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
Hi LARIS team,
Thank you for developing this excellent tool! I have several questions regarding visualization and multi-resolution support:
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?
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
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