@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},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{stardist_schmidt2018,
  author    = {Uwe Schmidt and
               Martin Weigert and
               Coleman Broaddus and
               Gene Myers},
  title     = {Cell Detection with Star-convex Polygons},
  journal   = {CoRR},
  volume    = {abs/1806.03535},
  year      = {2018}
}
@article{stardist3d_weigert2019,
  author =       {Martin Weigert and Uwe Schmidt and Robert Haase and
                  Ko Sugawara and Gene Myers},
  title =        {Star-convex Polyhedra for 3D Object Detection and
                  Segmentation in Microscopy},
  journal =      {arXiv:1908.03636},
  year =         2019
}


@InProceedings{unet_ronneberger2015,
  author       = "O. Ronneberger and P.Fischer and T. Brox",
  title        = "U-Net: Convolutional Networks for Biomedical Image Segmentation",
  booktitle    = "Medical Image Computing and Computer-Assisted Intervention (MICCAI)",
  series       = "LNCS",
  volume       = "9351",
  pages        = "234--241",
  year         = "2015",
  publisher    = "Springer",
  note         = "(available on arXiv:1505.04597 [cs.CV])",
  url          = "http://lmb.informatik.uni-freiburg.de/Publications/2015/RFB15a"
}

@article{deepws_bai2016,
  author    = {Min Bai and
               Raquel Urtasun},
  title     = {Deep Watershed Transform for Instance Segmentation},
  journal   = {CoRR},
  volume    = {abs/1611.08303},
  year      = {2016}
}

@inproceedings{chen2016dcan,
  title={DCAN: deep contour-aware networks for accurate gland segmentation},
  author={Chen, Hao and Qi, Xiaojuan and Yu, Lequan and Heng, Pheng-Ann},
  booktitle={Proceedings of the IEEE conference on Computer Vision and Pattern Recognition},
  pages={2487--2496},
  year={2016}
}

@inproceedings{guerrero2018multiclass,
  title={Multiclass weighted loss for instance segmentation of cluttered cells},
  author={Guerrero-Pena, Fidel A and Fernandez, Pedro D Marrero and Ren, Tsang Ing and Yui, Mary and Rothenberg, Ellen and Cunha, Alexandre},
  booktitle={2018 25th IEEE International Conference on Image Processing (ICIP)},
  pages={2451--2455},
  year={2018},
  organization={IEEE}
}

@inproceedings{heinrich2018synaptic,
  title={Synaptic cleft segmentation in non-isotropic volume electron microscopy of the complete drosophila brain},
  author={Heinrich, Larissa and Funke, Jan and Pape, Constantin and Nunez-Iglesias, Juan and Saalfeld, Stephan},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={317--325},
  year={2018},
  organization={Springer}
}

@article{funke2018large,
  title={Large scale image segmentation with structured loss based deep learning for connectome reconstruction},
  author={Funke, Jan and Tschopp, Fabian David and Grisaitis, William and Sheridan, Arlo and Singh, Chandan and Saalfeld, Stephan and Turaga, Srinivas C},
  journal={IEEE transactions on pattern analysis and machine intelligence},
  year={2018},
  publisher={IEEE}
}

@inproceedings{funke2018benchmark,
  title={A benchmark for epithelial cell tracking},
  author={Funke, Jan and Mais, Lisa and Champion, Andrew and Dye, Natalie and Kainmueller, Dagmar},
  booktitle={European Conference on Computer Vision},
  pages={437--445},
  year={2018},
  organization={Springer}
}

@article{long20093d,
  title={A 3D digital atlas of C. elegans and its application to single-cell analyses},
  author={Long, Fuhui and Peng, Hanchuan and Liu, Xiao and Kim, Stuart K and Myers, Eugene},
  journal={Nature methods},
  volume={6},
  number={9},
  pages={667},
  year={2009},
  publisher={Nature Publishing Group}
}

@article{caicedo2019evaluation,
  title={Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images},
  author={Caicedo, Juan C and Roth, Jonathan and Goodman, Allen and Becker, Tim and Karhohs, Kyle W and Broisin, Matthieu and Csaba, Molnar and McQuin, Claire and Singh, Shantanu and Theis, Fabian and Carpenter, Anne},
  journal={BioRxiv},
  pages={335216},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

@inproceedings{zhao2018deep,
  title={Deep Learning Based Instance Segmentation in 3D Biomedical Images Using Weak Annotation},
  author={Zhao, Zhuo and Yang, Lin and Zheng, Hao and Guldner, Ian H and Zhang, Siyuan and Chen, Danny Z},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={352--360},
  year={2018},
  organization={Springer}
}

@article{hollandi2019deep,
  title={A deep learning framework for nucleus segmentation using image style transfer},
  author={Hollandi, Reka and Szkalisity, Abel and Toth, Timea and Tasnadi, Ervin and Molnar, Csaba and Mathe, Botond and Grexa, Istvan and Molnar, Jozsef and Balind, Arpad and Gorbe, Mate and others},
  journal={bioRxiv},
  pages={580605},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

@inproceedings{he2017mask,
  title={Mask r-cnn},
  author={He, Kaiming and Gkioxari, Georgia and Doll{\'a}r, Piotr and Girshick, Ross},
  booktitle={Proceedings of the IEEE international conference on computer vision},
  pages={2961--2969},
  year={2017}
}

@article{falk2019u,
  title={U-Net: deep learning for cell counting, detection, and morphometry},
  author={Falk, Thorsten and Mai, Dominic and Bensch, Robert and {\c{C}}i{\c{c}}ek, {\"O}zg{\"u}n and Abdulkadir, Ahmed and Marrakchi, Yassine and B{\"o}hm, Anton and Deubner, Jan and J{\"a}ckel, Zoe and Seiwald, Katharina and others},
  journal={Nature methods},
  volume={16},
  number={1},
  pages={67},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{hofener2018deep,
  title={Deep learning nuclei detection: A simple approach can deliver state-of-the-art results},
  author={H{\"o}fener, Henning and Homeyer, Andr{\'e} and Weiss, Nick and Molin, Jesper and Lundstr{\"o}m, Claes F and Hahn, Horst K},
  journal={Computerized Medical Imaging and Graphics},
  volume={70},
  pages={43--52},
  year={2018},
  publisher={Elsevier}
}

@article{ljosa2012annotated,
  title={Annotated high-throughput microscopy image sets for validation.},
  author={Ljosa, Vebjorn and Sokolnicki, Katherine L and Carpenter, Anne E},
  journal={Nature methods},
  volume={9},
  number={7},
  pages={637--637},
  year={2012},
  publisher={NIH Public Access}
}

@article{kingma2014adam,
  title={Adam: A method for stochastic optimization},
  author={Kingma, Diederik P and Ba, Jimmy},
  journal={arXiv preprint arXiv:1412.6980},
  year={2014}
}

@INPROCEEDINGS{fowlkes_aff03,
  author =       {C. {Fowlkes} and D. {Martin} and J. {Malik}},
  booktitle =    {2003 IEEE Computer Society Conference on Computer
                  Vision and Pattern Recognition, 2003. Proceedings.},
  title =        {Learning affinity functions for image segmentation:
                  combining patch-based and gradient-based approaches},
  year =         2003,
  volume =       2,
  pages =        {II-54},
  doi =          {10.1109/CVPR.2003.1211452},
  ISSN =         {1063-6919},
  month =        {June},
}

@article{mahotas,
  author =       {Luis Pedro Coelho},
  title =        {Mahotas: Open source software for scriptable
                  computer vision},
  journal =      {Journal of Open Research Software},
  year =         2013,
  doi =          {http://dx.doi.org/10.5334/jors.ac},
  month =        {July},
  volume =       1
}

@misc{napari,
  author =        {napari contributors},
  title =        {napari: a multi-dimensional image viewer for python},
  year =         2019,
  url =          {https://github.com/napari/napari},
  doi =          {10.5281/zenodo.3555620},
}

@INPROCEEDINGS{li18_pixel_offset_reg,
  author =       {Y. {Li} and X. {Bian} and M. {Chang} and L. {Wen}
                  and S. {Lyu}},
  booktitle =    {2018 15th IEEE International Conference on Advanced
                  Video and Signal Based Surveillance (AVSS)},
  title =        {Pixel Offset Regression (POR) for Single-shot
                  Instance Segmentation},
  year =         2018,
  pages =        {1-6},
  doi =          {10.1109/AVSS.2018.8639428},
  ISSN =         {null},
  month =        {Nov},
}

@article{hirsch20_patch_instan_segmen,
  author =       {Hirsch, Peter and Mais, Lisa and Kainmueller,
                  Dagmar},
  title =        {Patch{P}er{P}ix for Instance Segmentation},
  journal =      {CoRR},
  year =         2020,
  url =          {http://arxiv.org/abs/2001.07626v1},
  archivePrefix ={arXiv},
  eprint =       {2001.07626},
  primaryClass = {cs.CV},
}

@InProceedings{cicek16_3d_unet,
  author =       "{\c{C}}i{\c{c}}ek, {\"O}zg{\"u}n and Abdulkadir,
                  Ahmed and Lienkamp, Soeren S.  and Brox, Thomas and
                  Ronneberger, Olaf",
  editor =       "Ourselin, Sebastien and Joskowicz, Leo and Sabuncu,
                  Mert R.  and Unal, Gozde and Wells, William",
  title =        "3D U-Net: Learning Dense Volumetric Segmentation
                  from Sparse Annotation",
  booktitle =    "Medical Image Computing and Computer-Assisted
                  Intervention -- MICCAI 2016",
  year =         2016,
  publisher =    "Springer International Publishing",
  address =      "Cham",
  pages =        "424--432",
  isbn =         "978-3-319-46723-8"
}

@InProceedings{xie15_deep_votin_a_robus_appro_towar_nucle_local_in_micro_image,
  author =       "Xie, Yuanpu and Kong, Xiangfei and Xing, Fuyong and
                  Liu, Fujun and Su, Hai and Yang, Lin",
  editor =       "Navab, Nassir and Hornegger, Joachim and Wells,
                  William M.  and Frangi, Alejandro F.",
  title =        "Deep Voting: A Robust Approach Toward Nucleus
                  Localization in Microscopy Images",
  booktitle =    "Medical Image Computing and Computer-Assisted
                  Intervention -- MICCAI 2015",
  year =         2015,
  publisher =    "Springer International Publishing",
  address =      "Cham",
  pages =        "374--382",
  isbn =         "978-3-319-24574-4"
}
