...

Visualize the annotated image from the automatically generated Spatial report task

With the pre-processed samples imported, we can begin analysis.

...

For now, the Analyses tab has only a singlestarting node, a circular node , called Single cell counts . As you perform the analysisand 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. A Spatial report task result node (rectangle) is automatically generated for this type of data. 

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

...

Visualize the annotated image from the Annotate Visium image task

If starting with with unprocessed fastq files, the Annotate Visium image task will create a new result node, Annotated counts. 

...

• 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. 

...

To color by the Cell attribute "Cell Type"  we  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. 

Image Added

...