aligning two H&E files - Githubissues

MathOnco / valis

Virtual Alignment of pathoLogy Image Series

https://valis.readthedocs.io/en/latest/

MIT License

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aligning two H&E files #48

Closed GlastonburyC closed 1 year ago

GlastonburyC commented 1 year ago

I have two H&E brightfield ome-tiffs one that's faded and one thats restained that I would like to register.

However, the results come out "pink" see attached. Is there any solution to this, as it renders the outputted registered tiff unusable.

cdgatenbee commented 1 year ago

Hi @GlastonburyC, I noticed the issue was closed pretty quickly. Were you able to resolve the issue? If so, what was the solution? If not, do you think it is similar to issue 26?

Best, -Chandler

GlastonburyC commented 1 year ago

Hey Chandler.

The issue was two-fold. Exporting the ome-tiff from QuPath added this red colour to my exported WSI, so of course, anything downstream with Valis also suffered from it.

And two, the compression method jpg2k used by Valis also adds a pink hue to the registered slides outputted. I circumvented that by defaulting to a different compression method.

Thanks for your quick response and interest, Craig