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

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...