> 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-connected-multiomics/icm-stratamap-walkthough.md).

# ICM StrataMap Walkthrough

When DRAGEN StrataMap completes, load its output into Illumina Connected Multiomics (ICM) for tertiary analysis. You can explore spatial data, create analyses, and save custom data-viewer sessions.

This walkthrough covers the current ICM workflow for DRAGEN StrataMap data. For platform-wide guidance, see the [Illumina Connected Multiomics User Guide](https://help.multiomics.illumina.com/icm).

* [Navigate to ICM](#navigating-to-icm)
* [Create a study](#creating-a-new-study)
* [Add StrataMap data](#adding-data-to-a-study)
* [Explore reports and run analyses](#explore-reports-and-run-analyses)

#### Video walkthrough (intro to StrataMap in ICM)

{% embed url="<https://www.youtube.com/watch?index=13&list=PLTxxnBBd6llQ&v=B3WvuBc3dNs>" %}

## Navigating to ICM

Open ICM directly at the regional URL, such as <https://use1.icm.illumina.com/icm/>. The region varies by deployment.

You can also open ICM from Illumina BioInsight Platform Core or BaseSpace by selecting the application icon in the top right navigation, then select **Illumina Connected Multiomics**.

Select the workgroup that contains the Core project with your StrataMap data.

ICM opens on the **Studies** page.

## Creating a new study

<figure><img src="https://1666731890-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F4oykwIlB6GxNkWm6RFlS%2Fuploads%2Fgit-blob-d4ff5dcbb8ebbd267976fcf92ad1c3ab29b953a7%2FScreenshot%202026-10-14%20at%202.59.15%E2%80%AFPM.png?alt=media" alt=""><figcaption></figcaption></figure>

To create a study:

1. Select **+ New Study**.
2. Enter a study name and description.
3. Select **I want to choose my preferred Platform Core project**.
4. Select the Core project that contains your data.
5. Select **Create**.

### Adding Data to a Study

Add DRAGEN StrataMap output from the linked Core project. A study can contain one or more samples. You can run analyses on one sample or across multiple samples.

<figure><img src="https://1666731890-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F4oykwIlB6GxNkWm6RFlS%2Fuploads%2Fgit-blob-b13197944c73d594ab7abbe7f4618d6b412df042%2FScreenshot%202026-10-14%20at%203.00.28%E2%80%AFPM.png?alt=media" alt=""><figcaption></figcaption></figure>

To add samples:

1. Open the study, then select **+ Add Data**.
2. Select **Select from Core project**.
3. Select **DRAGEN Spatial Transcriptome**. This format will be renamed **DRAGEN StrataMap**.
4. Under **Upload format**, select **Gzipped TAR archive (.tar.gz)**.
5. Navigate to the analysis `results` folder.
6. Select the sample folder or the top-level folder that contains the sample folders.
7. Select the `icm.tar.gz` file for each sample. If each sample folder contains one archive, select the top-level folder to add all samples.
8. Select **Add selected data to your study**.

The imported samples appear in the study. Select one or more samples, then create an analysis. Use the default pipeline. It will be renamed **Illumina StrataMap**.

{% hint style="info" %}
Importing can take several minutes. Open the analysis to monitor its task graph and status.
{% endhint %}

## Explore reports and run analyses

Open the **Analysis** to view the task graph. Squares represent tasks and circles represent data. Imported StrataMap data includes separate cell and grid-bin branches. The default grid-bin resolution is 10 µm. Additional grid sizes and nuclei-binning outputs appear as parallel branches when included in secondary analysis.

<figure><img src="https://1666731890-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F4oykwIlB6GxNkWm6RFlS%2Fuploads%2Fgit-blob-85a1146b3f7aa6575f841b2b210505b0f8eafdec%2FScreenshot%202026-10-14%20at%203.17.03%E2%80%AFPM.png?alt=media" alt="" width="563"><figcaption></figcaption></figure>

The tertiary tasks run upstream on BioInsight Platform are all included: filtering, normalization, PCA, UMAP, and Clustering. Each of these can be re-run with new parameters, or additional tasks can be run using the data.

### Explore spatial reports

Open a spatial report by double-clicking it in the analysis task graph. The cell report displays cells over the H\&E image, alongside a UMAP and Leiden-cluster chart. The grid-bin report displays a total-count heatmap by default, alongside a UMAP and Leiden-cluster chart.

<div><figure><img src="https://1666731890-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F4oykwIlB6GxNkWm6RFlS%2Fuploads%2Fgit-blob-6ce7045e0861361c23afe3e11aef5e6b4a51fe48%2FScreenshot%202026-10-14%20at%203.07.04%E2%80%AFPM.png?alt=media" alt=""><figcaption></figcaption></figure> <figure><img src="https://1666731890-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F4oykwIlB6GxNkWm6RFlS%2Fuploads%2Fgit-blob-6636a5780dc3fbe2a3e828a0e7e5fad85b07cb1e%2FScreenshot%202026-10-14%20at%203.05.43%E2%80%AFPM.png?alt=media" alt=""><figcaption></figcaption></figure></div>

Use the **Configure icon** in each plot to make changes to the plot. Change opacity to view the H\&E image beneath the cells. Selecting a Leiden cluster in the chart highlights it in the UMAP and spatial plot.

To preserve a custom view, select **Save** or **Save as**. Saving creates or updates a data-viewer session. It does not change the original report.

{% hint style="info" %}
Open **Settings** → **Spatial view** to control the scale bar and the mini map. For the grid binned plot, turn off dynamic resolution to load the full grid-bin resolution immediately.
{% endhint %}


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