Skip to main content
. Author manuscript; available in PMC: 2020 Mar 9.
Published in final edited form as: Nat Methods. 2019 Sep 9;16(10):987–990. doi: 10.1038/s41592-019-0548-y

Figure 2. HDST distinguishes cell types and niches in a breast cancer resection.

Figure 2.

(a) Labeling of morphological layers. HDST H&E image (left) of a breast cancer section and matching HDST (x,y) barcodes annotated into 13 morphological areas (right, color code). (b) Layer-specific spatial DE patterns in HDST. Summed normalized expression of positively enriched signature genes significantly (FDR<0.1, two-sided t-test) associated with each layer as in (a). (c) Cell type assignments by single nuclei as in (a). Two zoomed in regions (black and red squares) with H&E and color coded segments.