**segmentation** - [x] watershed, - [x] Cellpose - [ ] cellpose v4+ (Cellpose-SAM) - [x] [Stardist](https://github.com/stardist/stardist), - [x] Mesmer - [x] binning, - [ ] [SCS](https://www.nature.com/articles/s41592-023-01939-3) (designed for sequencing based ST, but also applicable to iST) - [ ] [BIDCell](https://www.nature.com/articles/s41467-023-44560-w), - [ ] [uber mask](https://www.biorxiv.org/content/10.1101/2025.04.03.646876v1), - [ ] ([SegJointGene](https://www.biorxiv.org/content/10.64898/2026.01.08.698474v1), [github](https://github.com/daifengwanglab/segjointgene)) **segmentation modification** - [x] nuclear expansion **transcript assignment** - [x] [pciseq](https://github.com/acycliq/pciSeq) - [x] [Baysor](https://github.com/kharchenkolab/Baysor) - [ ] [clustermap](https://www.nature.com/articles/s41467-021-26044-x), [github](https://github.com/wanglab-broad/ClusterMap) - [ ] [ComSeg](https://www.biorxiv.org/content/10.1101/2023.12.01.569528v1) - [ ] [JSTA](https://www.embopress.org/doi/full/10.15252/msb.202010108) - [ ] [proseg](https://www.nature.com/articles/s41592-025-02697-0), [github](https://github.com/dcjones/proseg), - [ ] [Segger](https://www.biorxiv.org/content/10.1101/2025.03.14.643160v1), [github](https://github.com/EliHei2/segger_dev) - [ ] [FastReseg](https://www.nature.com/articles/s41598-025-08733-5) - [ ] [Bering](https://www.biorxiv.org/content/10.1101/2023.09.19.558548v1) - [ ] [CelloType](https://www.nature.com/articles/s41592-024-02513-1) (tested by Leon ~25.02.25, not rly useable for Xenium) - [ ] [RNA2Seg](https://www.biorxiv.org/content/10.1101/2025.03.03.641259v2) ([github](https://github.com/fish-quant/rna2seg)) **cell volume calculation** - [ ] convex hull - [ ] nuclear segmentation - [ ] cell segmentation - [ ] alpha shape **normalization** - [ ] normalize by total counts - [ ] normalize by area ([ref1](https://link.springer.com/article/10.1186/s13059-024-03303-w), [ref2](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03241-7)) --> how to set factor? - [x] [SpaNorm](https://www.biorxiv.org/content/10.1101/2024.05.31.596908v1) **cell type annotation** - [x] majority vote - [x] [SSAM](https://www.nature.com/articles/s41467-021-23807-4), - [ ] pciseq - [x] [TACCO](https://www.nature.com/articles/s41587-023-01657-3) - [x] tangram - [x] [moscot](https://www.biorxiv.org/content/10.1101/2023.05.11.540374v2.abstract) - [ ] [CelloType](https://www.nature.com/articles/s41592-024-02513-1) - [ ] [SpatialMap](https://www.biorxiv.org/content/10.1101/2025.07.03.662904v1) - [ ] [insitutype](https://www.biorxiv.org/content/10.1101/2022.10.19.512902v1) - [ ] TODO: Add rest from txsim dev branch: https://github.com/theislab/txsim-pipeline/tree/dev/scripts - [ ] [BPcells](https://www.10xgenomics.com/analysis-guides/xenium-cell-type-annotation) - [x] [mapmycells](https://www.biorxiv.org/content/10.64898/2026.03.06.710160v1) **expression correction** - [ ] sc ref based probe efficiency correction - [ ] nr of probes based efficiency correction - [x] resolVI - [ ] [SPLIT](https://www.biorxiv.org/content/10.1101/2025.04.23.649965v1) - [ ] [DenoIST](https://www.biorxiv.org/content/10.1101/2025.11.13.688387v1) **qc filter** - [ ] ...
segmentation
segmentation modification
transcript assignment
cell volume calculation
normalization
cell type annotation
expression correction
qc filter