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MathOnco / valis

Virtual Alignment of pathoLogy Image Series
https://valis.readthedocs.io/en/latest/
MIT License
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Intermittent artifacts introduced in micro-registration step #30

Closed NichD closed 1 year ago

NichD commented 1 year ago

Greetings - I've been exploring VALIS for a month now and I've found it to be a very robust registration tool overall. Thank you and kudos for all the hard work!

I have encountered one issue that is intermittent. Most data I processed did not encounter this, but on a few datasets, there seems to be some artifacts introduced in the micro-registration step. I've included samples of the PNGs generated by VALIS for reference. Between the non-rigid and micro steps, some block artifacts are generated. I've confirmed these artifacts ARE present in the final transformed images (assuming they were generated).

After looking at the images, I'm guessing that data read/write using different pyramid / resolution levels is not properly updating regions that are outside of the tissue mask at the lower resolution level. I'm not sure if that's helpful, but I confess I didn't explore too deeply. I'll probably just omit the final micro-registration step and that should resolve the problem for my use case.

If I can test a solution for this, please let me know. Thanks again for your efforts!! rigid_registration non-rigid_registration micro_registration

cdgatenbee commented 1 year ago

Hi @NichD, apologies for the delayed response. This is indeed strange, I'll have to look into it. Would you happen to have any images you could share so that I could re-create the issue?

Best, -Chandler

NichD commented 1 year ago

Hi @cdgatenbee - I do have some data I can share for with you, as well as the parameters I used to generate the registered images. What is the best method to share that info with you? Email?

cdgatenbee commented 1 year ago

Hi @NichD, that would be great if you can share the images and parameters. E-mail would work if the images are small enough, but if not maybe something like WeTransfer or Google Drive or Dropbox? Either way, my e-mail is Chandler.Gatenbee@moffitt.org

NichD commented 1 year ago

@cdgatenbee thank you for the update. These images are quite large, so I'll confirm how best to share and shoot you an email and comment here once I've set that up. Cheers!

cdgatenbee commented 1 year ago

Hi @NichD, Unfortunately, I wasn't able to reproduce this error with the images you provided, but mostly because I ran into issues reading czi images with jpgxr compression (I think it's a mac M1 issue, and so that's why I added the CziJpgxrReader reader). Anyhow, I did recently run into something similar. I believe it was fixed in the last update, so I'm going to go ahead and close this issue, but please don't hesitate to re-open it if you run into it again.

Best, -Chandler

NichD commented 1 year ago

Hi @cdgatenbee - Thanks for the update. I hadn't encountered this issue further since skipping the micro-reg step. Thanks for your help and efforts!

Cheers,

Nich