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

License

Licensed under either of

• Apache License, Version 2.0 (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
• MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)

at your option.

Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.

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