> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-stratamap/dragen-spatial-transcriptome/overview.md). # Overview The DRAGEN Spatial Transcriptome analysis software processes spatial sequencing data along with the registered microscope image. It aligns sequencing reads to their respective spatial locations and organizes them into square grids and individual cells, using H\&E image processing for cell identification. The software performs filtering, normalization, dimensionality reduction, and clustering. The resulting spatial data can be explored using the Illumina Connected Multiomics (ICM) spatial data viewer for deeper insights and interaction. #### Illumina Connected Analytics Pipeline DRAGEN Spatial Transcriptome is available in the cloud as a hosted application on the Illumina Connected Analytics (ICA) platform. The Cloud App is designed for customers aiming to harness cloud computing capabilities for high performance analysis of sequencing data seamlessly integrated with the Illumina Connected Multiomics platform. #### DRAGEN App Manager Application DRAGEN Spatial Transcriptome is available locally through the use of the DRAGEN App Manager (DAM) platform which can be installed onto a locally managed DRAGEN Server. The Local App is designed for customers who require an on‑premises option for running analyses on their DRAGEN server. It provides a streamlined workflow that allows users to perform analysis without relying on external cloud services. In order to enable checking cell segmentation before sequencing, the cell segmentation portion of the pipeline is available as a standalone tool, see [Illumina Spatial Cell Segmentation Tool](broken://pages/ddfuxCpNGdSJtTNqap36). --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/dragen-stratamap/dragen-spatial-transcriptome/overview.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.