(SEA-AD) For the same donor, is it possible to map the small DAPI section to its IHC counterpart?

How To
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Hi there,

I am Jiqing, a post-doc researcher at the Department of Biomedical Engineering, University of Basel. Currently, we are working on a GenAI project that requires exactly paired spatial transcriptomic (ST) and bioimage data (e.g., DAPI, H&E, IHC, etc.).

I recently found this amazing SEA-AD cohort containing IHC-stained slides for pathology analysis and ST-associated DAPI/PolyT-stained slides. Based on the Extended Data Fig. 1 (a) of the nature paper, I am aware that these two types of slides come from consecutive tissue slabs at roughly the same localization. So I was wondering if it is possible to map (register) the DAPI/PolyT-stained small region to the corresponding IHC-stained slides from the same donor. If this is not possible, do the DAPI/PolyT slides have matched IHC slides at the very same location?

As mentioned above, the motivation behind my question is we would like to have exactly paired spatial molecular and bioimage data to train our GenAI model. In the current setting, it seems that we can only pair MERFISH data with DAPI/PolyT slides, while more informative IHC-stained slides are missing.

Thank you very much in advance!

Kind regards,
Jiqing

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This was addressed by e-mail, but for the benefit of other folks, Mariano Gabitto replied: “My understanding is that tissue for neuropathology and for spatial transcriptomics are collected from nearby slabs, not nearby section. For this reason, there is a considerable distance between them (0.5 cm), alignment would not make much sense here. I hope that this helps.”

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Thank you for following up on the question!