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Overview

• Data description

Image analysis

• Processing images - from images to intensities

• Image inspection
  • Inspect images with multiple nuclei
  • Inspect images with no nucleus
• Image intensities
  • CONFESS results
  • QC analysis including no. nuclei detected, DAPI, and intensity variation
  • Explore using log10 sum pixel intensity for signal metrics
  • Compare correction approaches using median versus mean background
• Shape metrics
  • Nucleus shape metrics versus intensities
• Normalize intensities by batch
  • Visualize signal variation by plate and individual identity
  • Visualize the structure of signal variation by individual identity
  • Quantile normalization for GFP, RFP and DAPI
• Fitting cellcycleR
  • Parametric model across plates and individuals
  • Model convergence assessment
• transgene count in sequencing data
  • Investigate zero-count transgenes

cell cycle genes

QC

• Sample QC and filtering
  • Sample QC criteria
    
  • Sequencing depth
    
  • Reads versus molecules
• Gene QC and filtering
  • gene filtering