Louis Benedikt Kuemmerle

The paper introduces SACCELERATOR, a framework for spatially aware clustering that improves benchmarking by incorporating expert feedback and consensus analysis across diverse datasets.

The paper benchmarks gene expression reconstruction from single-cell latent representations, finding autoencoders perform best at low dimensionality and foundation models depend on decoder architecture.

This paper introduces a tool to detect overlapping cells and segmentation errors in 3D spatial transcriptomics data.

The paper identifies region- and disease-specific transcriptomic changes in oligodendrocytes from Alzheimer's disease patients using single-nucleus RNA sequencing.

DISCO-seq enables 3D single-cell transcriptomics of whole tissues and organisms by combining tissue-clearing chemistry with imaging and transcriptomic profiling.

This study evaluates the Xenium In Situ spatial transcriptomics platform using mouse brain and human breast cancer datasets, comparing it to other technologies and benchmarking analysis tools.

Spapros selects optimal probe sets for targeted spatial transcriptomics to improve cell type identification and spatial variation detection across multiple datasets.

Squidpy extends Scanpy/AnnData with spatial neighbor graphs and a lazy-loading image container, enabling spatial statistics, ligand-receptor tests, image features, and ~10-fold faster neighborhood enrichment than Giotto.