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If you have not transferred files to the server already, click 
More details here.
- Select the fastq files in the upload folder used for file transfer
- Click Finish
The prefix used for R1 and R2 files should match.
Pre-processing the unaligned fastq files
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- From the unaligned reads node, select Space Ranger from the 10x Genomics drop-down in the toolbox. For more information about Space Ranger click here.
Annotate Visium image
To run Annotate cells:
- Click a Single cell counts data node
- Click the Pre-analysis tools section in the toolbox
- Click Annotate Visium image
You will be prompted to pick a Spatial image file for each sample you want to annotate (Figure 2).
Figure 2. Select the zipped image folder for each sample. The image zip file should contains 6 files including image files and tissue position text file with a scale factor json file
- Click Finish
A new data node, Annotated counts, will be generated (Figure 3).
Figure 3. Output of annotate counts
When the task report of the annotated counts node is opened (or double click on the Annotated counts node), the images will be displayed in data viewer (Figure 4)
Figure 4. Tissue image displayed in data viewer
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