spatial-transcriptomics-tutorials-with-omicverse

Guide users through omicverse spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modeling for Visium, Visium HD, Stereo-seq, and Slide-seq.

• Navigate spatial analysis tutorials in omicverse
• Cover preprocessing, deconvolution, and downstream modeling
• Supports Visium, Visium HD, Stereo-seq, and Slide-seq
• Includes notebooks for each workflow stage

• Preprocess spatial slides and coordinates
• Segment Visium HD tiles into cells
• Supports deconvolution via Tangram and cell2location
• Enables spatial clustering and integration
• Provides visualisation and QC tools
• Includes Starfysh archetypal deconvolution
• Uses shared references and spatial alignment
• Supports multi-slice dataset integration

1. 1.Load spatial slides and manipulate coordinates using omicverse and scanpy
2. 2.Run cell segmentation for Visium HD with CellPose variants
3. 3.Apply deconvolution methods like Tangram and cell2location
4. 4.Perform spatial clustering and integration workflows