Whole Slide Imaging

Resources related to Whole Slide Imaging (WSI) and its use in the context of the NGFF. Many of the examples come from the digital pathology community, but OME-Zarr may be used for other whole slide imaging applications.

Example

Note: expanding this loads real OME-Zarr data hosted on object storage.

Load example

Links

• QuPath - Open source software for digital pathology image analysis, with support for OME-Zarr.

Lazyslide & WSIData

• wsidata: Efficient data structures and IO for whole slide image analysis(Storage backed by SpatialData, so OME-NGFF at the core.)

• LazySlide: Accessible and interoperable whole slide image analysis uses WSIData at its core.

Other tools

• fastslide C++20 library for reading whole slide images, including support for OME-Zarr.

• raw2features Utility for generating embeddings from whole slide images saved in OME-Zarr format.

• kfb2zarr Rust converter for KFBio whole slide images (.kfb, .kfbf) to OME-Zarr

See also

• Bringing Open Data to Whole Slide Imaging (Besson et al, 2019.)

• DICOM WSI

• WSI on Wikipedia