Florian Muller

Impact of microbiota on spatial gene expression along the 3D colonic barrier Spatial organization at the cellular level is a fundamental aspect of complex life, orchestrating intricate biological processes with remarkable precision. This organization […]

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Imaging-based spatial transcriptomics (IST) enables high-resolution spatial mapping of RNA species. A key challenge in IST is accurate cell segmentation to assign each RNA molecule to the right cell. Here, we present RNA2seg, a […]

Recent progress in image-based spatial RNA profiling enables to spatially resolve tens to hundreds of distinct RNA species with high spatial resolution. It hence presents new avenues for comprehending tissue organization. In this context, […]

Regulation of RNA abundance and localization is a key step in gene expression control. Single-molecule RNA fluorescence in situ hybridization (smFISH) is a widely used single-cell-single-molecule imaging technique enabling quantitative studies of gene expression […]

A free Matlab-based toolbox to detect and count individual mRNA transcripts in single cells by automatic analysis of 3D RNA-FISH images. Software is available freely together with extensive instructions at : https://code.google.com/p/fish-quant/. The software […]

Single molecule FISH (smFISH) allows studying transcription and RNA localization by imaging individual mRNAs in single cells. We present smiFISH (single molecule inexpensive FISH), an easy to use and flexible RNA visualization and quantification […]