This is a QuPath extension for working with the Bioimage Model Zoo (https://bioimage.io).
You can download the .jar file from qupath-extension-bioimageio-0.1.0.jar
It's early and experimental - subject to change in later releases.
The main aim is to enable models kept in the Zoo to be imported into some QuPath-friendly form.
Currently, this extension adds a command to create pixel classifers from supported models:
- Extensions → Bioimage Model Zoo → Create pixel classifier (Bioimage Model Zoo)
Along the way, it adds some extra flexibility: choosing the resolution at which the model is applied, and adapting the input channels and output classifications.
Only a subset of models are currently supported, partly because
- not all models are Java-friendly, and
- some models require accessing all the pixels in the image... but QuPath is designed for huge images, and doesn't easily support these kinds of global calculations yet
As a result, applying the model in QuPath can sometimes give a different result to applying it in other software. The goal is to improve this in future releases.
