Spatial Cell Type Annotation (single-cell resolution)

Overview

Annotates cells and tissue niches in imaging-based spatial data, where each observation is one segmented cell. A tissue- and state-matched scRNA-seq reference is pulled from CELLxGENE, its labels are transferred with Harmony, and each cluster is then named from a table that puts its markers next to the transferred labels. Output: an AnnData with per-cell labels, confidence and niches, plus the evidence table behind every name.

Check the platform before anything else: