Fig 1.
Schematic illustrating the workflow and showcasing the core functionalities of BoReMi.
Fig 2.
Exemplary registration of MERFISH data to database HE images using BoReMi’s linear transformations.
a) BoReMi’s data/image view panel showcasing the different data/image manipulations enabling the registration of MERFISH data and HE images of mouse brain coronal sections. Panel i shows the unmanipulated data as they are obtained from their respective sources. Panels ii-ix show the data after consecutive application of the respective manipulations. b) BoReMi’s control panel that allows parameter selection for the data/image manipulations as shown in panel a):ii: Data point display size, iii: Data subsetting by cluster selection, iv: Scaling by setting the original resolution for data and image as well as the desired common display scale,v: Data orientation change by flipping, vi: Rotation by setting the angle, vii: Pan and zoom, viii: Translocation by setting x and y changes, and ix: Microscopy image selection. vii (pan and zoom) is controlled through mouse-interaction with the view panel. x shows the undo-redo buttons. xi shows the download buttons for the registered data and image. xii shows the data coordinate live-preview.
Fig 3.
a) Left: Non-linear manipulations control panel and functionalities. Manipulations are performed through mouse-interactions after activating the “point-select” widget; Right: Example for adjusting the position of slightly disconnected data points (possibly due to a tear) using BoReMi’s elastic non-linear transformation, building on the linear registration in Fig 2. The dragged cells as well as the “threshold of influence” (here set to 500 μm) are indicated by dashed circles. Arrows indicate the drag direction. b) Example for highly precise alignment which allows cell matching between cell-segmented data (as in panel a) and images (here DAPI) of the same tissue section by high magnification (zoom-in) and fine positional adjustment.
Fig 4.
Registration of multiple serial sections processed with MERFISH or Slide-seq.
a) Top: Data and HE images before alignment as displayed by BoReMi, with different sections accessible through different tabs. Bottom: Data and HE images after alignment. The percent overlap of data and HE is indicated and non-overlapping data points are highlighted in red. b) Histogram depicting spatial Spearman correlation of gene expression calculated for each gene across matched or randomly paired 100x100μm bins between pairs of tissue sections (as indicated).
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.