microbeSEG models

Trained models that can be used for the software microbeSEG. The models were trained on a dataset consisting of 826 320x320 px crops extracted from the Omnipose dataset (bact_fluor train, bact_phase train), the microbeSEG dataset, and the Cell Tracking Challenge datasets BF-C2DL-HSC, BF-C2DL-MuSC, Fluo-N2DL-HeLa, and PhC-C2DL-PSC. The training dataset is also provided.

Mean AJI+ scores on a test dataset with 32 320x320 px crops:
    - boundary_model_adam: 0.769
    - boundary_model_ranger: 0.783
    - distance_model_adam: 0.802
    - distance_model_ranger: 0.835

When using these models, please cite (and check if pre-prints have meanwhile been published in a journal/conference):
    - microbeSEG,
    - our method,
    - Omnipose,
    - the latest Cell Tracking Challenge publication: current paper.

Omnipose data license: www.cellpose.org/dataset_omnipose

Usage

Just download all files into the directory published in the microbeSEG repository. The models can then be selected in the graphical user interface of microbeSEG.