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

作者：Sebastian Tiesmeyer, Niklas Müller‐Bötticher, Alexander Malt, L.L. Ma, Sergio Marco Salas, Paul Kießling, Paul Horn, Adrien Guillot, Louis Kümmerle, Frank Tacke, Fabian J. Theis, Christoph Kuppe, Mats Nillson, Roland Eils, Brian Long, Naveed Ishaque · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2025 · DOI：10.1101/2025.01.13.632601 · 被引用次数：9 · 研究领域：Cell Image Analysis Techniques

Abstract Imaging-based spatially resolved transcriptomics can localize transcripts within tissue sections in 3D. Cell segmentation assigns transcripts to cells and precedes 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 by analyzing transcript localization in 3D.