MorphoDeep

MorphoDeep segments individual cells from grayscale 2D microscopy images or 3D volumes. It returns a label image with background value 0 and a distinct positive integer for each detected cell.

The package provides command line prediction, fine tuning on your own images, and napari widgets. The Python API is generated from the public code and its docstrings when this documentation is built.

Quick start

pip install morphodeep
morphodeep predict image.tif image_instances.tif --mode 2D

Model weights are separate from the Python distribution. See installation and weights before the first prediction.

The scripts used to make the paper figures, including figures/FineTuning/retrain.py, are research material in the source tree. They are not installed as the user fine tuning interface. Use morphodeep finetune or morphodeep.training.fine_tune for your own data.