@inproceedings{ronneberger2015u,
  title={U-net: Convolutional networks for biomedical image segmentation},
  author={Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
  booktitle={Medical Image Computing and Computer-Assisted Intervention--MICCAI 2015: 18th International Conference, Munich, Germany, October 5-9, 2015, Proceedings, Part III 18},
  pages={234--241},
  year={2015},
  organization={Springer}
}

@article{chen2017rethinking,
  title={Rethinking atrous convolution for semantic image segmentation},
  author={Chen, Liang-Chieh and Papandreou, George and Schroff, Florian and Adam, Hartwig},
  journal={arXiv preprint arXiv:1706.05587},
  year={2017}
}

@article{salvi2021automated,
  title={Automated assessment of glomerulosclerosis and tubular atrophy using deep learning},
  author={Salvi, Massimo and Mogetta, Alessandro and Gambella, Alessandro and Molinaro, Luca and Barreca, Antonella and Papotti, Mauro and Molinari, Filippo},
  journal={Computerized Medical Imaging and Graphics},
  volume={90},
  pages={101930},
  year={2021},
  publisher={Elsevier}
}

@article{fang2020multi,
  title={Multi-organ segmentation over partially labeled datasets with multi-scale feature abstraction},
  author={Fang, Xi and Yan, Pingkun},
  journal={IEEE Transactions on Medical Imaging},
  volume={39},
  number={11},
  pages={3619--3629},
  year={2020},
  publisher={IEEE}
}

@incollection{gonzalez2018multi,
  title={Multi-structure segmentation from partially labeled datasets. application to body composition measurements on ct scans},
  author={Gonz{\'a}lez, Germ{\'a}n and Washko, George R and San Jos{\'e} Est{\'e}par, Ra{\'u}l},
  booktitle={Image Analysis for Moving Organ, Breast, and Thoracic Images},
  pages={215--224},
  year={2018},
  publisher={Springer}
}


@article{bouteldja2021deep,
  title={Deep learning--based segmentation and quantification in experimental kidney histopathology},
  author={Bouteldja, Nassim and Klinkhammer, Barbara M and B{\"u}low, Roman D and Droste, Patrick and Otten, Simon W and von Stillfried, Saskia Freifrau and Moellmann, Julia and Sheehan, Susan M and Korstanje, Ron and Menzel, Sylvia and others},
  journal={Journal of the American Society of Nephrology},
  volume={32},
  number={1},
  pages={52--68},
  year={2021},
  publisher={Am Soc Nephrol}
}

@article{northcutt2021confident,
  title={Confident learning: Estimating uncertainty in dataset labels},
  author={Northcutt, Curtis and Jiang, Lu and Chuang, Isaac},
  journal={Journal of Artificial Intelligence Research},
  volume={70},
  pages={1373--1411},
  year={2021}
}

@inproceedings{fan2022pointly,
  title={Pointly-Supervised Panoptic Segmentation},
  author={Fan, Junsong and Zhang, Zhaoxiang and Tan, Tieniu},
  booktitle={Computer Vision--ECCV 2022: 17th European Conference, Tel Aviv, Israel, October 23--27, 2022, Proceedings, Part XXX},
  pages={319--336},
  year={2022},
  organization={Springer}
}


@article{li2022learning,
  title={Learning to segment subcortical structures from noisy annotations with a novel uncertainty-reliability aware learning framework},
  author={Li, Xiang and Wei, Ying and Hu, Qian and Wang, Chuyuan and Yang, Jingjing},
  journal={Computers in Biology and Medicine},
  volume={151},
  pages={106326},
  year={2022},
  publisher={Elsevier}
}

@inproceedings{deng2022single,
  title={Single Dynamic Network for Multi-label Renal Pathology Image Segmentation},
  author={Deng, Ruining and Liu, Quan and Cui, Can and Asad, Zuhayr and Huo, Yuankai and others},
  booktitle={International Conference on Medical Imaging with Deep Learning},
  pages={304--314},
  year={2022},
  organization={PMLR}
}

@article{imig2022interactions,
  title={Interactions Between Podocytes, Mesangial Cells, and Glomerular Endothelial Cells in Glomerular Diseases},
  author={Imig, John D and Zhao, Xueying and Elmarakby, Ahmed A and Pavlov, Tengis},
  journal={Frontiers in Physiology},
  pages={488},
  year={2022},
  publisher={Frontiers}
}

@article{comaniciu2002cell,
  title={Cell image segmentation for diagnostic pathology},
  author={Comaniciu, Dorin and Meer, Peter},
  journal={Advanced algorithmic approaches to medical image segmentation: State-of-the-art applications in cardiology, neurology, mammography and pathology},
  pages={541--558},
  year={2002},
  publisher={Springer}
}

@article{xing2016robust,
  title={Robust nucleus/cell detection and segmentation in digital pathology and microscopy images: a comprehensive review},
  author={Xing, Fuyong and Yang, Lin},
  journal={IEEE reviews in biomedical engineering},
  volume={9},
  pages={234--263},
  year={2016},
  publisher={IEEE}
}

@article{olindo2005htlv,
  title={HTLV-1 proviral load in peripheral blood mononuclear cells quantified in 100 HAM/TSP patients: a marker of disease progression},
  author={Olindo, St{\'e}phane and L{\'e}zin, Agn{\`e}s and Cabre, Philippe and Merle, Harold and Saint-Vil, Martine and Kaptue, Mireille Edimonana and Signate, A{\"\i}ssatou and C{\'e}saire, Raymond and Smadja, Didier},
  journal={Journal of the neurological sciences},
  volume={237},
  number={1-2},
  pages={53--59},
  year={2005},
  publisher={Elsevier}
}

@article{wijeratne2018quantification,
  title={Quantification of dengue virus specific T cell responses and correlation with viral load and clinical disease severity in acute dengue infection},
  author={Wijeratne, Dulharie T and Fernando, Samitha and Gomes, Laksiri and Jeewandara, Chandima and Ginneliya, Anushka and Samarasekara, Supun and Wijewickrama, Ananda and Hardman, Clare S and Ogg, Graham S and Malavige, Gathsaurie Neelika},
  journal={PLoS neglected tropical diseases},
  volume={12},
  number={10},
  pages={e0006540},
  year={2018},
  publisher={Public Library of Science San Francisco, CA USA}
}


@article{jimenez2006mast,
  title={Mast cell quantification in normal peritoneum and during peritoneal dialysis treatment},
  author={Jim{\'e}nez-Heffernan, Jos{\'e}A and Bajo, M Auxiliadora and Perna, Cristian and del Peso, Gloria and Larrubia, Juan R and Gamallo, Carlos and S{\'a}nchez-Tomero, Jos{\'e}A and L{\'o}pez-Cabrera, Manuel and Selgas, Rafael},
  journal={Archives of pathology \& laboratory medicine},
  volume={130},
  number={8},
  pages={1188--1192},
  year={2006}
}


@article{zheng2021deep,
  title={Deep-learning--driven quantification of interstitial fibrosis in digitized kidney biopsies},
  author={Zheng, Yi and Cassol, Clarissa A and Jung, Saemi and Veerapaneni, Divya and Chitalia, Vipul C and Ren, Kevin YM and Bellur, Shubha S and Boor, Peter and Barisoni, Laura M and Waikar, Sushrut S and others},
  journal={The American journal of pathology},
  volume={191},
  number={8},
  pages={1442--1453},
  year={2021},
  publisher={Elsevier}
}

@article{korzynska2021review,
  title={A review of current systems for annotation of cell and tissue images in digital pathology},
  author={Korzynska, Anna and Roszkowiak, Lukasz and Zak, Jakub and Siemion, Krzysztof},
  journal={Biocybernetics and Biomedical Engineering},
  volume={41},
  number={4},
  pages={1436--1453},
  year={2021},
  publisher={Elsevier}
}

@article{janowczyk2019histoqc,
  title={HistoQC: an open-source quality control tool for digital pathology slides},
  author={Janowczyk, Andrew and Zuo, Ren and Gilmore, Hannah and Feldman, Michael and Madabhushi, Anant},
  journal={JCO clinical cancer informatics},
  volume={3},
  pages={1--7},
  year={2019},
  publisher={American Society of Clinical Oncology}
}

@article{chen2020computer,
  title={A computer-aided diagnosis system for differentiation and delineation of malignant regions on whole-slide prostate histopathology image using spatial statistics and multidimensional DenseNet},
  author={Chen, Chiao-Min and Huang, Yao-Sian and Fang, Pei-Wei and Liang, Cher-Wei and Chang, Ruey-Feng},
  journal={Medical physics},
  volume={47},
  number={3},
  pages={1021--1033},
  year={2020},
  publisher={Wiley Online Library}
}

@article{das2020computer,
  title={Computer-aided histopathological image analysis techniques for automated nuclear atypia scoring of breast cancer: a review},
  author={Das, Asha and Nair, Madhu S and Peter, S David},
  journal={Journal of digital imaging},
  volume={33},
  pages={1091--1121},
  year={2020},
  publisher={Springer}
}

@article{hollandi2020annotatorj,
  title={AnnotatorJ: an ImageJ plugin to ease hand annotation of cellular compartments},
  author={Hollandi, R{\'e}ka and Di{\'o}sdi, {\'A}kos and Hollandi, G{\'a}bor and Moshkov, Nikita and Horv{\'a}th, P{\'e}ter},
  journal={Molecular biology of the cell},
  volume={31},
  number={20},
  pages={2179--2186},
  year={2020},
  publisher={Am Soc Cell Biol}
}

@article{koohbanani2020nuclick,
  title={NuClick: a deep learning framework for interactive segmentation of microscopic images},
  author={Koohbanani, Navid Alemi and Jahanifar, Mostafa and Tajadin, Neda Zamani and Rajpoot, Nasir},
  journal={Medical Image Analysis},
  volume={65},
  pages={101771},
  year={2020},
  publisher={Elsevier}
}


@article{bankhead2017qupath,
  title={QuPath: Open source software for digital pathology image analysis},
  author={Bankhead, Peter and Loughrey, Maurice B and Fern{\'a}ndez, Jos{\'e} A and Dombrowski, Yvonne and McArt, Darragh G and Dunne, Philip D and McQuaid, Stephen and Gray, Ronan T and Murray, Liam J and Coleman, Helen G and others},
  journal={Scientific reports},
  volume={7},
  number={1},
  pages={1--7},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{day2013fluorescently,
  title={Fluorescently labeled therapeutic antibodies for detection of microscopic melanoma},
  author={Day, Kristine E and Beck, Lauren N and Deep, Nicholas L and Kovar, Joy and Zinn, Kurt R and Rosenthal, Eben L},
  journal={The Laryngoscope},
  volume={123},
  number={11},
  pages={2681--2689},
  year={2013},
  publisher={Wiley Online Library}
}

@article{moore2017effects,
  title={Effects of an unlabeled loading dose on tumor-specific uptake of a fluorescently labeled antibody for optical surgical navigation},
  author={Moore, Lindsay S and Rosenthal, Eben L and de Boer, Esther and Prince, Andrew C and Patel, Neel and Richman, Joshua M and Morlandt, Anthony B and Carroll, William R and Zinn, Kurt R and Warram, Jason M},
  journal={Molecular Imaging and Biology},
  volume={19},
  pages={610--616},
  year={2017},
  publisher={Springer}
}

@article{zhan2019learning,
  title={Learning from multi-annotator data: A noise-aware classification framework},
  author={Zhan, Xueying and Wang, Yaowei and Rao, Yanghui and Li, Qing},
  journal={ACM Transactions on Information Systems (TOIS)},
  volume={37},
  number={2},
  pages={1--28},
  year={2019},
  publisher={ACM New York, NY, USA}
}

@inproceedings{long2015multi,
  title={Multi-class multi-annotator active learning with robust gaussian process for visual recognition},
  author={Long, Chengjiang and Hua, Gang},
  booktitle={Proceedings of the IEEE international conference on computer vision},
  pages={2839--2847},
  year={2015}
}



@inproceedings{li2021dual,
  title={Dual-stream multiple instance learning network for whole slide image classification with self-supervised contrastive learning},
  author={Li, Bin and Li, Yin and Eliceiri, Kevin W},
  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
  pages={14318--14328},
  year={2021}
}

@article{deng2021map3d,
  title={Map3D: Registration-Based Multi-Object Tracking on 3D Serial Whole Slide Images},
  author={Deng, Ruining and Yang, Haichun and Jha, Aadarsh and Lu, Yuzhe and Chu, Peng and Fogo, Agnes B and Huo, Yuankai},
  journal={IEEE transactions on medical imaging},
  volume={40},
  number={7},
  pages={1924--1933},
  year={2021},
  publisher={IEEE}
}

@article{sandkuhler2018airlab,
  title={AirLab: autograd image registration laboratory},
  author={Sandk{\"u}hler, Robin and Jud, Christoph and Andermatt, Simon and Cattin, Philippe C},
  journal={arXiv preprint arXiv:1806.09907},
  year={2018}
}


@article{graham2019hover,
  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}
}

@article{ruifrok2001quantification,
  title={Quantification of histochemical staining by color deconvolution},
  author={Ruifrok, Arnout C and Johnston, Dennis A and others},
  journal={Analytical and quantitative cytology and histology},
  volume={23},
  number={4},
  pages={291--299},
  year={2001},
  publisher={St. Louis, MO: Science Printers and Publishers, 1985-}
}

@article{oberg2012statistical,
  title={Statistical methods for quantitative mass spectrometry proteomic experiments with labeling},
  author={Oberg, Ann L and Mahoney, Douglas W},
  journal={BMC bioinformatics},
  volume={13},
  number={16},
  pages={1--18},
  year={2012},
  publisher={BioMed Central}
}


@article{englbrecht2021automatic,
  title={Automatic image annotation for fluorescent cell nuclei segmentation},
  author={Englbrecht, Fabian and Ruider, Iris E and Bausch, Andreas R},
  journal={PloS one},
  volume={16},
  number={4},
  pages={e0250093},
  year={2021},
  publisher={Public Library of Science San Francisco, CA USA}
}

@inproceedings{hsueh2009data,
  title={Data quality from crowdsourcing: a study of annotation selection criteria},
  author={Hsueh, Pei-Yun and Melville, Prem and Sindhwani, Vikas},
  booktitle={Proceedings of the NAACL HLT 2009 workshop on active learning for natural language processing},
  pages={27--35},
  year={2009}
}

@inproceedings{marzahl2020crowd,
  title={Is crowd-algorithm collaboration an advanced alternative to crowd-sourcing on cytology slides?},
  author={Marzahl, Christian and Aubreville, Marc and Bertram, Christof A and Gerlach, Stefan and Maier, Jennifer and Voigt, J{\"o}rn and Hill, Jenny and Klopfleisch, Robert and Maier, Andreas},
  booktitle={Bildverarbeitung f{\"u}r die Medizin 2020: Algorithmen--Systeme--Anwendungen. Proceedings des Workshops vom 15. bis 17. M{\"a}rz 2020 in Berlin},
  pages={26--31},
  year={2020},
  organization={Springer}}

@article{amgad2022nucls,
  title={NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer},
  author={Amgad, Mohamed and Atteya, Lamees A and Hussein, Hagar and Mohammed, Kareem Hosny and Hafiz, Ehab and Elsebaie, Maha AT and Alhusseiny, Ahmed M and AlMoslemany, Mohamed Atef and Elmatboly, Abdelmagid M and Pappalardo, Philip A and others},
  journal={GigaScience},
  volume={11},
  year={2022},
  publisher={Oxford Academic}
}


@article{caicedo2017data,
  title={Data-analysis strategies for image-based cell profiling},
  author={Caicedo, Juan C and Cooper, Sam and Heigwer, Florian and Warchal, Scott and Qiu, Peng and Molnar, Csaba and Vasilevich, Aliaksei S and Barry, Joseph D and Bansal, Harmanjit Singh and Kraus, Oren and others},
  journal={Nature methods},
  volume={14},
  number={9},
  pages={849--863},
  year={2017},
  publisher={Nature Publishing Group US New York}
}

@article{deng2020deep,
  title={Deep learning in digital pathology image analysis: a survey},
  author={Deng, Shujian and Zhang, Xin and Yan, Wen and Chang, Eric I-Chao and Fan, Yubo and Lai, Maode and Xu, Yan},
  journal={Frontiers of medicine},
  volume={14},
  pages={470--487},
  year={2020},
  publisher={Springer}
}


@article{greenwald2022whole,
  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}
}


@article{keren2018structured,
  title={A structured tumor-immune microenvironment in triple negative breast cancer revealed by multiplexed ion beam imaging},
  author={Keren, Leeat and Bosse, Marc and Marquez, Diana and Angoshtari, Roshan and Jain, Samir and Varma, Sushama and Yang, Soo-Ryum and Kurian, Allison and Van Valen, David and West, Robert and others},
  journal={Cell},
  volume={174},
  number={6},
  pages={1373--1387},
  year={2018},
  publisher={Elsevier}
}


@article{pratapa2021image,
  title={Image-based cell phenotyping with deep learning},
  author={Pratapa, Aditya and Doron, Michael and Caicedo, Juan C},
  journal={Current opinion in chemical biology},
  volume={65},
  pages={9--17},
  year={2021},
  publisher={Elsevier}
}

@article{litjens2017survey,
  title={A survey on deep learning in medical image analysis},
  author={Litjens, Geert and Kooi, Thijs and Bejnordi, Babak Ehteshami and Setio, Arnaud Arindra Adiyoso and Ciompi, Francesco and Ghafoorian, Mohsen and Van Der Laak, Jeroen Awm and Van Ginneken, Bram and S{\'a}nchez, Clara I},
  journal={Medical image analysis},
  volume={42},
  pages={60--88},
  year={2017},
  publisher={Elsevier}
}

@article{guo2024good,
  title={How Good Are We? Evaluating Cell AI Foundation Models in Kidney Pathology with Human-in-the-Loop Enrichment},
  author={Guo, Junlin and Lu, Siqi and Cui, Can and Deng, Ruining and Yao, Tianyuan and Tao, Zhewen and Lin, Yizhe and Lionts, Marilyn and Liu, Quan and Xiong, Juming and others},
  journal={arXiv preprint arXiv:2411.00078},
  year={2024}
}


@inproceedings{deng2023democratizing,
  title={Democratizing pathological image segmentation with lay annotators via molecular-empowered learning},
  author={Deng, Ruining and Li, Yanwei and Li, Peize and Wang, Jiacheng and Remedios, Lucas W and Agzamkhodjaev, Saydolimkhon and Asad, Zuhayr and Liu, Quan and Cui, Can and Wang, Yaohong and others},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={497--507},
  year={2023},
  organization={Springer}
}

@inproceedings{vuadineanu2022analysis,
  title={An analysis of the impact of annotation errors on the accuracy of deep learning for cell segmentation},
  author={V{\u{a}}dineanu, {\c{S}}erban and Pelt, Dani{\"e}l Maria and Dzyubachyk, Oleh and Batenburg, Kees Joost},
  booktitle={International Conference on Medical Imaging with Deep Learning},
  pages={1251--1267},
  year={2022},
  organization={PMLR}
}

@article{karimi2020deep,
  title={Deep learning with noisy labels: Exploring techniques and remedies in medical image analysis},
  author={Karimi, Davood and Dou, Haoran and Warfield, Simon K and Gholipour, Ali},
  journal={Medical image analysis},
  volume={65},
  pages={101759},
  year={2020},
  publisher={Elsevier}
}


@article{zhang2018generalized,
  title={Generalized cross entropy loss for training deep neural networks with noisy labels},
  author={Zhang, Zhilu and Sabuncu, Mert},
  journal={Advances in neural information processing systems},
  volume={31},
  year={2018}
}


@article{wang2020noise,
  title={A noise-robust framework for automatic segmentation of COVID-19 pneumonia lesions from CT images},
  author={Wang, Guotai and Liu, Xinglong and Li, Chaoping and Xu, Zhiyong and Ruan, Jiugen and Zhu, Haifeng and Meng, Tao and Li, Kang and Huang, Ning and Zhang, Shaoting},
  journal={IEEE Transactions on Medical Imaging},
  volume={39},
  number={8},
  pages={2653--2663},
  year={2020},
  publisher={IEEE}
}


@inproceedings{ma2020normalized,
  title={Normalized loss functions for deep learning with noisy labels},
  author={Ma, Xingjun and Huang, Hanxun and Wang, Yisen and Romano, Simone and Erfani, Sarah and Bailey, James},
  booktitle={International conference on machine learning},
  pages={6543--6553},
  year={2020},
  organization={PMLR}
}


@inproceedings{zhang2020robust,
  title={Robust medical image segmentation from non-expert annotations with tri-network},
  author={Zhang, Tianwei and Yu, Lequan and Hu, Na and Lv, Su and Gu, Shi},
  booktitle={Medical Image Computing and Computer Assisted Intervention--MICCAI 2020: 23rd International Conference, Lima, Peru, October 4--8, 2020, Proceedings, Part IV 23},
  pages={249--258},
  year={2020},
  organization={Springer}
}


@article{han2018co,
  title={Co-teaching: Robust training of deep neural networks with extremely noisy labels},
  author={Han, Bo and Yao, Quanming and Yu, Xingrui and Niu, Gang and Xu, Miao and Hu, Weihua and Tsang, Ivor and Sugiyama, Masashi},
  journal={Advances in neural information processing systems},
  volume={31},
  year={2018}
}

@article{lu2023uncertainty,
  title={Uncertainty-aware pseudo-label and consistency for semi-supervised medical image segmentation},
  author={Lu, Liyun and Yin, Mengxiao and Fu, Liyao and Yang, Feng},
  journal={Biomedical Signal Processing and Control},
  volume={79},
  pages={104203},
  year={2023},
  publisher={Elsevier}
}


@article{guo2023sac,
  title={SAC-Net: Learning with weak and noisy labels in histopathology image segmentation},
  author={Guo, Ruoyu and Xie, Kunzi and Pagnucco, Maurice and Song, Yang},
  journal={Medical Image Analysis},
  volume={86},
  pages={102790},
  year={2023},
  publisher={Elsevier}
}



@article{oquab2023dinov2,
  title={Dinov2: Learning robust visual features without supervision},
  author={Oquab, Maxime and Darcet, Timoth{\'e}e and Moutakanni, Th{\'e}o and Vo, Huy and Szafraniec, Marc and Khalidov, Vasil and Fernandez, Pierre and Haziza, Daniel and Massa, Francisco and El-Nouby, Alaaeldin and others},
  journal={arXiv preprint arXiv:2304.07193},
  year={2023}
}


@inproceedings{huang2021gloria,
  title={Gloria: A multimodal global-local representation learning framework for label-efficient medical image recognition},
  author={Huang, Shih-Cheng and Shen, Liyue and Lungren, Matthew P and Yeung, Serena},
  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision},
  pages={3942--3951},
  year={2021}
}


@inproceedings{deng2024hats,
  title={HATs: Hierarchical Adaptive Taxonomy Segmentation for Panoramic Pathology Image Analysis},
  author={Deng, Ruining and Liu, Quan and Cui, Can and Yao, Tianyuan and Xiong, Juming and Bao, Shunxing and Li, Hao and Yin, Mengmeng and Wang, Yu and Zhao, Shilin and others},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={155--166},
  year={2024},
  organization={Springer}
}



@inproceedings{deng2024prpseg,
  title={PrPSeg: Universal Proposition Learning for Panoramic Renal Pathology Segmentation},
  author={Deng, Ruining and Liu, Quan and Cui, Can and Yao, Tianyuan and Yue, Jialin and Xiong, Juming and Yu, Lining and Wu, Yifei and Yin, Mengmeng and Wang, Yu and others},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages={11736--11746},
  year={2024}
}

@inproceedings{lucarelli2024computational,
  title={Computational integration of CODEX and brightfield histology for cell annotation using deep learning},
  author={Lucarelli, Nicholas and Laszik, Zoltan and Winfree, Seth and El-Achkar, Tarek M and Eadon, Michael and Jain, Sanjay and Sarder, Pinaki},
  booktitle={Medical Imaging 2024: Digital and Computational Pathology},
  volume={12933},
  pages={347--350},
  year={2024},
  organization={SPIE}
}

@article{border2024investigating,
  title={Investigating quantitative histological characteristics in renal pathology using HistoLens},
  author={Border, Samuel P and Tomaszewski, John E and Yoshida, Teruhiko and Kopp, Jeffrey B and Hodgin, Jeffrey B and Clapp, William L and Rosenberg, Avi Z and Buyon, Jill P and Sarder, Pinaki},
  journal={Scientific reports},
  volume={14},
  number={1},
  pages={17528},
  year={2024},
  publisher={Nature Publishing Group UK London}
}


@article{zhang2020disentangling,
  title={Disentangling human error from ground truth in segmentation of medical images},
  author={Zhang, Le and Tanno, Ryutaro and Xu, Mou-Cheng and Jin, Chen and Jacob, Joseph and Cicarrelli, Olga and Barkhof, Frederik and Alexander, Daniel},
  journal={Advances in Neural Information Processing Systems},
  volume={33},
  pages={15750--15762},
  year={2020}
}

@inproceedings{dang2024singr,
  title={Singr: Brain tumor segmentation via signed normalized geodesic transform regression},
  author={Dang, Trung and Nguyen, Huy Hoang and Tiulpin, Aleksei},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={593--603},
  year={2024},
  organization={Springer}
}


@article{goldsborough2024instanseg,
  title={InstanSeg: an embedding-based instance segmentation algorithm optimized for accurate, efficient and portable cell segmentation},
  author={Goldsborough, Thibaut and Philps, Ben and O'Callaghan, Alan and Inglis, Fiona and Leplat, Leo and Filby, Andrew and Bilen, Hakan and Bankhead, Peter},
  journal={arXiv preprint arXiv:2408.15954},
  year={2024}
}


@article{horst2024cellvit,
  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}
}


@article{israel2024foundation,
  title={A foundation model for cell segmentation},
  author={Israel, Uriah and Marks, Markus and Dilip, Rohit and Li, Qilin and Yu, Changhua and Laubscher, Emily and Li, Shenyi and Schwartz, Morgan and Pradhan, Elora and Ates, Ada and others},
  journal={bioRxiv},
  pages={2023--11},
  year={2024}
}


@article{deng2025kpis,
  title={KPIs 2024 Challenge: Advancing Glomerular Segmentation from Patch-to Slide-Level},
  author={Deng, Ruining and Yao, Tianyuan and Tang, Yucheng and Guo, Junlin and Lu, Siqi and Xiong, Juming and Yu, Lining and Cap, Quan Huu and Cai, Pengzhou and Lan, Libin and others},
  journal={arXiv preprint arXiv:2502.07288},
  year={2025}
}


@article{ke2023clusterseg,
  title={Clusterseg: A crowd cluster pinpointed nucleus segmentation framework with cross-modality datasets},
  author={Ke, Jing and Lu, Yizhou and Shen, Yiqing and Zhu, Junchao and Zhou, Yijin and Huang, Jinghan and Yao, Jieteng and Liang, Xiaoyao and Guo, Yi and Wei, Zhonghua and others},
  journal={Medical Image Analysis},
  volume={85},
  pages={102758},
  year={2023},
  publisher={Elsevier}
}


@inproceedings{zhu2023anti,
  title={An Anti-biased TBSRTC-Category Aware Nuclei Segmentation Framework with a Multi-label Thyroid Cytology Benchmark},
  author={Zhu, Junchao and Shen, Yiqing and Zhang, Haolin and Ke, Jing},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={580--590},
  year={2023},
  organization={Springer}
}


@article{zhu2024cross,
  title={Cross-Species Data Integration for Enhanced Layer Segmentation in Kidney Pathology},
  author={Zhu, Junchao and Yin, Mengmeng and Deng, Ruining and Long, Yitian and Wang, Yu and Wang, Yaohong and Zhao, Shilin and Yang, Haichun and Huo, Yuankai},
  journal={arXiv preprint arXiv:2408.09278},
  year={2024}
}