Visium HD

[bmateosa]

Hello,
is it possible to use this tool for Visium HD?
Thank you

[ankitbioinfo]

Thank you for your insightful question.

If I understand correctly, Visium HD utilizes 2×2 micron barcoded squares, meaning that an individual cell may span multiple such squares. To accurately analyze cell-level transcriptomics data, the first step is to aggregate these pixels to construct a gene count matrix at the cellular level.

Once the data is aggregated, you can apply the NiCo method for further analysis. Since Visium HD captures the full transcriptome, alternative approaches such as RCTD and Cell2location can also be employed for cell type annotation.

For a practical implementation, you may find Tutorial 2 helpful:
📌 NiCo Analysis for Low-Resolution Sequencing Technologies

I hope this helps! Let me know if you need further clarification.