# View tissue images

* [Visualize the annotated image from the automatically generated Spatial report task](#visualize-the-annotated-image-from-the-automatically-generated-spatial-report-task)
* [Visualize the annotated image from the Annotate Visium image task](#visualize-the-annotated-image-from-the-annotate-visium-image-task)
* [Modify Style](#modify-style)
* [Modify Axes](#modify-axes)
* [Color by gene expression and attributes](#color-by-gene-expression-and-attributes)

## Visualize the annotated image from the automatically generated Spatial report task

[With the pre-processed samples imported, we can begin analysis.](/partek/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/start-with-pre-processed-space-ranger-output-files.md)

* Click **Analyses** to switch to the *Analyses* tab

For now, the *Analyses* tab has a starting node, a circular node called *Single cell* counts and also a rectangular task node called *Spatial report* which was automatically generated for this type of data. As you [perform analyses, additional nodes representing tasks and new data will be created](/partek/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/spatial-data-analysis-steps.md), forming a visual representation of your analysis pipeline.

* Click the **Spatial report** node
* Click **Task report** on the task menu

![](/files/wLXMMzAT7MedhvZmSt13)

The spatial report will display the first sample (Replicate 1). We want to visualize all of the samples using the steps below.

* Duplicate the plot by clicking the **Duplicate plot** button in the upper right controls (arrow 1)
* Open the **Axes** configuration option (arrow 2)
* Change the Sample on the duplicated image under *Misc* (arrow 3)

![](/files/Tz7gfm020wsjbblNxy42)

Each data point is a tissue spot. Duplicate and change the sample to view multiple samples.

## Visualize the annotated image from the Annotate Visium image task

If starting with unprocessed [fastq files](https://github.com/illumina-swi/partek-docs/blob/main/docs/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/start-with-10x-genomics-visium-fastq-files/README.md), the *Annotate Visium image* task will create a new result node, *Annotated counts*.

* Double click on the **Annotated counts** node to invoke the *Data Viewer* showing data points overlaid on top of the microscopy image
* Follow the steps outlined above by duplicating the image to visualize the multiple samples

## Modify Style

To modify the points on the image to show more of the background image use the Style configuration option.

* Press and hold Ctrl or Shift to select both plots
* Click **Style** in the left panel
* Move the *Opacity* slider to the left
* Change the *Point size* to 3

![](/files/xG233t7qoOB5aQedkg2Y)

* Click **Save** in the left panel and give the session an appropriate name

![](/files/2SOLWnaKsVabhA7v6KSq)

## Modify Axes

Modify the axes to remove the X and Y coordinates from the tissue image.

* Press and hold Ctrl or Shift to select both plots
* Click **Axes** in the left panel
* Toggle off *Show lines* for both the X & Y axis
* Toggle off *Show title* and *Show axis* for both the X & Y axis

![](/files/JXxRtnm1ZmR7GLyE5b8v)

## Color by gene expression and attributes

Style the image and color by normalized gene expression using three genes of interest.

* Press and hold Ctrl or Shift to select both plots
* Click **Style**
* Click the blue circle node ![image2023-12-12\_13-21-34](/files/2DpHsNhOrREG01GakzfU) to the right of the *Color by* drop-down
* Select the *Normalized counts* node as the source
* Choose to **Color by** *Numeric triad*
* Use the Green drop-down to select IL32, Red drop-down to select DES, and Blue drop-down to select PTGDS genes (type in name of gene in drop-down)
* Increase the *Point size* to 11

![](/files/wBRbbTvvFniasFd5wSNr)

To color by the [Cell attribute "Cell Type"](/partek/partek-flow/tutorials/10x-genomics-visium-spatial-data-analysis/spatial-data-analysis-steps.md#publish-cell-attributes-to-project) which we previously determined in this tutorial, use the **Color by** drop-down and select Cell Type. Cell type is a blue categorical attribute while green attributes are numerical.

![](/files/kuaLgswvMH9eYAze43Yj)

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.


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