Question: How can I estimate the number of tissue covered spots in my Visium sample? Can I use the Loupe Browser to do that?
Answer: Yes, you can use the Loupe Browser to estimate the number of tissue covered spots in your Visium sample. The manual image alignment tool will return the number of tissue covered spots.
For detailed instruction on how to use the Visium Manual Alignment Wizard please see our support site here. For a quick walk through on how to estimate the number of tissue covered spots please see below.
1. Open the alignment tool by clicking on the icon in the lower left corner of the Loupe Browser:
2. Follow the promptings from the Visium Manual Alignment Wizard to upload your image, align the fiducial spots, and identify the tissue:
3. Once you have used the lasso and brush tools to label the tissue, the number of spots that are labeled as tissue will be reported on the left panel:
In this example there are 3108 spots labeled as under the tissue. This number can then be used in the equation for calculating the number of reads you should sequence described in the Visium Sequencing Requirements document.
Product: Visium, Visium for FFPE