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NHPatterson / wsireg

multimodal whole slide image registration in a graph structure
MIT License
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Gigapixel WSI deformable registration #16

Closed omayrkhan closed 2 years ago

omayrkhan commented 3 years ago

Firstly, thank you for developing this library. It looks very promising. Secondly, apologies for posting this question in the issues section. I would like to ask if the library supports deformable registration of gigapixel WSI. I need to register H&E stained (RGB) WSI to the unstained equivalent WSI. The tool that I am using currently does an okay high-level rigid registration - but at the tile level, the registration is below par.

NHPatterson commented 3 years ago

Hi @omayrkhan, glad to see you found this library. Indeed, registering gigapixel WSIs is exactly the purpose of this library. Some of the challenges of this task are WSI image formats, memory management with large image planes, and writing pyramidal formats that can work for downstream analysis (wsireg outputs pyramidal OME-TIFF). wsireg takes care of these issues.

A first considerations about your actual data.. Are the images you wish to register from the same tissue section or an adjacent one? Usually if they are from the same tissue section, using linear transformation models can be successful and can be transformed efficiently. I would recommend using the bleeding edge version of wsireg for your task as I've recently implemented tile-by-tile image writing for RGB images that can transform such images with a really small memory footprint. I have yet to cut a release with these updates on pip but I will soon.

I'm happy to correspond here to help you get starting, and if you'd like, I'm happy to test out the software with your data (confidentially, of course) to help get over any potential snags!

Heath

omayrkhan commented 3 years ago

Thanks for the prompt and detailed response. The images are from the same tissue sections, first scanned unstained and then with H&E. Based on your answer, I'll first try to tweak the parameters of the tool that I am currently using, and then I'll also try wsireg to at least compare the quality. I hope in the meanwhile you'll be able to push a new release with the aforementioned new features.

omayrkhan commented 2 years ago

Hi @NHPatterson - I am returning to this conversation after a long time. Just wanted to let you know that I used the tool for unstained-stained tissue WSI registration and worked like a charm. So, once again thank you for your efforts to build such a useful tool.

Secondly, how do I cite this WSI registration tool in my publication?

Regards, Umair