Remove label and macro from a WSI

I have some WSI from Leica (svs), Roche (bif) and ome.tiff with label image information like the following:

I would like to remove this information from the slide. Is there any way to do this?

Not sure of any other answers than what is listed here.

Just out of curiosity, if you used QuPath to write out the image as an OME.TIFF file using the whole slide image builder, wouldn’t that remove the other two images? @petebankhead

This would be painfully slow compared to removing the label image but… should work I think.

Hi @Joan_Gibert_Fernande, if you wish to remove it you could convert only the the required series into a new file. You can do this using the Bio-Formats command line tools from: https://www.openmicroscopy.org/bio-formats/downloads/

Then you can run the below:
bfconvert -series 0 path/to/originalFile.ome-tiff path/to/newFile.ome-tiff

See https://docs.openmicroscopy.org/bio-formats/6.5.1/users/comlinetools/conversion.html for the full docs

If you want to use libvips, get the precompiled binaries from the github release page. It uses openslide to read whole slide image files, so make sure to get the version with openslide binaries ( vips-dev-w64-all-8.10.2.zip).

Using command line try:

vips copy input.svs output.ome.tif[pyramid,subifd]

I found libvips to be very fast at reading whole slide images and writing ome.tiff.

Read here for more details on libvips support for ome.tif:

I wrote a small GUI with .Net Framework for my personal use. It uses libvips, NetVips and openslide to batch convert svs files to tiff (or OME-TIFF). I am not sure if this will help you, give it a try. Here is a Dropbox Link: SVS2TIFF

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