Segmentation with nnInteractive

nnInteractive is an automated segmentation tool

https://github.com/MIC-DKFZ/napari-nninteractive?tab=readme-ov-file

https://arxiv.org/abs/2503.08373

The nnInteractive napari plugin is pre-installed on the maxwell cluster, so users do not need their own installation. To start Napari, use:

module load maxwell napari

napari -w napari-nninteractive

Start loading your image stack, e.g. via file-> open files as stack

After the stack is loaded, you can first need to click Initialize on the right side.

Then you can select a specific object, e.g. by selecting the point interaction tool, each time you click in the image, the selection is refined, also in the adjacent slices. The tool is designed to select single, interconnected objects. If you need to select a second object, click on “Next Object” and it will create a new layer for the second object. The different layers can be saved by using the export button on the lower right.

More details on how to use the plugin can be found in the arxiv paper.