Quantitative Pathology & BioImage Analysis: QuPath

• Site Web de QuPath
• Documentation en ligne
• QuPath - [NEUBIASAcademy@Home] Webinar
• QuPath Workshop From Samples to Knowledge 2020 - Day 1
• QuPath Workshop From Samples to Knowledge 2020 - Day 2

• QuPath in 5 minutes
• QuPath for H&E
• QuPath for Ki67

QuPath tutorial #2 - IHC analysis

• 1 - Introduction to QuPath for IHC analysis
• 2 - Setting stain vectors
• 3 - Command List
• 4 - Cell detection vs Positive cell detection
• 5 - Choosing the detection image
• 6 - Requested pixel size
• 7 - Thresholds and background
• 8 - Smoothing and fragmented nuclei
• 9 - Cell size filters
• 10 - Avoiding tissue folds
• 11 - Split by shape
• 12 - Avoiding non nuclear staining
• 13 - Cell expansion
• 14 - Other cell detection parameters
• 15 - Recovering parameters from the Workflow history
• 16 - Local measurements and the object hierarchy
• 17 - A click too far
• 18 - Learning lessons or not
• 19 - Measurement maps
• 20 - Displaying cells
• 21 - Smoothed measurements
• 22 - Training a cell classifier
• 23 - More classifier suggestions
• 24 - Toggle displaying classes
• 25 - Revisiting past mistakes
• 26 Applying intensity classifications
• 27 - Finishing one image
• 28 - Scripting the analysis
• 29 - Remembering to select
• 30 - Batch processing
• 31 - Simple tissue detection
• 32 - Finishing up