Tutorials

• Automatic H&E alignment
  • Align H&E with Visium data
  • Align H&E with Seq-scope data
• Manual H&E alignment
  • Before you begin
  • Step 1 - generate an expression image
  • Step 2 - load images into Fiji
  • Step 3 - select corresponding points
  • Step 4 - align the images
  • Step 5 - attach the aligned image
• Processing a custom single-cell sample
  • Step 1: install and initialize spacemake
  • Step 2: download test data
  • Step 3: add a new species
  • Step 4: add a new barcode_flavor
  • Step 5: add a new run_mode
  • Step 6: add the sample
  • Step 7: runn spacemake
  • Step 8: results
• Longreads Integration
  • Building blocks and Signatures
  • What happens?
  • A nanopre example
  • Graphical reports
    • Library overview plot
    • Oligo alignment quality plot
    • Histograms
• Single-cell data integration with novosparc
  • Reconstructing a tissue de-novo with novosparc
  • Mapping single cell data onto spatial data using novosparc