napari-wsi 1.0.0

A plugin to read whole-slide images within napari.

napari-wsi

A plugin to read whole-slide images within napari.

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Installation

You can install napari-wsi via pip:

pip install napari-wsi[all]

This automatically installs all optional backends, as a shortcut for:

pip install napari-wsi[openslide,rasterio,wsidicom]

In addition, to be able to read images using the openslide backend, it is required to install the OpenSlide library itself, for example by installing the openslide-bin python package (also via pip).

Description

This napari plugin provides a widget for reading various whole-slide image formats using a common zarr store inteface, based on the libraries openslide, rasterio, and wsidicom.

Quickstart

After installation, open the Plugins menu in the viewer and select WSI Reader to open the widget. Then select a Backend to use, select a Path to open, and click Load.

If sRGB is selected in the Color Space menu and an ICC profile is attached to the given image, a transformation to this color space will be applied when the image data is read. Otherwise, the raw RGB image data will be displayed.

This plugin can also be used to open image files via drag and drop into the viewer window. The file suffixes '.bif', '.ndpi', '.scn', '.svs' are registered with the openslide backend, while the suffixes '.tif' and '.tiff' are registered with the rasterio backend. These files can also be opened directly from the command line or from a python script:

napari CMU-1.svs

from napari.viewer import Viewer

viewer = Viewer()
viewer.open("CMU-1.svs", plugin="napari-wsi")