wsi
License: Apache-2.0
Author: Philipp Plewa
Author-email: philipp.plewa@astrazeneca.com
Maintainer: Philipp Plewa
Maintainer-email: philipp.plewa@astrazeneca.com
Requires-Python: >=3.10,<3.12
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Dist: dask[array] (>=2023)
Requires-Dist: imagecodecs (>=2023.9.18)
Requires-Dist: magicgui (>=0.7.3)
Requires-Dist: matplotlib (>=3.8)
Requires-Dist: napari (>=0.4.18)
Requires-Dist: numpy (>=1.26)
Requires-Dist: rasterio (>=1.3)
Requires-Dist: tifffile (>=2023)
Requires-Dist: zarr (>=2.16)
Project-URL: Repository, https://github.com/AstraZeneca/napari-wsi
Description-Content-Type: text/markdown

# napari-wsi

[![PyPI](https://img.shields.io/pypi/v/napari-wsi.svg?color=green)](https://pypi.org/project/napari-wsi)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-wsi)](https://napari-hub.org/plugins/napari-wsi)
[![Tests](https://github.com/AstraZeneca/napari-wsi/actions/workflows/main.yml/badge.svg)](https://github.com/AstraZeneca/napari-wsi/actions)
![Maturity Level-1](https://img.shields.io/badge/Maturity%20Level-ML--1-yellow)

A plugin to read whole slide images within [napari].

---

## Installation

You can install `napari-wsi` via [pip]:

```bash
pip install napari-wsi
```

To install the latest development version, run:
```bash
pip install git+https://github.com/AstraZeneca/napari-wsi.git
```

# Description

This [napari] plugin provides a reader for various whole slide image formats.

By default, any of the following formats is read using the [tifffile] library.
If the image file contains a tag `GDAL_METADATA`, the [rasterio] library is used
instead.

- .bif
- .ndpi
- .qptiff
- .scn
- .svs
- .tif
- .tiff

# Quickstart

From the terminal:

```bash
napari CMU-1.svs
```

From python:

```python
import napari

viewer = napari.Viewer()
viewer.open("CMU-1.svs")
```

[napari]: https://github.com/napari/napari
[pip]: https://pypi.org/project/pip/
[rasterio]: https://github.com/rasterio/rasterio
[tifffile]: https://github.com/cgohlke/tifffile

