Biology subjects

Malt, A.

Publications and source records attributed to Malt, A..

2 recordsLinked to original sources

bioRxiv2026

Atlas-scale spatially aware clustering with support for 3D and multimodal data using SpatialLeiden

Here we extend SpatialLeiden, our spatial clustering algorithm, to enable generalised atlas-scale multi-sample, 3D serial-section, and multimodal spatial omics via flexible neighbour-graph multiplexing on batch-corrected latent spaces. It delivers coherent domains aligning with brain atlases across >100 samples, stable 3D reconstruction of cancer tissue structures, and integrated multimodal features, outperforming specialized tools in modularity and scalability on standard hardware. SpatialLeiden is compatible with scverse for broad and intuitive adoption.

bioinformatics↗

bioRxiv2025

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

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.

bioinformatics↗