WSI Reader

napari-wsi

A plugin to read whole slide images within napari.

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

From the terminal:

napari CMU-1.svs

From python:

import napari

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

Version:

  • 0.1.1

Last updated:

  • 06 March 2023

First released:

  • 01 February 2023

License:

  • Apache-2.0

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 7
  • Forks: 1
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • dask (>=2022)
  • imagecodecs (>=2022)
  • magicgui (<1.0.0)
  • matplotlib (>=3.0.0,<4.0.0)
  • napari (>=0.4.0,<0.5.0)
  • numpy (>=1.0.0,<2.0.0)
  • pydantic (!=1.10.0)
  • rasterio (>=1.0.0,<2.0.0)
  • tifffile (>=2022)
  • zarr (>=2.0.0,<3.0.0)

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