Once your 3D sample is reconstructed, you can rotate, take virtual sections in any orientation, project gene expression through depth, link 3D space with UMAP, and compute spatial differential expression on the reconstructed volume to find region-enriched genes.

To turn spatial data into a 3D object, check our protocol (open source, napari plug-in). @guignardlab.bsky.social @adrianobolondi.bsky.social @ibdm.bsky.social
For example, if you have spatial RNA-seq as sections, you can align them automatically to analyse directly in 3D.
bio-protocol.org/e5607

Once your 3D sample is reconstructed, you can rotate, take virtual sections in any orientation, project gene expression through depth, link 3D space with UMAP, and compute spatial differential expression on the reconstructed volume to find region-enriched genes.

Here we study the origin of the cardiac cell lineages in the mouse embryo. Separate but coordinated lineages independently specified at gastrulation generate the myocardium and endocardium. Credits: Miquel Sendra & coll: Jorge Dominguez, K. McDole and L. Guinard
authors.elsevier.com/sd/article/S...