Not able to use map function (like in FICTURE) in punkst for reference-based mapping

[sabir-yas]

Hi,

I’ve been exploring punkst for visualizing MERFISH/Xenium-style spatial transcriptomics data, and I noticed something I want to clarify.

In the FICTURE paper and documentation, there is a map command that allows users to integrate a reference scRNA-seq dataset (e.g., Allen Brain Atlas h5ad) with a query dataset (MERFISH/Xenium counts):

ficture map
--reference /path/to/reference_cell_types.h5ad
--query /path/to/MERFISH_counts.csv
--output /path/to/output_directory
--n-processors 8

This is useful for label transfer / reference-guided mapping, where query pixels/cells are assigned to known cell types.

My question is:

Does punkst include or plan to include a similar map function?

Or is punkst meant to focus purely on visualization, with the assumption that mapping/classification should be done with external tools (e.g., FICTURE, Seurat, scANVI, cell2location), and then the results imported into punkst (via cells.csv and transcripts.csv)?

If punkst does not currently handle reference-based mapping, are there any recommended workflows for combining punkst with FICTURE or other tools?

Thanks for clarifying — I want to make sure I’m not missing a hidden feature, and it would help other users understand the division between analysis and visualization.

This is part of an effort to do supervised learning through punkst.

Thanks