Overview
Here’s an overview of the general concepts in QuPath:
Your images may (and probably should) be organized in a
Project
Each image in the project is represented by a
ProjectImageEntry
When you open a
ProjectImageEntry
, you get anImageData
displayed in the viewerThe
ImageData
stores a few things, including:The
ImageType
(e.g. Brightfield, Fluorescence)Any
ColorDeconvolutionStains
required (if brightfield)An
ImageServer
, for accessing pixels and metadataA
PathObjectHierarchy
, containingPathObjects
in a tree-like structureEach
PathObject
contains aROI
and aMeasurementList
When you analyze an image in QuPath, you take your ImageData
, access pixels from the ImageServer
and try to represent what the image contains in the PathObjectHierarchy
.
Then you query the object hierarchy to extract some kind of summary measurements.