Export Ventana bif to OME-TIFF


Since bif are not well supported in openslide (and libvips) I was wondering how could I batch export Ventana bif files to OME-TIFF using command line and using Bio-formats support. I found TileExported from QuPath (awesome resource!) but, since I have 1K images, I was wondering if there is something a little bit faster.

If this could be a plus, I have acces to GPUs but I am not aware of any tool that could use them.


QuPath’s export to OME-TIFF is as fast as I could succeed in making it (optionally parallelizing the tile requests), but ultimately relies on Bio-Formats’ TIFF-writing at the end. I have seen some cases with very large images where it was too slow for me to realistically use and I wasn’t able to figure out a way to overcome that.

There’s a thread here on Bio-Formats’ TIFF-writing performance: Bioformats saving with compression is too slow – you might find Glencoe’s pipeline a bit faster.


Supplementing Pete’s answer, the aforementioned pipeline is described in this post and is certainly worth a try

Ultimately, this tool also consumes the low-level Bio-Formats TIFF saving API but unlike the Bio-Formats command line tools, the input data is structured in a way which allow to make assumptions on how to write the data on disk.