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The result of Space Ranger task is the Single cell counts data node, which contains the gene expression data. Double click the Single cell counts node to invoke the report the task report (Figure 76) which is the same as the ‘Summary HTML’ from Space Ranger output. Task report is sample based. You can use the dropdown list in top left to switch samples (not shown in Figure 6).  Each report consists of two pages: Summary and Analysis. For deatails, please visit 10x Genomics web page.

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Annotate Visium image

After creating the Single cell counts node, the next step is to associate the microscopy image image with the expression data. To start, select the Single cell counts data node and then go to Annotate Visium image in the toolbox (Figure 7). 

The setup page shows the sample table (one sample per row; Figure 8). Click on the Browse button to open the file browser and point to the file <project-name>_spatial.zip, created by the Space Ranger task. After that, click on Finish to launch the Annotate task.  

You can find the location of the <project-name>_spatial.zip file using the following seps. Selcte the Space Ranger task node (i.e. the rectangle) and then click on the Task Details (toolbox). Click on the Output files link to open the page with the list of files created by the Space Ranger task. Mouse over any of the files to see the directory in which the file is located. Figure 9 shows the path to the .zip file which is required for Annotate Visium image.