Föreläsningar och seminarier Cell-resolved 3D transcriptomics from sequencing-native proximity graphs - Cloned

About this talk

A recurring limitation in single-cell genomics is that while molecular states can be measured at scale, capturing the three-dimensional microenvironments where development and disease unfold remains challenging. Dr Weinstein will present volumetric DNA microscopy (vDM), an optics-free spatial-genomics platform that encodes local molecular proximity relationships directly into DNA inside intact specimens and reads them out using standard sequencing. The resulting data forms a molecular contact graph (barcoded molecules as nodes and proximity events as edges). From this graph, the Weinstein lab reconstructs global 3D organization using geodesic spectral embeddings, a scalable graph-embedding approach. A key advance he will highlight is that the contact graph's community structure can be leveraged not only for coordinate reconstruction, but also to segment individual cells directly from sequencing-derived connectivity. This enables increasingly cell-resolved 3D transcriptomes along with quantitative neighborhood features such as cell-cell adjacency and local contact density. In whole zebrafish embryos, vDM yields datasets of ~10 million tagged molecules per organism at ~1-2 µm neighborhood-scale resolution, recovering anatomical compartments, developmental gradients, and cellular organization in 3D. 

Finally, Dr Weinstein will outline how these contact-first measurements connect to broader computational questions in high-dimensional biological data and future applications in complex tissues and microenvironments.