> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/dragen-stratamap/illumina-stratamap-image-tool/overview.md). # Overview The Illumina StrataMap Image Tool (ISIT) processes stitched microscope or slide scanner images of tissue sections placed on the StrataMap slide. For each sample, it registers the image, performs quality control checks, and generates a tissue mask. The software enables direct export of registered images with tissue masks in OME-TIFF format, along with associated sample information, to the cloud and/or a local storage location. When using the cloud export feature, the OME-TIFF files and sample information are exported to the selected account within BSSH Run Planner. This facilitates use in run setup, sample sheet generation, and downstream analysis using the DRAGEN StrataMap analysis software. Additionally, the same data is made accessible within the selected account on the Illumina BioInsight Platform Core (Core), where it can be used to manually launch the DRAGEN StrataMap analysis. {% hint style="info" %} Illumina recommends using a slide scanner for imaging, as microscopes require manual adjustments, more experience with imaging principles, and additional training and practice for accurate results. {% endhint %} #### Video walkthrough {% embed url="" %} --- # 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 by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.illumina.com/dragen-stratamap/illumina-stratamap-image-tool/overview.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. 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.