User Guide: From Raw FASTQ to STOmics StereoMap Visualization

Processing a spatial omics experiment generates a unique set of data files, with raw sequencing FASTQ files representing a crucial starting point. The journey from these files to an interpretable spatial visualization is a defined computational pathway. At STOmics, we have structured this workflow into two primary stages of spatial omics software: initial data processing with SAW and subsequent in-depth exploration with stomics stereoMap. This guide outlines the key steps in this transition, turning raw data into biological insight.

Stage One: Foundational Processing with SAW

The first phase happens within our SAW pipeline. This essential piece of spatial omics software is designed for the initial heavy lifting. Its primary role is spatial localization—precisely mapping where each sequencing read originated on the tissue sample. SAW integrates the raw sequencing data (FASTQ files) with the high-resolution tissue images captured by our Go Optical imager. Through alignment and quantification algorithms, it processes these inputs to generate a standardized spatial expression matrix. This matrix is the foundational output where every row is a gene or protein, and every column is a uniquely identified spatial barcode linked to a coordinate on the tissue. Completing this stage with SAW transforms your raw FASTQ files into a structured, spatially-aware data resource ready for specialized analysis.

Stage Two: Interactive Analysis with STOmics StereoMap

With the spatial expression matrix generated, the next phase is exploration and discovery using stomics stereoMap. This is where our analytical spatial omics software shifts from processing to interrogation. STOmics stereoMap is built to handle the complexity and scale of high-resolution spatial data. Researchers can load their SAW-processed matrices directly into this environment to perform a wide array of analyses. Key functions include spatial clustering to identify distinct tissue regions based on expression profiles, differential expression analysis across these clusters or user-defined regions of interest, and the creation of detailed spatial visualizations for specific genes or protein targets. This software environment allows you to ask direct questions of your data and receive visual, spatially-contextual answers.

A Cohesive Software Ecosystem for the Full Workflow

The strength of this process lies in the seamless connection between SAW and stomics stereoMap. They are not isolated tools but integrated components of the STOmics platform. SAW establishes the definitive spatial map, ensuring data integrity from the raw FASTQ stage. stomics stereoMap then unlocks that mapped data for scientific discovery without requiring users to manage complex format conversions or coordinate alignments manually. This end-to-end software approach, from raw data to visualization, ensures efficiency and reduces potential technical errors. It allows researchers to focus on their biological questions, supported by a computational workflow that maintains the fidelity of spatial information at every step.

Moving from raw sequencing files to a clear spatial visualization is a multi-step computational journey. By utilizing the SAW pipeline for robust spatial localization and data structuring, followed by the analytical power of STOmics  stereoMap for exploration and visualization, researchers can fully leverage the information contained within their experiments. This integrated software strategy is a core part of the STOmics offering, providing a complete and reliable path from the sequencer to the screen. Our goal is to ensure that the technical pathway from FASTQ to final map is clear, managed, and empowers your spatial omics research.