Methods to add

[LouisK92]

segmentation

• watershed,
• Cellpose
• cellpose v4+ (Cellpose-SAM)
• Stardist,
• Mesmer
• binning,
• SCS (designed for sequencing based ST, but also applicable to iST)
• BIDCell,
• uber mask,
• (SegJointGene, github)

segmentation modification

• nuclear expansion

transcript assignment

• pciseq
• Baysor
• clustermap, github
• ComSeg
• JSTA
• proseg, github,
• Segger, github
• FastReseg
• Bering
• CelloType (tested by Leon ~25.02.25, not rly useable for Xenium)
• RNA2Seg (github)

cell volume calculation

• convex hull
• nuclear segmentation
• cell segmentation
• alpha shape

normalization

• normalize by total counts
• normalize by area (ref1, ref2) --> how to set factor?
• SpaNorm

cell type annotation

• majority vote
• SSAM,
• pciseq
• TACCO
• tangram
• moscot
• CelloType
• SpatialMap
• insitutype
• TODO: Add rest from txsim dev branch: https://github.com/theislab/txsim-pipeline/tree/dev/scripts
• BPcells

expression correction

• sc ref based probe efficiency correction
• nr of probes based efficiency correction
• resolVI
• SPLIT
• DenoIST

qc filter

• ...