QuPath
0.2
Contents:
Introduction
Getting started
Tutorials
Projects
Separating stains
Detecting tissue
Measuring areas
Cell detection
Cell classification
Exporting measurements
Multiplexed analysis
Pixel classification
Superpixels
Concepts
Advanced
Scripting
Reference
QuPath
Docs
»
Tutorials
Edit on GitHub
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
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v: 0.2
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