Data exchange
QuPath is intended to make it easy to start to bring together different open source tools, and apply them to whole slide image analysis. The goal is to help researchers to use the best tool for the job when it comes to performing their analysis, and to help make use of code that they may already have that has been written for a different platform.
Sometimes this works by launching QuPath from within another application, sometimes by launching the other application from within QuPath. Also, the integration of some tools is at a more advanced (and useful) stage than others. This is something that ought to improve over time.
The following links outline the current situation and how to get started with a few common tools.
These docs are for QuPath ≤ v0.1.2.
For more up-to-date information, see https://qupath.readthedocs.io
- Video tutorials
- First steps
- Viewing images
- Drawing regions
- Counting cells
- Projects
- Multiple images
- Preferences
- Getting help
- Object-oriented analysis
- Types of object
- Object measurements
- Object classifications
- Object hierarchies
- Working with objects
- Workflows
- From workflows to scripts
- Writing custom scripts
- Advanced scripting with IntelliJ
- Scripting examples