We at STOmics recognize that a robust and integrated spatial biology workflow is the backbone of any successful research project. Moving from a tissue sample to a detailed map of gene expression requires a series of deliberate, connected steps. Each phase must be executed with precision to ensure the final spatial coordinates are accurate and biologically meaningful. This article outlines the key stages of this process and how integrated spatial omics solutions are designed to support consistency and reliability from start to finish.

Tissue Preparation and Imaging

The initial phase is critical for preserving spatial information. The process begins with preparing thin tissue sections and mounting them onto specialized capture arrays. For studies utilizing our technology, this means placing sections onto STOmics Stereo-seq Chips or Slides. Following this, staining is performed to visualize the tissue morphology. Options include fluorescent dyes for nuclei or traditional H&E staining. High-quality imaging of this stained tissue is then completed, generating a histological reference map. This optical image will later become the foundational layer upon which all molecular spatial coordinates are overlaid, allowing for direct visual correlation between tissue structure and gene activity.

Molecular Capture and Library Construction

The next stage involves capturing the tissue's biomolecules directly onto the array. For fresh frozen samples, permeabilization releases mRNA, which then binds to spatially barcoded probes on the chip. Each probe carries a unique molecular address that tags every captured transcript with its location of origin. In the case of FFPE samples, a similar in situ process captures and converts RNA. This step is where the spatial biology workflow transitions from physical tissue to digital information. The captured molecules are then amplified and converted into sequencing-ready libraries. This entire wet-lab process is a core component of the complete spatial omics solutions we provide, ensuring the spatial barcodes are faithfully maintained for downstream analysis.

Sequencing and Data Generation

With libraries prepared, high-throughput sequencing is the engine that reads the output. The spatially barcoded libraries are sequenced on platforms like the DNBSEQ series. This step generates vast amounts of raw data files, where each sequence read is associated with its unique spatial barcode from the chip. The accuracy and depth of this sequencing run directly influence the resolution and quality of the final spatial map. It transforms the analog biological sample into a digital dataset poised for computational reconstruction, forming the raw material for the final phase of the spatial biology workflow.

Bioinformatics and Visualization

The final phase is where spatial coordinates are fully realized and interpreted. The sequencing data is processed through a dedicated bioinformatics pipeline, such as our Stereo-seq Analysis Workflow (SAW). This pipeline aligns reads, filters data, and, most importantly, uses the spatial barcodes to map each gene expression signal back to its specific x,y location on the original tissue image. The result is a rich, layered spatial dataset. Researchers then use visualization software like StereoMap to explore this data, overlaying gene expression patterns on the tissue image to identify spatially distinct regions, cell communities, and molecular gradients.

A seamless spatial biology workflow is not a collection of disjointed steps but a unified pipeline. From careful sample preparation on our chips to the final visualization of data, each stage builds upon the last to generate reliable spatial maps. At STOmics, our goal is to offer cohesive spatial omics solutions that integrate the necessary tools and protocols across this entire journey. By providing an optimized, end-to-end system, we support researchers in efficiently translating tissue samples into actionable, spatially resolved insights, solidifying the foundational role of workflow in spatial discovery.