2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices

Imaging-based spatially resolved transcriptomics can localise transcripts within cells in 3D. Cell segmentation precedes assignment of transcripts to cells and annotation of cell function. However, cell segmentation is usually performed in 2D, thus unable to deal with spatial doublets arising from overlapping cells, resulting in segmented cells containing transcripts originating from multiple cell-types. Here we present a computational tool called ovrlpy that identifies overlapping cells, tissue folds and inaccurate cell-segmentation.