Using InstanSeg in QuPath

InstanSeg has its own extension for QuPath, so you can segment images without writing any code. Because the whole InstanSeg model, including postprocessing, compiles to TorchScript, the extension runs it directly inside QuPath without Python.

InstanSeg is included in recent QuPath releases. The source code of the extension is in the qupath-extension-instanseg repository.

GeoJSON files saved by InstanSeg in Python (see Running inference) can also be imported into QuPath.