Inquiry about 3D Model Z-axis Coordinate Calculation in Spateo

[WangyangLiu-Bio]

Dear Spateo Developers,

First, I want to express my sincere gratitude for developing such a powerful and comprehensive package for spatial transcriptomics analysis. Spateo has been instrumental in advancing our research, and we truly appreciate the effort you've put into creating this excellent tool.

I've been thoroughly studying the Spateo documentation and tutorials, and while I found the 2D spatial analysis features exceptionally well-documented, I'm having some difficulty understanding how to properly calculate and assign z-axis coordinates when building 3D models from multiple tissue slices.

Specifically, in our current project we have:

Multiple aligned 2D spatial transcriptomics slices

Successfully performed 2D alignment using Spateo's alignment functions

Now need to reconstruct these into a proper 3D model

From the documentation, I can see functions for 3D visualization and analysis, but I couldn't find clear guidance on:

How to determine appropriate z-spacing between slices

Whether Spateo provides automatic z-coordinate calculation

Best practices for assigning z-values when building 3D models from sequential sections

Could you please provide some guidance on:

What is the recommended workflow for 3D reconstruction in Spateo?

Are there specific functions for calculating optimal z-axis coordinates?

Should we use equal spacing, tissue thickness-based spacing, or is there a more sophisticated method available?

Thank you again for your incredible work on Spateo, and I would be extremely grateful for any advice you could offer on 3D model construction.