Obtain and add files to the project

The sample used for this tutorial can be found in the 10x Genomics Datasets. We will use the Control, replicate 1 mouse brain sample which can found here. 

• Choose the 10x Genomics Visium fastq import format
• Click Next

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 fastq files should match. 

The fastq files will be imported into the project as a unaligned reads node. 

Pre-processing the unaligned fastq files

The unaligned reads must be preprocessed before proceeding with the analysis steps covered here: Spatial data analysis. 

• 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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