> 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/illumina-spatial-image-tool/overview.md). # Overview The Illumina Spatial Image Tool (ISIT) processes stitched microscope or slide scanner images of tissue sections placed on the Spatial Transcriptome 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 Spatial Transcriptome analysis software. Additionally, the same data is made accessible within the selected account on the Illumina Connected Analytics (ICA) platform, where it can be used to manually launch the DRAGEN Spatial Transcriptome 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 %} --- # 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/illumina-spatial-image-tool/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.