module QuPath

[heylf]

Description of feature

Description

https://qupath.github.io/ https://www.10xgenomics.com/support/software/xenium-explorer/latest/tutorials/xe-image-file-conversion

Can we implement this?

[jwrth]

Hi @heylf, what exactly was your idea to implement here? A general conversion of image files from different formats to Xenium Explorer compatible formats? I already implemented the function that is shown on the 10x website in my analysis workflow and use it regularly.

[heylf]

Yes exactly

[jwrth]

Yes I think that might be useful and relatively easy to achieve with a combination of aicsimageio and slideio.

However, it might be even more interesting to implement something that also registers such post-Xenium stained images to the Xenium data. I already have a opencv-based workflow set up to automatically register images to xenium data. I think it might be very useful to the community to implement this as a nf-core module.

My workflow currently is structured like that:

1. Selection and naming of individual regions on post-Xenium stained image in QuPath:
2. Export of the regions using a script in QuPath
3. Registration of images to xenium data

By using a fixed naming scheme in the export, I think we could implement this in a quite generalized way which would work then also if there are multiple post-Xenium stainings of the same Xenium slide (e.g. HE, IHC and IF). And I think this would be very useful because the manual alignment in Xenium explorer can be very painful... What do you think?

[heylf]

That would be awesome. We could make then two distinct tracks in the pipeline. One for preprocessing and one for re-processing of the data.

[jwrth]

Preprocessing would be then the integration of images and the qc pipeline? And re-processing things like cell segmentation?