BoReMi: Bokeh-based jupyter-interface for registering spatio-molecular data to related microscopy images
Fig 5
Alignment of mouse hippocampus Slide-seq data to HE with STalign and BoReMi.
a) Overview of the inputs Slide-seq puck and an Allen Brain Atlas HE image. Leiden clusters (resolution 0.3) are indicated and show internal structure, while bead distribution (beads > 50 UMIs) itself does not show structure. b) STalign and BoReMi visual interface and setup. STalign landmarks were set to the best of our ability. c) Final alignment results produced by STalign and BoReMi, respectively. The region of over-distortion by STalign is amplified for both alignments.