View tissue images

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

• Visualize the annotated image from the Annotate Visium image task

• Modify Style

• Modify Axes

• 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.

• 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, forming a visual representation of your analysis pipeline.

• Click the Spatial report node

• Click Task report on the task menu

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)

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, 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

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

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

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 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

To color by the Cell attribute "Cell Type" 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.

Additional Assistance

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