This repository serves as as a platform to facilitate researchers to reuse the methods of the Cell Tracking Challenge in an easy and direct way.
It contains Colab Notebooks to reproduce the training and inference of the following contestants, that were presented in the 2021 edition:
Respective links to the contestant's repositories are here, together with the repositories of other teams that already prepared their submission for reusability and created their own Colab notebooks.
- BGU-IL (5): https://github.com/talbenha/cell-tracker-gnn
- DKFZ-GE: https://github.com/MIC-DKFZ/nnUNet
- IGFL-FR (*): https://github.com/ksugar/CTC-IGFL-FR
- KIT-GE (3):https://git.scc.kit.edu/KIT-Sch-GE/2021_segmentation
- KIT-GE (4): https://git.scc.kit.edu/kit-loe-ge/embedtrack
- KTH-SE (1*): https://github.com/klasma/BaxterAlgorithms/tree/ctc2021
- MU-CZ (2*): https://gitlab.fi.muni.cz/xlux/deepwater
- MU-US (4*): https://github.com/CIVA-Lab/U-SE-ResNet-for-Cell-Tracking-Challenge
- PURD-US (*): https://github.com/westgate458/XB-Net
- MU-US (3*): https://github.com/CIVA-Lab/DMNet_Rina/
Notebooks for CALT-US (), MU-US (4**), PURD-US and MU-CZ (2**) created by Estibaliz Gómez de Mariscal. Notebook for DKFZ-GE created by Pablo Delgado Rodríguez*
If you experience any issue while using the notebooks provided here, please, open a GitHub issue.
If you find this work useful for your research, please do not forget citing the work representing the chosen method and the Cell Tracking Challenge paper:
@article{ulman2017objective,
title={An objective comparison of cell-tracking algorithms},
author={Ulman, Vladim{\'\i}r and Ma{\v{s}}ka, Martin and Magnusson, Klas EG and Ronneberger, Olaf and Haubold, Carsten and Harder, Nathalie and Matula, Pavel and Matula, Petr and Svoboda, David and Radojevic, Miroslav and others},
journal={Nature methods},
volume={14},
number={12},
pages={1141--1152},
year={2017},
publisher={Nature Publishing Group}
}