Napari plugin

Install morphodeep[napari] and start napari:

napari

Open the MorphoDeep plugin from napari's Plugins menu. Predict instances works on the selected image layer and adds an instance labels layer. Choose the dimension, model patch size, tiling option, and, for volumes, the voxel spacing. To use your own model, select a local weights file.

Fine tune model asks for separate image and instance mask directories, an output directory, and optional validation directories and initial weights. It trains in the background. Once it finishes, use the reported best weights in the prediction widget.

See fine tuning for input format and output files.