Software
Software for the Visium Solution
- Fiducial frame is not visible in the IF image
- Testing microscope image compatibility with Space Ranger
- How do I know if I used the correct image?
- How can I change spaceranger filtering for FFPE probes?
- Is my gene in the Visium for FFPE probe set?
- Do misprinted fiducial frame spots affect the performance of automated image alignment?
- The fiducials are misaligned in my web summary — how can I fix this?
- How can I transfer pathologist annotations to Loupe Browser?
- TinyImageError: My image resolution is too low for Space Ranger. How can I fix it?
- Why is my Space Ranger run failing with manual alignment?
- Can I aggregate data from different samples or staining protocols using spaceranger aggr?
- How can I convert the feature-barcode matrix from Space Ranger 1.x to a CSV file?
- Can I manually mark spots covered by tissue in my Visium experiment?
- Where can I find the Space Ranger barcode whitelist and their coordinates on the slide?
- How do I use the Loupe Browser to estimate the number of tissue covered spots in my Visium sample?
- How can I demultiplex my data if I sequenced 8bp of the index reads instead of 10bp?
- How much of the fiducial frame needs to be left uncovered for the automatic image alignment to work in Space Ranger?
- Can Space Ranger and Loupe be used to analyze data from the product developed by Spatial Transcriptomics before 10x acquired it?