Table 2 Best pairwise agreement (Cohen’s Kappa) between individual matching methods for each protocol.

From: Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain

Protocol

Method 1

Method 2

Kappa

MERFISH

map.cells*

mfishtools

0.70

smFISH

FR-Match

mfishtools

0.84

BaristaSeq

Tangram

ATLAS

0.23

ExSeq

mfishtools

pciSeq

0.75

  1. See full table in Supplementary Table S2. Kappa values: ≤ 0 indicates no agreement, 0.01–0.20 indicates slight agreement, 0.21–0.40 fair agreement, 0.41–0.60 moderate agreement, 0.61–0.80 substantial agreement, and 0.81–1.00 almost perfect agreement37.
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