Table 2.

The overview of widely-used spatial technologies.

Methods	Company	Imaging/Sequencing technology	Resolution	N_readouts	(Processed) Representation
Imaging mass cytometry (IMC) [2]	Standard BioTools	Multiplexed mass spectrometry (MMS)	Sub-cellular	<50 protein markers	learned latent representation
Multiplexed ion beam imaging (MIBI) [48]	Ionpath	MMS	Sub-cellular	<50 protein markers	learned latent representation
Co-detection by indexing (CODEX) [6]	Akoya Biosciences	Cyclic immunofluorescence (IF)	Diffraction-limited	Up to 60 protein markers	learned latent representation
COMET [51]	Lunaphore	Cyclic IF	Diffraction-limited	Up to 40 protein markers	learned latent representation
GeoMX DSP [27]	Nanostring	Light-based dissection	<10 microns	Whole transcriptome and >570 proteins	Imputed readouts between the spot gap
Visium [49]	10x	Spatial barcoding	55 microns in diameter	Whole transcriptome	Imputed readouts between the spot gap
Visum HD [46]	10x	Spatial barcoding	2 × 2 microns in square	Whole transcriptome	Processed readouts through bin aggregation
Stereo-seq [15]	BGI	Spatial barcoding	220 nm in diameter	Whole transcriptome	Processed readouts through bin aggregation
CosMx [25]	Nanostring	Multiplexed in situ hybridization (ISH)	Sub-cellular	Up to 6000 RNAs and 64 proteins	Raw readouts
Xenium [30]	10x	Multiplexed ISH	Sub-cellular	Up to 5000 RNAs	Raw readouts
MERFISH [68]	Vizgen	Multiplexed ISH	Sub-cellular	Up to 1000 RNAs	Raw readouts