pyMarAI: nnU-Net-based Tumor Spheroids Auto Delineation

Collection of neural network models for automatic image segmentation of microscopic tumor spheroids. Intended to be used with nnU-Net deep-learning framework. Trained and tested on a total of microscopic images of mouse pheochromocytoma (MPC) tumor cells. In addition to the trained network model, a PyQt5-based graphical user interface tool is provided. This tool provides a complete pipeline for handling microscopic spheroid image data, running deep-learning–based delineation, and curating results for continuous model improvement. For installation and usage instructions, please visit https://github.com/hzdr-MedImaging/pyMarAI Please cite nnU-Net and the respective paper when using pyMarAI. List of available model types: pyMarAI-1.0.0-ecat.zip: nnUNetv2 ready network (for ECAT7) pyMarAI-1.0.0-nifti.zip: nnUNetv2 ready network (for NIFTI)