# sopa proposal comparison

| Feature | mcmicro | molkart | spatialxe | spatialvi | sopa | iss-nf (https://github.com/BioImageTools/iss-nf) | Image-ST (https://github.com/cellgeni/Image-ST) | Panorama-seq |
| ---------------------- | ------- | ------- | --------- | --------- | ---- | ---- | ---- | ------------ |
| uses spatialdata | | | ✓ | yes | ✓ | no | partially | yes |
| supported modalities | spatial proteomics | spatial transcriptomics | spatial transcriptomics | spatial transcriptomics | spatial proteomics / transcriptomics, H&E | spatial transcriptomics | spatial transcriptomics | spatial transcriptomics |
| supported technologies | Cycif, PhenoImager, PhenoCycler, COMET, Orion, MACSima (any antibody-based multiplexed IF; raw data preprocessing supported) | Resolve Biosciences | 10x Xenium | 10x Visium, VisiumHD | Xenium, CosMX, MERSCOPE, VisiumHD, PhenoCycler, Resolve Biosciences, MACSima, Hyperion, WSI | Cartana-like In-situ sequencing | Cartana-like In-situ sequencing, RNAscope | Any sequencing-based technology that uses barcoded in-situ arrays|
| cell segmentations | Cellpose, Stardist, Mesmer, Ilastik, other methods planned for integration | Cellpose, Stardist, Mesmer, Ilastik, other methods planned for integration | Cellpose, Baysor, Proseg, Segger, xeniumranger resegment, boms, ficture & other methods are planned for integration | | Cellpose, Baysor, Proseg, Stardist, Comseg | CellPose | CellPose, Stardist, Instanseg, Mesmer | |
| tissue segmentations | | | grandqc | | H&E or staining based | | | |
| supported aggregations | | basic QC metrics | single-cell/transcript QC | QC metrics | transcript count, channel min/max/mean, bins aggregation transcript count | transcript count | transcript count | QC metrics |
| visualization | Napari, Minerva | Napari | QC plots & spatialdata visualizations, napari, Xenium Explorer | QC plots, spatial visualisations, clustering, spatially variable genes; output compatible with TissUUmaps | via SpatialData (napari / spatialdata-plot) or Xenium Explorer | | Napari (via napari-spatialdata), Vitessce, | QC plots, SpatialData, spatial visualisations Napari, clustering, spatially variable gene |
| H&E tools | | | | | patches embeddings, clustering, join over spatial omics | | | |