Thomas Defard

The paper describes an optimized spatial transcriptomics workflow for Xenopus embryos, enabling high-resolution gene expression mapping across developmental stages.

RNA2seg is a cell segmentation model for spatial transcriptomics trained on MERFISH and CosMx data, showing superior performance in zero-shot and few-shot settings.

autoFISH provides a modular toolbox for automated smFISH experiments, including equipment plans, software, protocols, and analysis workflows validated on cell lines and tissues.

This paper introduces ComSeg, a segmentation algorithm for image-based spatial transcriptomics that outperforms existing methods in cell type calling and handles complex tissue structures.

The paper provides a DIY guide for image-based spatial transcriptomics using TLS as an example, covering experimental design, wet lab methods, and analysis.