> 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/get-started/readme.md).

# Introduction

## Illumina Spatial Transcriptome software

Welcome to the user documentation for the Illumina Spatial Transcriptome analysis software.

For guidance on the assay workflow, please refer to your PDF of the Illumina Spatial Transcriptome user documentation.

## Software user guide format

This software user guide is separated into three sections corresponding to the three software components of the Illumina Spatial Transcriptome analysis software in order of use.

<figure><img src="/files/oSRzoePJdbCgVtNJTubz" alt=""><figcaption><p>High level software workflow, the numbers indicate the relevant sections of the user guide, see below</p></figcaption></figure>

1. **Illumina Spatial Image Tool (ISIT)**: the desktop image processing app.

{% hint style="info" %}
Note: If planning to export sample files from ISIT directly to the cloud, ensure the application is installed on a PC with a stable network connection. On PCs without a stable network connection, export sample files using the local export feature in ISIT. For further assistance, please contact Illumina Support.
{% endhint %}

2. **DRAGEN Spatial Transcriptome**: the secondary and initial tertiary analysis cloud software run on Illumina Connected Analytics (ICA). This section of the guide also explains how to use the Base Space Sequence Hub (BSSH) Run Planning tool to create a run for sequencing and analysis.
3. **Illumina Connected Multiomics** (ICM): the visualization and additional tertiary analysis cloud platform. This section of the guide explains portions of the ICM platform specific for spatial visualization and analysis, see the ICM guide for more information about the platform itself.


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