Swapped channels when converting from VSI

I’m using bfconvert 6.2.1 to convert vsi files to tiff and the resulting files have the red and blue channels swapped, compared to the original. It’s similar to Converting Vsi to Tiff causes undesired color changes but as I’m using the compiled version of bfconvert, I don’t have control on what channel get assigned to what color in the output.

1 Like

Hi @nmatasci, would you be able to upload a sample file to https://www.openmicroscopy.org/qa2/qa/upload/ for testing?

Thanks David. I’ve just uploaded an example. I had to create a zip archive to preserve the folder structure. Note that I’ve tried to crop a smaller area from a larger slide using Olympus VS-DESKTOP software which resulted in a self-contained VSI file. The self-contained VSI did not result in swapped RB channels.

Thanks for uploading the sample file. My apologies for the delay in getting it tested, I was able to reproduce what you were seeing with bfconvert this afternoon. I will try and get a workaround solution for you by tomorrow if possible.

What software are you using to read in the converted TIFF’s after conversion?