A typical Visium data analysis pipeline

A basic example of a spatial data analysis is outlined below. 

Performing tasks in the Analyses tab

A context-sensitive menu will appear on the right side of the pipeline. Use the drop-downs in the toolbox to open available tasks for the selected data node. 

An important step in analyzing single cell RNA-Seq data is to filter out low-quality cells. A few examples of low-quality cells are doublets, cells damaged during cell isolation, or cells with too few counts to be analyzed. Click here for more information on Single cell QA/QC. We will not perform Single cell QA/QC in this tutorial. 

Filter Features

• Click the Filtering drop-down in the toolbox
• Click the Filter Features task 
• Choose Noise reduction
• Exclude features where value <= 0.0 in at least 99.0% of the cells 
• Click Finish

A task node, Filtered counts, is produced. Initially, the node will be semi-transparent to indicate that it has been queued, but not completed. A progress bar will appear on the Filter features task node to indicate that the task is running.

Normalization

• Select the Filtered Counts result node
• Choose the Normalization task from the toolbox 

• Click Use recommended  
• Click Finish

Exploratory analysis

• Click the Normalized counts results node
• Select the PCA task under Exploratory analysis in the toolbox
• Unselect Split by Sample
• Click Finish

• Click the PCA result node
• Select the Graph-based clustering task 
• Click Finish

• Click the Graph-based clustering result node
• Select the UMAP task
• Click Finish

Statistics