@article{chandrasekaran2024three,
  title={Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations},
  author={Chandrasekaran, Srinivas Niranj and Cimini, Beth A and Goodale, Amy and Miller, Lisa and Kost-Alimova, Maria and Jamali, Nasim and Doench, John G and Fritchman, Briana and Skepner, Adam and Melanson, Michelle and others},
  journal={Nature Methods},
  volume={21},
  number={6},
  pages={1114--1121},
  year={2024},
  url={https://doi.org/10.1038/s41592-024-02241-6}
}

@article{lange2024multimodal,
  title={A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors},
  author={Lange, Merlin and Granados, Alejandro and VijayKumar, Shruthi and Bragantini, Jord{\~a}o and Ancheta, Sarah and Kim, Yang-Joon and Santhosh, Sreejith and Borja, Michael and Kobayashi, Hirofumi and McGeever, Erin and others},
  journal={Cell},
  volume={187},
  number={23},
  pages={6742--6759},
  year={2024},
  publisher={Elsevier},
  url={https://doi.org/10.1016/j.cell.2024.09.047}
}

@article{cellpose,
  title={Cellpose: a generalist algorithm for cellular segmentation},
  author={Stringer, Carsen and Wang, Tim and Michaelos, Michalis and Pachitariu, Marius},
  journal={Nature Methods},
  volume={18},
  number={1},
  pages={100--106},
  year={2021},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41592-020-01018-x}
}

@inproceedings{stardist,
  title={Cell detection with star-convex polygons},
  author={Schmidt, Uwe and Weigert, Martin and Broaddus, Coleman and Myers, Gene},
  booktitle={International conference on medical image computing and computer-assisted intervention},
  pages={265--273},
  year={2018},
  organization={Springer},
  url={https://doi.org/10.1007/978-3-030-00934-2_30}
}

@article{hovernet,
  title={Hover-net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images},
  author={Graham, Simon and Vu, Quoc Dang and Raza, Shan E Ahmed and Azam, Ayesha and Tsang, Yee Wah and Kwak, Jin Tae and Rajpoot, Nasir},
  journal={Medical image analysis},
  volume={58},
  pages={101563},
  year={2019},
  publisher={Elsevier},
  url={https://doi.org/10.1016/j.media.2019.101563}
}

@article{mitonet,
  title={Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset},
  author={Conrad, Ryan and Narayan, Kedar},
  journal={Cell Systems},
  volume={14},
  number={1},
  pages={58--71},
  year={2023},
  publisher={Elsevier},
  url={https://doi.org/10.1016/j.cels.2022.12.006}
}

@article{synapsenet,
  title={SynapseNet: deep learning for automatic synapse reconstruction},
  author={Muth, Sarah and Moschref, Frederieke and Freckmann, Luca and Mutschall, Sophia and Hojas-Garcia-Plaza, Ines and Bahr, Julius N and Petrovic, Arsen and Do, Thanh Thao and Schwarze, Valentin and Archit, Anwai and others},
  journal={Molecular Biology of the Cell},
  volume={36},
  number={10},
  pages={ar127},
  year={2025},
  publisher={The American Society for Cell Biology},
  url={https://doi.org/10.1091/mbc.E24-11-0519}
}

@article{bioimageio,
  title={Bioimage model zoo: a community-driven resource for accessible deep learning in bioimage analysis},
  author={Ouyang, Wei and Beuttenmueller, Fynn and G{\'o}mez-de-Mariscal, Estibaliz and Pape, Constantin and Burke, Tom and Garcia-L{\'o}pez-de-Haro, Carlos and Russell, Craig and Moya-Sans, Luc{\'\i}a and De-La-Torre-Guti{\'e}rrez, Cristina and Schmidt, Deborah and others},
  journal={BioRxiv},
  pages={2022--06},
  year={2022},
  publisher={Cold Spring Harbor Laboratory},
  url={https://doi.org/10.1101/2022.06.07.495102}
}

@article{deepimagej,
  title={DeepImageJ: A user-friendly environment to run deep learning models in ImageJ},
  author={G{\'o}mez-de-Mariscal, Estibaliz and Garc{\'\i}a-L{\'o}pez-de-Haro, Carlos and Ouyang, Wei and Donati, Laur{\`e}ne and Lundberg, Emma and Unser, Michael and Mu{\~n}oz-Barrutia, Arrate and Sage, Daniel},
  journal={Nature Methods},
  volume={18},
  number={10},
  pages={1192--1195},
  year={2021},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41592-021-01262-9}
}

@article{ilastik,
  title={Ilastik: interactive machine learning for (bio) image analysis},
  author={Berg, Stuart and Kutra, Dominik and Kroeger, Thorben and Straehle, Christoph N and Kausler, Bernhard X and Haubold, Carsten and Schiegg, Martin and Ales, Janez and Beier, Thorsten and Rudy, Markus and others},
  journal={Nature Methods},
  volume={16},
  number={12},
  pages={1226--1232},
  year={2019},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41592-019-0582-9}
}

@article{micro-sam,
  title={Segment anything for microscopy},
  author={Archit, Anwai and Freckmann, Luca and Nair, Sushmita and Khalid, Nabeel and Hilt, Paul and Rajashekar, Vikas and Freitag, Marei and Teuber, Carolin and Spitzner, Melanie and Tapia Contreras, Constanza and others},
  journal={Nature Methods},
  volume={22},
  number={3},
  pages={579--591},
  year={2025},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41592-024-02580-4}
}

@article{cellpose-sam,
  title={Cellpose-SAM: superhuman generalization for cellular segmentation},
  author={Pachitariu, Marius and Rariden, Michael and Stringer, Carsen},
  journal={bioRxiv},
  pages={2025--04},
  year={2025},
  publisher={Cold Spring Harbor Laboratory},
  url={https://doi.org/10.1101/2025.04.28.651001}
}

@article{cell-sam,
  title = {CellSAM: a foundation model for cell segmentation},
  author = {Marks,  Markus and Israel,  Uriah and Dilip,  Rohit and Li,  Qilin and Yu,  Changhua and Laubscher,  Emily and Iqbal,  Ahamed and Pradhan,  Elora and Ates,  Ada and Abt,  Martin and Brown,  Caitlin and Pao,  Edward and Li,  Shenyi and Pearson-Goulart,  Alexander and Perona,  Pietro and Gkioxari,  Georgia and Barnowski,  Ross and Yue,  Yisong and Van Valen,  David},
  journal = {Nature Methods},
  volume = {22},
  number = {12},
  pages = {2585–2593},
  year = {2025},
  url = {http://doi.org/10.1038/s41592-025-02879-w},
}

@article{cell-vit,
  title={Cellvit: Vision transformers for precise cell segmentation and classification},
  author={H{\"o}rst, Fabian and Rempe, Moritz and Heine, Lukas and Seibold, Constantin and Keyl, Julius and Baldini, Giulia and Ugurel, Selma and Siveke, Jens and Gr{\"u}nwald, Barbara and Egger, Jan and others},
  journal={Medical Image Analysis},
  volume={94},
  pages={103143},
  year={2024},
  publisher={Elsevier},
  url={https://doi.org/10.1016/j.media.2024.103143}
}

@inproceedings{patho-sam,
    title={Segment Anything for Histopathology},
    author={Titus Griebel and Anwai Archit and Constantin Pape},
    booktitle={Medical Imaging with Deep Learning},
    year={2025},
    url={https://openreview.net/forum?id=EWGV97ESaP}
}

@InProceedings{SAM,
    author = {Kirillov, Alexander and Mintun, Eric and Ravi, Nikhila and Mao, Hanzi and Rolland, Chloe and Gustafson, Laura and Xiao, Tete and Whitehead, Spencer and Berg, Alexander C. and Lo, Wan-Yen and Dollar, Piotr and Girshick, Ross},
    title = {Segment Anything},
    booktitle = {Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV)},
    month = {October},
    year = {2023},
    pages = {4015-4026},
    url = {https://openaccess.thecvf.com/content/ICCV2023/html/Kirillov_Segment_Anything_ICCV_2023_paper.html}
}

@inproceedings{SAM2,
    title={{SAM} 2: Segment Anything in Images and Videos},
    author={Nikhila Ravi and Valentin Gabeur and Yuan-Ting Hu and Ronghang Hu and Chaitanya Ryali and Tengyu Ma and Haitham Khedr and Roman R{\"a}dle and Chloe Rolland and Laura Gustafson and Eric Mintun and Junting Pan and Kalyan Vasudev Alwala and Nicolas Carion and Chao-Yuan Wu and Ross Girshick and Piotr Dollar and Christoph Feichtenhofer},
    booktitle={The Thirteenth International Conference on Learning Representations},
    year={2025},
    url={https://openreview.net/forum?id=Ha6RTeWMd0}
}

@article{SAM3,
  title={Sam 3: Segment anything with concepts},
  author={Carion, Nicolas and Gustafson, Laura and Hu, Yuan-Ting and Debnath, Shoubhik and Hu, Ronghang and Suris, Didac and Ryali, Chaitanya and Alwala, Kalyan Vasudev and Khedr, Haitham and Huang, Andrew and others},
  journal={arXiv preprint},
  year={2025},
  url={https://doi.org/10.48550/arXiv.2511.16719}
}

@article{gpt3,
  title={Language models are few-shot learners},
  author={Brown, Tom and Mann, Benjamin and Ryder, Nick and Subbiah, Melanie and Kaplan, Jared D and Dhariwal, Prafulla and Neelakantan, Arvind and Shyam, Pranav and Sastry, Girish and Askell, Amanda and others},
  journal={Advances in neural information processing systems},
  volume={33},
  pages={1877--1901},
  year={2020},
  url={https://papers.nips.cc/paper/2020/hash/1457c0d6bfcb4967418bfb8ac142f64a-Abstract.html}
}

@inproceedings{clip,
  title={Learning transferable visual models from natural language supervision},
  author={Radford, Alec and Kim, Jong Wook and Hallacy, Chris and Ramesh, Aditya and Goh, Gabriel and Agarwal, Sandhini and Sastry, Girish and Askell, Amanda and Mishkin, Pamela and Clark, Jack and others},
  booktitle={International conference on machine learning},
  pages={8748--8763},
  year={2021},
  organization={PmLR},
  url={https://proceedings.mlr.press/v139/radford21a.html}
}

@inproceedings{siglip,
  title={Sigmoid loss for language image pre-training},
  author={Zhai, Xiaohua and Mustafa, Basil and Kolesnikov, Alexander and Beyer, Lucas},
  booktitle={Proceedings of the IEEE/CVF international conference on computer vision},
  pages={11975--11986},
  year={2023},
  url={https://openaccess.thecvf.com/content/ICCV2023/html/Zhai_Sigmoid_Loss_for_Language_Image_Pre-Training_ICCV_2023_paper.html}
}

@article{dino-v2,
    title={{DINO}v2: Learning Robust Visual Features without Supervision},
    author={Maxime Oquab and Timoth{\'e}e Darcet and Th{\'e}o Moutakanni and Huy V. Vo and Marc Szafraniec and Vasil Khalidov and Pierre Fernandez and Daniel HAZIZA and Francisco Massa and Alaaeldin El-Nouby and Mido Assran and Nicolas Ballas and Wojciech Galuba and Russell Howes and Po-Yao Huang and Shang-Wen Li and Ishan Misra and Michael Rabbat and Vasu Sharma and Gabriel Synnaeve and Hu Xu and Herve Jegou and Julien Mairal and Patrick Labatut and Armand Joulin and Piotr Bojanowski},
    journal={Transactions on Machine Learning Research},
    issn={2835-8856},
    year={2024},
    url={https://openreview.net/forum?id=a68SUt6zFt},
    note={Featured Certification}
}

@article{dino-v3,
  title={Dinov3},
  author={Sim{\'e}oni, Oriane and Vo, Huy V and Seitzer, Maximilian and Baldassarre, Federico and Oquab, Maxime and others},
  journal={arXiv preprint},
  volume={2},
  number={4},
  pages={5},
  year={2025},
  url={https://doi.org/10.48550/arXiv.2508.10104}
}

@InProceedings{seg-gpt,
    author = {Wang, Xinlong and Zhang, Xiaosong and Cao, Yue and Wang, Wen and Shen, Chunhua and Huang, Tiejun},
    title = {SegGPT: Towards Segmenting Everything in Context},
    booktitle = {Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV)},
    month = {October},
    year = {2023},
    pages = {1130-1140},
    url = {https://openaccess.thecvf.com/content/ICCV2023/html/Wang_SegGPT_Towards_Segmenting_Everything_in_Context_ICCV_2023_paper.html}
}

@article{SEEM,
  title={Segment everything everywhere all at once},
  author={Zou, Xueyan and Yang, Jianwei and Zhang, Hao and Li, Feng and Li, Linjie and Wang, Jianfeng and Wang, Lijuan and Gao, Jianfeng and Lee, Yong Jae},
  journal={Advances in neural information processing systems},
  volume={36},
  pages={19769--19782},
  year={2023},
  url={https://proceedings.neurips.cc/paper_files/paper/2023/hash/3ef61f7e4afacf9a2c5b71c726172b86-Abstract-Conference.html}
}

@InProceedings{LISA,
    author = {Lai, Xin and Tian, Zhuotao and Chen, Yukang and Li, Yanwei and Yuan, Yuhui and Liu, Shu and Jia, Jiaya},
    title = {LISA: Reasoning Segmentation via Large Language Model},
    booktitle = {Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
    month = {June},
    year = {2024},
    pages = {9579-9589},
    url = {https://openaccess.thecvf.com/content/CVPR2024/html/Lai_LISA_Reasoning_Segmentation_via_Large_Language_Model_CVPR_2024_paper.html}
}

@inproceedings{vista-3d,
  title={VISTA3D: A unified segmentation foundation model for 3D medical imaging},
  author={He, Yufan and Guo, Pengfei and Tang, Yucheng and Myronenko, Andriy and Nath, Vishwesh and Xu, Ziyue and Yang, Dong and Zhao, Can and Simon, Benjamin and Belue, Mason and others},
  booktitle={Proceedings of the Computer Vision and Pattern Recognition Conference},
  pages={20863--20873},
  year={2025},
  url={https://doi.ieeecomputersociety.org/10.1109/CVPR52734.2025.01943}
}

@article{MedSAM,
  title={Segment anything in medical images},
  author={Ma, Jun and He, Yuting and Li, Feifei and Han, Lin and You, Chenyu and Wang, Bo},
  journal={Nature Communications},
  volume={15},
  number={1},
  pages={654},
  year={2024},
  publisher={Nature Publishing Group UK London},
  url={https://doi.org/10.1038/s41467-024-44824-z}
}

@article{MedicoSAM,
  title = {MedicoSAM: Robust Improvement of SAM for Medical Imaging},
  ISSN = {1558-254X},
  url = {http://doi.org/10.1109/TMI.2025.3644811},
  DOI = {10.1109/tmi.2025.3644811},
  journal = {IEEE Transactions on Medical Imaging},
  publisher = {Institute of Electrical and Electronics Engineers (IEEE)},
  author = {Archit,  Anwai and Freckmann,  Luca and Pape,  Constantin},
  year = {2025},
  pages = {1–1}
}

@article{SAMed2d,
  title={Sam-med2d},
  author={Cheng, Junlong and Ye, J and Deng, Z and Chen, J and Li, T and Wang, H and Su, Y and Huang, Z and Chen, J and Jiang, L and others},
  journal={arXiv preprint},
  year={2023},
  url={https://doi.org/10.48550/arXiv.2308.16184}
}

@inproceedings{peft-sam,
    title={Parameter Efficient Fine-Tuning of Segment Anything Model for Biomedical Imaging},
    author={Carolin Teuber and Anwai Archit and Constantin Pape},
    booktitle={Medical Imaging with Deep Learning},
    year={2025},
    url={https://openreview.net/forum?id=TWPnpixpW2}
}

@article{cellseg1,
  title={CellSeg1: Robust Cell Segmentation with One Training Image},
  author={Zhou, Peilin and Du, Bo and Xu, Yongchao},
  journal={arXiv preprint},
  year={2024},
  url={https://doi.org/10.48550/arXiv.2412.01410}
}

@inproceedings{DETR,
  title={End-to-end object detection with transformers},
  author={Carion, Nicolas and Massa, Francisco and Synnaeve, Gabriel and Usunier, Nicolas and Kirillov, Alexander and Zagoruyko, Sergey},
  booktitle={European conference on computer vision},
  pages={213--229},
  year={2020},
  organization={Springer},
  url={https://www.ecva.net/papers/eccv_2020/papers_ECCV/papers/123460205.pdf}
}

@article{un-sam,
  title={Un-sam: Universal prompt-free segmentation for generalized nuclei images},
  author={Chen, Zhen and Xu, Qing and Liu, Xinyu and Yuan, Yixuan},
  journal={arXiv preprint},
  year={2024},
  url={https://doi.org/10.48550/arXiv.2402.16663}
}

@article{cellpose3,
  title={Cellpose3: one-click image restoration for improved cellular segmentation},
  author={Stringer, Carsen and Pachitariu, Marius},
  journal={Nature Methods},
  volume={22},
  number={3},
  pages={592--599},
  year={2025},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41592-025-02595-5}
}

@article{msa,
  title={Segmentation metric misinterpretations in bioimage analysis},
  author={Hirling, Dominik and Tasnadi, Ervin and Caicedo, Juan and Caroprese, Maria V and Sj{\"o}gren, Rickard and Aubreville, Marc and Koos, Krisztian and Horvath, Peter},
  journal={Nature Methods},
  volume={21},
  number={2},
  pages={213--216},
  year={2024},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41592-023-01942-8}
}

% Datasets:
% Label-free

@article{livecell,
  title={LIVECell—A large-scale dataset for label-free live cell segmentation},
  author={Edlund, Christoffer and Jackson, Timothy R and Khalid, Nabeel and Bevan, Nicola and Dale, Timothy and Dengel, Andreas and Ahmed, Sheraz and Trygg, Johan and Sj{\"o}gren, Rickard},
  journal={Nature Methods},
  volume={18},
  number={9},
  pages={1038--1045},
  year={2021},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41592-021-01249-6}
}

@article{omnipose,
  title={Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation},
  author={Cutler, Kevin J and Stringer, Carsen and Lo, Teresa W and Rappez, Luca and Stroustrup, Nicholas and Brook Peterson, S and Wiggins, Paul A and Mougous, Joseph D},
  journal={Nature Methods},
  volume={19},
  number={11},
  pages={1438--1448},
  year={2022},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41592-022-01639-4}
}

@article{deepbacs,
  title={DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches},
  author={Spahn, Christoph and G{\'o}mez-de-Mariscal, Estibaliz and Laine, Romain F and Pereira, Pedro M and von Chamier, Lucas and Conduit, Mia and Pinho, Mariana G and Jacquemet, Guillaume and Holden, S{\'e}amus and Heilemann, Mike and others},
  journal={Communications Biology},
  volume={5},
  number={1},
  pages={688},
  year={2022},
  publisher={Nature Publishing Group UK London},
  url={https://doi.org/10.1038/s42003-022-03634-z}
}

@article{usiigaci,
  title={Usiigaci: Instance-aware cell tracking in stain-free phase contrast microscopy enabled by machine learning},
  author={Tsai, Hsieh-Fu and Gajda, Joanna and Sloan, Tyler FW and Rares, Andrei and Shen, Amy Q},
  journal={SoftwareX},
  volume={9},
  pages={230--237},
  year={2019},
  publisher={Elsevier},
  url={https://doi.org/10.1016/j.softx.2019.02.007}
}

@article{vicar,
  title={Self-supervised pretraining for transferable quantitative phase image cell segmentation},
  author={Vicar, Tomas and Chmelik, Jiri and Jakubicek, Roman and Chmelikova, Larisa and Gumulec, Jaromir and Balvan, Jan and Provaznik, Ivo and Kolar, Radim},
  journal={Biomedical optics express},
  volume={12},
  number={10},
  pages={6514--6528},
  year={2021},
  publisher={Optical Society of America},
  url={https://doi.org/10.1364/BOE.433212}
}

@article{deepsea,
  title={DeepSea is an efficient deep-learning model for single-cell segmentation and tracking in time-lapse microscopy},
  author={Zargari, Abolfazl and Lodewijk, Gerrald A and Mashhadi, Najmeh and Cook, Nathan and Neudorf, Celine W and Araghbidikashani, Kimiasadat and Hays, Robert and Kozuki, Sayaka and Rubio, Stefany and Hrabeta-Robinson, Eva and others},
  journal={Cell Reports Methods},
  volume={3},
  number={6},
  year={2023},
  publisher={Elsevier},
  url={https://doi.org/10.1016/j.crmeth.2023.100500}
}

@inproceedings{toiam,
  title={Tracking one-in-a-million: Large-scale benchmark for microbial single-cell tracking with experiment-aware robustness metrics},
  author={Seiffarth, Johannes and Bl{\"o}baum, Luisa and Paul, Richard D and Friederich, Nils and Sitcheu, Angelo Jovin Yamachui and Mikut, Ralf and Scharr, Hanno and Gr{\"u}nberger, Alexander and N{\"o}h, Katharina},
  booktitle={European Conference on Computer Vision},
  pages={318--334},
  year={2024},
  organization={Springer},
  url={https://doi.org/10.1007/978-3-031-91721-9_20}
}

% Nuclei (Fluo):
% "dynamicnuclearnet", "u20s", "arvidsson", "ifnuclei",
% "gonuclear", "nis3d", "parhyale_regen", "dsb",
% "bitdepth_nucseg"

@article{dynamicnuclearnet,
  title = {Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning},
  volume = {40},
  ISSN = {1546-1696},
  url = {http://doi.org/10.1038/s41587-021-01094-0},
  DOI = {10.1038/s41587-021-01094-0},
  number = {4},
  journal = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  author = {Greenwald,  Noah F. and Miller,  Geneva and Moen,  Erick and Kong,  Alex and Kagel,  Adam and Dougherty,  Thomas and Fullaway,  Christine Camacho and McIntosh,  Brianna J. and Leow,  Ke Xuan and Schwartz,  Morgan Sarah and Pavelchek,  Cole and Cui,  Sunny and Camplisson,  Isabella and Bar-Tal,  Omer and Singh,  Jaiveer and Fong,  Mara and Chaudhry,  Gautam and Abraham,  Zion and Moseley,  Jackson and Warshawsky,  Shiri and Soon,  Erin and Greenbaum,  Shirley and Risom,  Tyler and Hollmann,  Travis and Bendall,  Sean C. and Keren,  Leeat and Graf,  William and Angelo,  Michael and Van Valen,  David},
  year = {2021},
  month = nov,
  pages = {555–565}
}

@article{paryhale_regen,
  title={Live imaging reveals the progenitors and cell dynamics of limb regeneration},
  author={Alwes, Frederike and Enjolras, Camille and Averof, Michalis},
  journal={Elife},
  volume={5},
  pages={e19766},
  year={2016},
  publisher={eLife Sciences Publications, Ltd},
  url={https://doi.org/10.7554/eLife.19766}
}


@article{ifnuclei,
  title={An annotated fluorescence image dataset for training nuclear segmentation methods},
  author={Kromp, Florian and Bozsaky, Eva and Rifatbegovic, Fikret and Fischer, Lukas and Ambros, Magdalena and Berneder, Maria and Weiss, Tamara and Lazic, Daria and D{\"o}rr, Wolfgang and Hanbury, Allan and others},
  journal={Scientific Data},
  volume={7},
  number={1},
  pages={262},
  year={2020},
  publisher={Nature Publishing Group UK London},
  url={https://doi.org/10.1038/s41597-020-00608-w}
}

@article{arvidsson,
  title={An annotated high-content fluorescence microscopy dataset with Hoechst 33342-stained nuclei and manually labelled outlines},
  author={Arvidsson, Malou and Rashed, Salma Kazemi and Aits, Sonja},
  journal={Data in Brief},
  volume={46},
  pages={108769},
  year={2023},
  publisher={Elsevier},
  url={https://doi.org/10.1016/j.dib.2022.108769}
}

@article{u20s,
  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},
  year={2012},
  url={https://doi.org/10.1038/nmeth.2083}
}

@article{gonuclear,
  title={A deep learning-based toolkit for 3D nuclei segmentation and quantitative analysis in cellular and tissue context},
  author={Vijayan, Athul and Mody, Tejasvinee Atul and Yu, Qin and Wolny, Adrian and Cerrone, Lorenzo and Strauss, Soeren and Tsiantis, Miltos and Smith, Richard S and Hamprecht, Fred A and Kreshuk, Anna and others},
  journal={Development},
  volume={151},
  number={14},
  pages={dev202800},
  year={2024},
  publisher={The Company of Biologists Ltd},
  url={https://doi.org/10.1242/dev.202800}
}

@article{nis3d,
  title={NIS3D: a completely annotated benchmark for dense 3D nuclei image segmentation},
  author={Zheng, Wei and Peng, Cheng and Hou, Zeyuan and Lyu, Boyu and Wang, Mengfan and Mi, Xuelong and Qiao, Shuoxuan and Wan, Yinan and Yu, Guoqiang},
  journal={Advances in neural information processing systems},
  volume={36},
  pages={4741--4752},
  year={2023},
  url={https://proceedings.neurips.cc/paper_files/paper/2023/hash/0f2cd3d09a132757555b602e2dd43784-Abstract-Datasets_and_Benchmarks.html}
}

@article{dsb,
  title={Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl},
  author={Caicedo, Juan C and Goodman, Allen and Karhohs, Kyle W and Cimini, Beth A and Ackerman, Jeanelle and Haghighi, Marzieh and Heng, CherKeng and Becker, Tim and Doan, Minh and McQuin, Claire and others},
  journal={Nature Methods},
  volume={16},
  number={12},
  pages={1247--1253},
  year={2019},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41592-019-0612-7}
}

@article{bitseg,
  title={Investigating the impact of the bit depth of fluorescence-stained images on the performance of deep learning-based nuclei instance segmentation},
  author={Mahbod, Amirreza and Schaefer, Gerald and L{\"o}w, Christine and Dorffner, Georg and Ecker, Rupert and Ellinger, Isabella},
  journal={Diagnostics},
  volume={11},
  number={6},
  pages={967},
  year={2021},
  publisher={MDPI},
  url={https://doi.org/10.3390/diagnostics11060967}
}

% Histopathology
% ihc_tma", "lynsec", "pannuke", "monuseg", "tnbc", "nuinsseg", "puma", "cytodark0"
@article{lynsec,
  title={HoLy-Net: Segmentation of histological images of diffuse large B-cell lymphoma},
  author={Naji, Hussein and Sancere, Lucas and Simon, Adrian and B{\"u}ttner, Reinhard and Eich, Marie-Lisa and Lohneis, Philipp and Bo{\.z}ek, Katarzyna},
  journal={Computers in Biology and Medicine},
  volume={170},
  pages={107978},
  year={2024},
  publisher={Elsevier},
  url={https://doi.org/10.1016/j.compbiomed.2024.107978}
}

@article{ihc-tma,
  title={Simultaneously segmenting and classifying cell nuclei by using multi-task learning in multiplex immunohistochemical tissue microarray sections},
  author={Wang, Ranran and Qiu, Yusong and Hao, Xinyu and Jin, Shan and Gao, Junxiu and Qi, Heng and Xu, Qi and Zhang, Yong and Xu, Hongming},
  journal={Biomedical Signal Processing and Control},
  volume={93},
  pages={106143},
  year={2024},
  publisher={Elsevier},
  url={https://doi.org/10.1016/j.bspc.2024.106143}
}

@article{monuseg,
  title={A multi-organ nucleus segmentation challenge},
  author={Kumar, Neeraj and Verma, Ruchika and Anand, Deepak and Zhou, Yanning and Onder, Omer Fahri and Tsougenis, Efstratios and Chen, Hao and Heng, Pheng-Ann and Li, Jiahui and Hu, Zhiqiang and others},
  journal={IEEE Transactions on Medical Imaging},
  volume={39},
  number={5},
  pages={1380--1391},
  year={2019},
  publisher={IEEE},
  url={https://doi.org/10.1109/TMI.2019.2947628}
}

@article{tnbc,
  title={Segmentation of nuclei in histopathology images by deep regression of the distance map},
  author={Naylor, Peter and La{\'e}, Marick and Reyal, Fabien and Walter, Thomas},
  journal={IEEE Transactions on Medical Imaging},
  volume={38},
  number={2},
  pages={448--459},
  year={2018},
  publisher={IEEE},
  url={https://doi.org/10.1109/TMI.2018.2865709}
}

@article{nuinsseg,
  title={Nuinsseg: a fully annotated dataset for nuclei instance segmentation in h\&e-stained histological images},
  author={Mahbod, Amirreza and Polak, Christine and Feldmann, Katharina and Khan, Rumsha and Gelles, Katharina and Dorffner, Georg and Woitek, Ramona and Hatamikia, Sepideh and Ellinger, Isabella},
  journal={Scientific Data},
  volume={11},
  number={1},
  pages={295},
  year={2024},
  publisher={Nature Publishing Group UK London},
  url={https://doi.org/10.1038/s41597-024-03117-2}
}

@article{cytodark0,
  title={Cisca and cytodark0: a cell instance segmentation and classification method for histo(patho)logical image analyses and a new, open, nissl-stained dataset for brain cytoarchitecture studies},
  author={Vadori, Valentina and Gra{\"\i}c, Jean-Marie and Peruffo, Antonella and Vadori, Giulia and Finos, Livio and Grisan, Enrico},
  journal={Computers in Biology and Medicine},
  volume={197},
  pages={111018},
  year={2025},
  publisher={Elsevier},
  url={https://doi.org/10.1016/j.compbiomed.2025.111018}
}

@article{puma,
  title={A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks},
  author={Schuiveling, Mark and Liu, Hong and Eek, Daniel and Breimer, Gerben E and Suijkerbuijk, Karijn PM and Blokx, Willeke AM and Veta, Mitko},
  journal={GigaScience},
  volume={14},
  pages={giaf011},
  year={2025},
  publisher={Oxford University Press},
  url={https://doi.org/10.1093/gigascience/giaf011}
}

@article{pannuke,
  title={Pannuke dataset extension, insights and baselines},
  author={Gamper, Jevgenij and Koohbanani, Navid Alemi and Benes, Ksenija and Graham, Simon and Jahanifar, Mostafa and Khurram, Syed Ali and Azam, Ayesha and Hewitt, Katherine and Rajpoot, Nasir},
  journal={arXiv preprint},
  year={2020},
  url={https://doi.org/10.48550/arXiv.2003.10778}
}

% Cells Fluo
% "cellpose", "cellbindb", "tissuenet", "plantseg_root", 
% "covid_if", "hpa", "plantseg_ovules", "pnas_arabidopsis"

@article{cellbindb,
  title={CellBinDB: a large-scale multimodal annotated dataset for cell segmentation with benchmarking of universal models},
  author={Shi, Can and Fan, Jinghong and Deng, Zhonghan and Liu, Huanlin and Kang, Qiang and Li, Yumei and Guo, Jing and Wang, Jingwen and Gong, Jinjiang and Liao, Sha and others},
  journal={GigaScience},
  volume={14},
  pages={giaf069},
  year={2025},
  publisher={Oxford University Press},
  url={https://doi.org/10.1093/gigascience/giaf069}
}

@article{tissuenet,
  title={Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning},
  author={Greenwald, Noah F and Miller, Geneva and Moen, Erick and Kong, Alex and Kagel, Adam and Dougherty, Thomas and Fullaway, Christine Camacho and McIntosh, Brianna J and Leow, Ke Xuan and Schwartz, Morgan Sarah and others},
  journal={Nature Biotechnology},
  volume={40},
  number={4},
  pages={555--565},
  year={2022},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41587-021-01094-0}
}

@article{plantseg,
  title={Accurate and versatile 3D segmentation of plant tissues at cellular resolution},
  author={Wolny, Adrian and Cerrone, Lorenzo and Vijayan, Athul and Tofanelli, Rachele and Barro, Amaya Vilches and Louveaux, Marion and Wenzl, Christian and Strauss, S{\"o}ren and Wilson-S{\'a}nchez, David and Lymbouridou, Rena and others},
  journal={Elife},
  volume={9},
  pages={e57613},
  year={2020},
  publisher={eLife Sciences Publications, Ltd},
  url={https://doi.org/10.7554/eLife.57613}
}

@article{covid-if,
  title={Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera: A semi-quantitative, high throughput, microscopy-based assay expands existing approaches to measure SARS-CoV-2 specific antibody levels in human sera},
  author={Pape, Constantin and Remme, Roman and Wolny, Adrian and Olberg, Sylvia and Wolf, Steffen and Cerrone, Lorenzo and Cortese, Mirko and Klaus, Severina and Lucic, Bojana and Ullrich, Stephanie and others},
  journal={Bioessays},
  volume={43},
  number={3},
  pages={2000257},
  year={2021},
  publisher={Wiley Online Library},
  url={https://doi.org/10.1002/bies.202000257}
}

@article{pnas_arabidopsis,
  title={Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche},
  author={Willis, Lisa and Refahi, Yassin and Wightman, Raymond and Landrein, Benoit and Teles, Jos{\'e} and Huang, Kerwyn Casey and Meyerowitz, Elliot M and J{\"o}nsson, Henrik},
  journal={Proceedings of the National Academy of Sciences},
  volume={113},
  number={51},
  pages={E8238--E8246},
  year={2016},
  publisher={National Academy of Sciences},
  url={https://doi.org/10.1073/pnas.1616768113}
}

@article{hpa,
  title={Analysis of the human protein atlas image classification competition},
  author={Ouyang, Wei and Winsnes, Casper F and Hjelmare, Martin and Cesnik, Anthony J and {\AA}kesson, Lovisa and Xu, Hao and Sullivan, Devin P and Dai, Shubin and Lan, Jun and Jinmo, Park and others},
  journal={Nature Methods},
  volume={16},
  number={12},
  pages={1254--1261},
  year={2019},
  publisher={Nature Publishing Group US New York},
  url={https://doi.org/10.1038/s41592-019-0658-6}
}

@article{mouse-embryo,
  title = {Embryo‐uterine interaction coordinates mouse embryogenesis during implantation},
  volume = {42},
  ISSN = {1460-2075},
  url = {http://doi.org/10.15252/embj.2022113280},
  DOI = {10.15252/embj.2022113280},
  number = {17},
  journal = {The EMBO Journal},
  publisher = {Springer Science and Business Media LLC},
  author = {Bondarenko,  Vladyslav and Nikolaev,  Mikhail and Kromm,  Dimitri and Belousov,  Roman and Wolny,  Adrian and Blotenburg,  Marloes and Zeller,  Peter and Rezakhani,  Saba and Hugger,  Johannes and Uhlmann,  Virginie and Hufnagel,  Lars and Kreshuk,  Anna and Ellenberg,  Jan and van Oudenaarden,  Alexander and Erzberger,  Anna and Lutolf,  Matthias P and Hiiragi,  Takashi},
  year = {2023},
  month = jul 
}

@article{yeaz,
  title = {A convolutional neural network segments yeast microscopy images with high accuracy},
  volume = {11},
  ISSN = {2041-1723},
  url = {http://doi.org/10.1038/s41467-020-19557-4},
  DOI = {10.1038/s41467-020-19557-4},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Dietler,  Nicola and Minder,  Matthias and Gligorovski,  Vojislav and Economou,  Augoustina Maria and Joly,  Denis Alain Henri Lucien and Sadeghi,  Ahmad and Chan,  Chun Hei Michael and Koziński,  Mateusz and Weigert,  Martin and Bitbol,  Anne-Florence and Rahi,  Sahand Jamal},
  year = {2020},
  month = nov 
}

@article{segpc,
  title = {SegPC-2021: A challenge \& dataset on segmentation of Multiple Myeloma plasma cells from microscopic images},
  volume = {83},
  ISSN = {1361-8415},
  url = {http://doi.org/10.1016/j.media.2022.102677},
  DOI = {10.1016/j.media.2022.102677},
  journal = {Medical Image Analysis},
  publisher = {Elsevier BV},
  author = {Gupta,  Anubha and Gehlot,  Shiv and Goswami,  Shubham and Motwani,  Sachin and Gupta,  Ritu and Faura,  Álvaro García and Štepec,  Dejan and Martinčič,  Tomaž and Azad,  Reza and Merhof,  Dorit and Bozorgpour,  Afshin and Azad,  Babak and Sulaiman,  Alaa and Pandey,  Deepanshu and Gupta,  Pradyumna and Bhattacharya,  Sumit and Sinha,  Aman and Agarwal,  Rohit and Qiu,  Xinyun and Zhang,  Yucheng and Fan,  Ming and Park,  Yoonbeom and Lee,  Daehong and Park,  Joon Sik and Lee,  Kwangyeol and Ye,  Jaehyung},
  year = {2023},
  month = jan,
  pages = {102677}
}

@article{cryonuseg,
  title = {CryoNuSeg: A dataset for nuclei instance segmentation of cryosectioned H\&E-stained histological images},
  volume = {132},
  ISSN = {0010-4825},
  url = {http://doi.org/10.1016/j.compbiomed.2021.104349},
  DOI = {10.1016/j.compbiomed.2021.104349},
  journal = {Computers in Biology and Medicine},
  publisher = {Elsevier BV},
  author = {Mahbod,  Amirreza and Schaefer,  Gerald and Bancher,  Benjamin and L\"{o}w,  Christine and Dorffner,  Georg and Ecker,  Rupert and Ellinger,  Isabella},
  year = {2021},
  month = may,
  pages = {104349}
}