Table 1 Qualitative summary of findings in iST benchmarking

Total transcripts

Total transcripts detected. Note the big difference of panel size between platforms. Xenium (<=377); MERSCOPE( < = 255); CosMx(1000).

Supp. Table 6

Great

Great

Great

Sample quality impact on transcript detection

Comparison of total transcript detected between different tissue microarrays

Supp. Table 6

Great

Poor

Great

Reproducibility (panel to panel)

Spearman correlation coefficient of core-level cumulative gene expression levels of shared genes between two panels within each platform, captured from matched tissue cores.

Supp. Figure 1

Great

Great

N/A

Reproducibility (sample to sample)

Spearman correlation coefficient of gene expression levels of every shared gene between two cores of the same tissue type from the same patient.

Supp. Figure 2

Great

Great

Great

Sensitivity

Gene-by-gene plot between platform and panels

Fig. 2a-c, Supp. Figure 2

Great

OK

Good

Specificity

On-target fraction and FDR

Fig. 2d-f, Supp. Figure 2

Great

Good

OK

Genes above noise

Percentage of genes above noise

Fig. 2h, Supp. Figure 2

Great

OK

Great

Concordance with TCGA

Gene-by-gene plot between iST data and orthogonal TCGA database

Fig. 3a

Great

Great

Great

Concordance with GTEx

Gene-by-gene plot between iST data and orthogonal GTEx database

Fig. 3b

Great

OK

Great

Concordance with scRNA-seq data

Gene-by-gene plot between iST data and paired sc-RNA-seq data

Fig. 3c-e

Great

OK

Great

Transcript per cell (share genes only)

Transcript per cell using share genes only

Fig. 4e

Great

Poor

OK

Cell segmentation accuracy

Precision, Recall, F1 score

Fig. 4b

Great

Good

Great

Cell segmentation biological performance

Co-expression plot of disjoint markers

Fig. 4g

Great

Good

OK

Cell typing performance

Clustering analysis

Fig. 5

Great

OK

Good