To systematically address these hurdles, STOmics introduced the Stereo Data Analysis Solution (SDAS) Webinar Series delivers an end-to-end bioinformatics roadmap tailored for spatial omics, especially Stereo-seq data.

A Nature study combines Stereo-seq with single-nucleus RNA sequencing to examine how gene-expression programs unfold across space, time, organs and anatomical substructures during early human development.

SDAS is an "unzip-and-run" Linux command-line toolkit specifically developed for Stereo-seq spatiotemporal data. Covering the entire workflow from raw data preprocessing to publication-ready figure output, it eliminates the need to manually stitch scripts together, ensuring standardized, high-quality spatial omics analysis.

By introducing multi-modal imaging (nucleus, cytoplasm, and membrane), we can define cellular territories using actual biological boundaries. Instead of guessing or inferring where a cell ends, we let the image data tell us exactly where the physical borders lie. This "What You See Is What You Get" segmentation approach ensures that every single molecule is accurately assigned to its rightful cellular home, ultimately yielding a far more biologically meaningful CellBin matrix.

Traditional tools simply cannot answer a foundational biological question: On exactly which side of the cellular layer within the root nodule did this core nitrogen-fixing regulatory gene undergo targeted up-regulation?STOmics' Stereo-seq provides a transformative solution to overcome these bottlenecks in soybean research by seamlessly balancing sub-micron resolution with an expansive field of view (Liu et al., 2023

By profiling multi-ovary (MO) and near-isogenic single-ovary (SO) wheat lines at the decisive lemma primordium (LP) stage, the study delineates the exact spatial coordinates of cell populations and gene networks governing floral meristem maintenance. This research provides a definitive spatial framework for understanding how elevated WUS-D1 gene activity prolongs floral meristem competence and delays termination. By resolving these micro-scale regulatory programs, the study offers a precise developmental ro

The thymus is the primary site of T cell maturation, where adaptive immunity and central tolerance are established to prevent autoimmunity. Within this highly organized organ, developing T cells undergo stepwise selection across distinct compartments. In the cortex, cortical thymic epithelial cells (cTECs) support T-lineage commitment and positive selection. Surviving thymocytes then migrate to the medulla, where medullary thymic epithelial cells (mTECs) and dendritic cells (DCs) present peripheral tissue a

The thymus is a small, bilobed organ nestled behind the sternum, yet it fundamentally dictates the balance of human immunity. As the essential training ground for the adaptive immune system, it is the sole reason your T cells target foreign pathogens rather than your own tissues. Every single T cell defending your body today was rigorously tested and certified within this transient organ (one that naturally shrinks after puberty). For decades, immunologists could profile the cellular composition of the thym

Stereo-seq LCD is the first spatial transcriptomics solution to combine a centimeter-scale field of view with true nanoscale resolution—a distinction that matters enormously in practice. The platform currently offers three standardized chip sizes: 1 cm × 2 cm, 2 cm × 2 cm, and 2 cm × 3 cm. For projects with exceptional scale requirements, customized configurations are available up to 13 × 13 cm, subject to project design and regional support agreements.

In the standard STOmics analysis workflow, SAW generates Cellbin GEF files containing gene expression matrices and spatial coordinates. While SAW provides initial clustering, researchers often perform advanced downstream analysis using third-party tools such as Scanpy, Seurat, or specialized algorithms like cell2location or RCTD (Robust Cell Type Decomposition) to identify precise cell types or functional states.