Visium HD Analysis
- Dena Leshkowitz
10X Resources of information
https://www.10xgenomics.com/blog/getting-started-with-visium-hd-data-analysis-and-third-party-tools
10X Nuclei Segmentation (Python)
https://www.10xgenomics.com/analysis-guides/segmentation-visium-hd
Seurat
https://satijalab.org/seurat/articles/visiumhd_analysis_vignette
Bin2cell
Visium HD captures gene expression data at a subcellular 2um resolution. It should be possible to use this data to reconstruct cells more accurately than just using the next resolution up (8um), especially if additionally using the available high resolution morphology images.
https://github.com/Teichlab/bin2cell . The final output can be anndata output of cells. (Python)
ENACT
https://github.com/Sanofi-Public/enact-pipeline . Suppose to be end-to-end analysis for visium hd, including bin 2 cell and annotations. The output can also be good for TissUUmap. (Python)
TissUUmap
TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample.
https://tissuumaps.github.io/TissUUmaps-docs/index.html . This is a browser-based tool. You can use it from windows and you can upload directly anndata objects.
Introduction to the SpatialFeatureExperiment class
Lambda Moses, Lior Pachter Jan 30, 2025
Convert formats
https://www.youtube.com/watch?v=como93CmnS8 This is a 4 min video
That explains how to convert the h5ad and the notebook here - https://github.com/mousepixels/sanbomics_scripts/blob/main/h5ad_to_seurat.ipynb
https://github.com/xleizi/easySCF – convert easily between Seurat object an anndata object. Can also be used with spatial data.