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Description
Hi LARIS team,
Thank you for developing this excellent tool! I have several questions regarding visualization and multi-resolution support:
- Multi-resolution parameter settings
For spatial transcriptomics data with different binning resolutions, what are the recommended parameter settings?
Examples:
Visium HD: 8μm bins vs 16μm bins
Stereo-seq: bin1 (500nm) vs bin10 vs bin50
Xenium: subcellular resolution
Questions:
Should we adjust k (number of nearest neighbors) based on bin size?
How should mu (distance decay parameter) be scaled for different resolutions?
Are there any recommended parameter combinations for each resolution?
- HE image overlay visualization
Can LARIS overlay ligand-receptor interaction results on H&E stained tissue images, similar to what Scanpy or Squidpy offers?
Desired features:
Display interaction scores as heatmaps on H&E images
Visualize cell type-specific interactions with spatial context like stlearn
Export high-resolution figures with tissue morphology
- Cell-cell interaction visualization on spatial slices
Similar to stlearn's CCI visualization, can LARIS display:
Sender cells and receiver cells highlighted on tissue sections
Lines/arrows connecting interacting cell pairs
4 is there a demo compare different cci like cellchat
5 does it support singlecell, Llike 10x or DNB C4