Paper Review
Spatial Transcriptomics (ST) methods supplement the location information lost using scRNA-seq approaches for spatial biology research. Emerging large field-of-view (FOV) ST platforms enable whole-embryo-scale spatiotemporal research at different time points. However, how to do the downstream computational analysis for 3D reconstruction, spatial domain digitization, and cell-cell interaction still blocks the way for further digging embryo-scale and 3D ST dataset.
An international team of scientists from leading research institutes worldwide collaborated to conduct pioneering research in building a 3D spatiotemporal modeling framework—Spateo (https://github.com/aristoteleo/spateo-release). Their accomplishment was published in Cell, titled “Spatiotemporal modeling of molecular holograms”.
Spateo is built on four key phases for advanced spatiotemporal modeling: (1) It reconstructs 3D embryo and organ models from sequential 2D serial sections using a scalable and precise algorithm that enables partial, non-rigid alignment, multi-slice refinement, and mesh correction. (2) It develops a multi-scale spatial digitization framework to explore biological processes across levels, from single-cell to whole-embryo resolution. (3) It analyzes left-right (L:R) interactions and predicts their downstream effects on gene expression in 3D structures such as the zona limitans intrathalamica (ZLI), midbrain-hindbrain boundary (MHB) organizers, and spinal cord, employing a spatially aware regression model at single-cell resolution. (4) It derives morphometric vector fields to map cellular migration patterns, uncovering regulatory mechanisms that drive cell movement and morphogenesis. For example, Spateo unveils the molecular programs driving asymmetrical heart development in mice, linking cellular dynamics to organ-level changes. Researchers expect future molecular and genetic studies to validate these predictions, advancing our understanding of embryogenesis and disease.
“We are now at the dawn of a new era of spatial biology, with subcellular resolution, large FOV methods such as Stereo-seq theoretically enabling construction of time-resolved embryo-scale datasets in 3D space.”, mentioned in this paper. The raw data of the E9.5 and E11.5 whole mouse embryo 3D spatial transcriptomics dataset and the S11 and S13 Drosophila whole-embryo datasets generated on Stereo-seq platform were used in this study. The processed data could be download via https://spateodata.aristoteleo.com/
Learn more about the research: https://www.cell.com/cell/fulltext/S0092-8674(24)01159-0
About STOmics Stereo-seq:
STOmics Stereo-seq Transcriptomics for Large Chip Designs (LCD) pioneers the whole transcriptome study for entire tissue sections. Stereo-seq for Large Chip Designs is firstly offered to the market - 1cm x 2cm, 2cm x 2cm, 2cm x 3cm. Compatible for all species (FF samples), it enables a “tissue-to-data” solution through in situ capture of the whole transcriptome, at nanoscale resolution and centimeter-sized field of view.
Find out more about Stereo-seq Large Chip Design? https://en.stomics.tech/products/stereo-seq-transcriptomics-large-chip-design/list.html
