kfb2zarr

Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr.

Installation

via cargo:

cargo install kfb2zarr

via conda:

conda install bioconda::kfb2zarr

Usage

kfb2zarr slide.kfb slide.ome.zarr

To replace an existing output store:

kfb2zarr slide.kfb slide.ome.zarr --overwrite

To limit CPU usage (default uses all cores):

kfb2zarr slide.kfb slide.ome.zarr --threads 4

Viewing the output

The output .ome.zarr can be viewed locally with:

• QuPath ≥ 0.7.0 via drag & drop
• napari via the napari-ome-zarr plugin

Acknowledgements

Sample data used during development was kindly provided by KFBio. kfb2zarr is not an official product of KFBio.

kfb2zarr writes Zarr stores with:

Deakin, L. (2025). zarrs: A High-Performance Rust Library for the Zarr Array Storage Format (Version 0.22.10) [Computer software]. https://github.com/zarrs/zarrs