petebankhead/qupath-extension-bioimageio

A QuPath extension for working with the Bioimage Model Zoo (https://bioimage.io)

QuPath Bioimage Model Zoo extension

This is a QuPath extension for working with the Bioimage Model Zoo (https://bioimage.io).

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

1. not all models are Java-friendly, and
2. 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.