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  1. 10X Genomics
  2. Visium
  3. Software

Software

Software for the Visium Solution

  • Visium CNV calling
  • 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?
  • 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?
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