Tutorials

• Projects
  • Create a project
  • Working with projects
• Separating stains
  • Fluorescence images
  • Brightfield images
• Detecting tissue
  • Thresholders in QuPath
  • Thresholds in action
  • Adjusting parameters
  • Saving your thresholder
  • Creating objects
• Measuring areas
  • Define the region of interest
  • Threshold stained areas
  • Viewing measurements
  • Generating results
• Cell detection
  • Annotate a region of interest
  • Run Positive cell detection
  • View cell-by-cell results
  • Analyze additional annotations
  • View results
• Cell classification
  • Annotate the main region of interest
  • Run Cell detection command
  • View cell measurements (if you want)
  • Calculate additional features
  • Annotate regions containing different cell types
  • Train a cell classifier based on annotations
  • Save the classifier
  • Apply intensity classification
  • View the results
• Exporting measurements
  • Via the measurement table
  • Via the Measurement Exporter
  • Via scripting
• Multiplexed analysis
  • Before we begin…
  • Detect & measure cells
  • Create a classifier for each marker
  • Combine the classifiers
• Pixel classification
  • Stained areas (again)
  • More complex classifications
  • Handling variation
• Superpixels
  • Generating superpixels
  • Adding features
  • Training a classifier
  • Merging tiles