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Xenium bundle
gene panel
relabel
import-segmentation
Bundle redefinition Xenium Ranger
segger
xeniumranger resegment
Segmentation refinement
Coordinates/ mask
FICTURE
Proseg
Segmentation-free approach
BOMS
Cellpose
Image-based segmentation approach
Baysor
tiff
csv
JSON
morphology
transcripts
Xenium bundle (redefined)
spatialxe QC
spatialxe meta
SpatialData Domain
html
QC reports
JSON
Metadata
Coordinates/ mask
RO-crate output
SpatialData integration
Approach: image-based (Cellpose, BOMS)
Approach: image-based and segmentation-free (Baysor)
Approach: segmentation-free (Proseg, FICTURE)
Optional step
Outputs
Xenium onboard analysis (XOA)
Inputs
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