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Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images.
A new measure of rank correlation
Maurice G Kendall · 1938
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Elliptic fourier features of a closed contour
Frank P Kuhl and Charles R Giardina · 1982
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Seeded region growing
Rolf Adams and Leanne Bischof · 1994
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Faster r-cnn: Towards real-time object detection with region proposal networks
Shaoqing Ren, Kaiming He, Ross Girshick, and Jian Sun · 2015
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U-net: Convolutional networks for biomedical image segmentation
Olaf Ronneberger, Philipp Fischer, and Thomas Brox · 2015
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Deep residual learning for image recognition
Kaiming He, Xiangyu Zhang, Shaoqing Ren, and Jian Sun · 2016
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Deeplab: Semantic image segmentation with deep convolutional nets, atrous convolution, and fully connected crfs
Liang-Chieh Chen, George Papandreou, Iasonas Kokkinos, Kevin Murphy, and Alan L Yuille · 2017
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Mask r-cnn
Kaiming He, Georgia Gkioxari, Piotr Dollár, and Ross Girshick · 2017
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An objective comparison of cell-tracking algorithms
Vladimír Ulman, Martin Maška, Klas EG Magnusson, Olaf Ronneberger, Carsten Haubold, Nathalie Harder, Pavel Matula, Petr Matula, David Svoboda, Miroslav Radojevic, et al · 2017
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Attention is all you need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin · 2017
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Cell detection with star-convex polygons
Uwe Schmidt, Martin Weigert, Coleman Broaddus, and Gene Myers · 2018
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Why rankings of biomedical image analysis competitions should be interpreted with care
Lena Maier-Hein, Matthias Eisenmann, Annika Reinke, Sinan Onogur, Marko Stankovic, Patrick Scholz, Tal Arbel, Hrvoje Bogunovic, Andrew P Bradley, Aaron Carass, et al · 2018
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Nucleus segmentation across imaging experiments: the 2018 data science bowl
Juan C Caicedo, Allen Goodman, Kyle W Karhohs, Beth A Cimini, Jeanelle Ackerman, Marzieh Haghighi, CherKeng Heng, Tim Becker, Minh Doan, Claire McQuin, et al · 2019
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Multi-task attention-based semi-supervised learning for medical image segmentation
Shuai Chen, Gerda Bortsova, Antonio García-Uceda Juárez, Gijs Van Tulder, and Marleen De Bruijne · 2019
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U-net: deep learning for cell counting, detection, and morphometry
Thorsten Falk, Dominic Mai, Robert Bensch, Özgün Çiçek, Ahmed Abdulkadir, Yassine Marrakchi, Anton Böhm, Jan Deubner, Zoe Jäckel, Katharina Seiwald, et al · 2019
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Hover-net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images
Simon Graham, Quoc Dang Vu, Shan E Ahmed Raza, Ayesha Azam, Yee Wah Tsang, Jin Tae Kwak, and Nasir Rajpoot · 2019
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Consistency-based semi-supervised learning for object detection
Jisoo Jeong, Seungeui Lee, Jeesoo Kim, and Nojun Kwak · 2019
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Continual lifelong learning with neural networks: A review
German I Parisi, Ronald Kemker, Jose L Part, Christopher Kanan, and Stefan Wermter · 2019
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Generalized intersection over union: A metric and a loss for bounding box regression
Hamid Rezatofighi, Nathan Tsoi, JunYoung Gwak, Amir Sadeghian, Ian Reid, and Silvio Savarese · 2019
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Yolov4: Optimal speed and accuracy of object detection
Alexey Bochkovskiy, Chien-Yao Wang, and Hong-Yuan Mark Liao · 2020
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A convolutional neural network segments yeast microscopy images with high accuracy
Nicola Dietler, Matthias Minder, Vojislav Gligorovski, Augoustina Maria Economou, Denis Alain Henri Lucien Joly, Ahmad Sadeghi, Chun Hei Michael Chan, Mateusz Koziński, Martin Weigert, Anne-Florence Bitbol, et al · 2020
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An image is worth 16x16 words: Transformers for image recognition at scale
Alexey Dosovitskiy, Lucas Beyer, Alexander Kolesnikov, Dirk Weissenborn, Xiaohua Zhai, Thomas Unterthiner, Mostafa Dehghani, Matthias Minderer, Georg Heigold, Sylvain Gelly, et al · 2020
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Ma-net: A multi-scale attention network for liver and tumor segmentation
Tongle Fan, Guanglei Wang, Yan Li, and Hongrui Wang · 2020
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The single-cell pathology landscape of breast cancer
Hartland W Jackson, Jana R Fischer, Vito RT Zanotelli, H Raza Ali, Robert Mechera, Savas D Soysal, Holger Moch, Simone Muenst, Zsuzsanna Varga, Walter P Weber, et al · 2020
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Mish: A self regularized non-monotonic activation function, 2020
Diganta Misra · 2020
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J regularization improves imbalanced multiclass segmentation
Fidel A Guerrero Pena, Pedro D Marrero Fernandez, Paul T Tarr, Tsang Ing Ren, Elliot M Meyerowitz, and Alexandre Cunha · 2020
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Unbiased teacher v2: Semi-supervised object detection for anchor-free and anchor-based detectors
Yen-Cheng Liu, Chih-Yao Ma, and Zsolt Kira · 2022
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A convnet for the 2020s
Zhuang Liu, Hanzi Mao, Chao-Yuan Wu, Christoph Feichtenhofer, Trevor Darrell, and Saining Xie · 2022
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Cellpose 2.0: how to train your own model
Marius Pachitariu and Carsen Stringer · 2022
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Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma
Tyler Risom, David R Glass, Inna Averbukh, Candace C Liu, Alex Baranski, Adam Kagel, Erin F McCaffrey, Noah F Greenwald, Belen Rivero-Gutierrez, Siri H Strand, et al · 2022
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napari: a multi-dimensional image viewer for Python, 2022
Nicholas Sofroniew, Talley Lambert, Kira Evans, Juan Nunez-Iglesias, Grzegorz Bokota, Philip Winston, Gonzalo Peña-Castellanos, Kevin Yamauchi, Matthias Bussonnier, Draga Doncila Pop, Ahmet Can Solak, Ziyang Liu, Pam Wadhwa, Alister Burt, Genevieve Buckley, Andrew Sweet, Lukasz Migas, Volker Hilsenstein, Lorenzo Gaifas, Jordão Bragantini, Jaime Rodríguez-Guerra, Hector Muñoz, Jeremy Freeman, Peter Boone, Alan Lowe, Christoph Gohlke, Loic Royer, Andrea PIERRÉ, Hagai Har-Gil, and Abigail McGovern · 2022
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Cell segmentation and tracking using cnn-based distance predictions and a graph-based matching strategy
Tim Scherr, Katharina Löffler, Moritz Böhland, and Ralf Mikut · 2020
Cited alongside, same era.
Embracing imperfect datasets: A review of deep learning solutions for medical image segmentation
Nima Tajbakhsh, Laura Jeyaseelan, Qian Li, Jeffrey N Chiang, Zhihao Wu, and Xiaowei Ding · 2020
Cited alongside, same era.
Using hindsight to anchor past knowledge in continual learning
Arslan Chaudhry, Albert Gordo, Puneet Dokania, Philip Torr, and David Lopez-Paz · 2021
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A continual learning survey: Defying forgetting in classification tasks
Matthias De Lange, Rahaf Aljundi, Marc Masana, Sarah Parisot, Xu Jia, Aleš Leonardis, Gregory Slabaugh, and Tinne Tuytelaars · 2021
Cited alongside, same era.
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning
Noah F Greenwald, Geneva Miller, Erick Moen, Alex Kong, Adam Kagel, Thomas Dougherty, Christine Camacho Fullaway, Brianna J McIntosh, Ke Xuan Leow, Morgan Sarah Schwartz, et al · 2021
Cited alongside, same era.
nnu-net: a self-configuring method for deep learning-based biomedical image segmentation
Fabian Isensee, Paul F Jaeger, Simon AA Kohl, Jens Petersen, and Klaus H Maier-Hein · 2021
Cited alongside, same era.
Cellpose: a generalist algorithm for cellular segmentation
Carsen Stringer, Tim Wang, Michalis Michaelos, and Marius Pachitariu · 2021
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Later among the works it cites.
Aggregated residual transformations for deep neural networks
Saining Xie, Ross Girshick, Piotr Dollár, Zhuowen Tu, and Kaiming He · 2022
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Contour proposal networks for biomedical instance segmentation
Eric Upschulte, Stefan Harmeling, Katrin Amunts, and Timo Dickscheid · 2022
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Segpc-2021: A challenge & dataset on segmentation of multiple myeloma plasma cells from microscopic images
Anubha Gupta, Shiv Gehlot, Shubham Goswami, Sachin Motwani, Ritu Gupta, Álvaro García Faura, Dejan Štepec, Tomaž Martinčič, Reza Azad, Dorit Merhof, et al · 2023
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Segmentation metric misinterpretations in bioimage analysis
Dominik Hirling, Ervin Tasnadi, Juan Caicedo, Maria V Caroprese, Rickard Sjögren, Marc Aubreville, Krisztian Koos, and Peter Horvath · 2023
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Mediar: Harmony of data-centric and model-centric for multi-modality microscopy
Gihun Lee, SangMook Kim, Joonkee Kim, and Se-Young. Yun · 2023
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Multiplexed 3d atlas of state transitions and immune interaction in colorectal cancer
Jia-Ren Lin, Shu Wang, Shannon Coy, Yu-An Chen, Clarence Yapp, Madison Tyler, Maulik K. Nariya, Cody N. Heiser, Ken S. Lau, Sandro Santagata, and Peter K. Sorger · 2023
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Multi-stream cell segmentation with low-level cues for multi-modality images
Wei Lou, Xinyi Yu, Chenyu Liu, Xiang Wan, Guanbin Li, Siqi Liu, and Haofeng Li · 2023
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Towards foundation models of biological image segmentation
Jun Ma and Bo Wang · 2023
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The cell tracking challenge: 10 years of objective benchmarking
Martin Maška, Vladimír Ulman, Pablo Delgado-Rodriguez, Estibaliz Gómez-de Mariscal, Tereza Nečasová, Fidel A Guerrero Peña, Tsang Ing Ren, Elliot M Meyerowitz, Tim Scherr, Katharina Löffler, et al · 2023
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Uncertainty-aware contour proposal networks for cell segmentation in multi-modality high-resolution microscopy images
Eric Upschulte, Stefan Harmeling, Katrin Amunts, and Timo Dickscheid · 2023
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Maunet: Modality-aware anti-ambiguity u-net for multi-modality cell segmentation
Li Wangkai, Li Zhaoyang, Sun Rui, Mai Huayu, Luo Naisong, Yuan Wang, Pan Yuwen, Xiong Guoxin, Lai Huakai, Xiong Zhiwei, and Zhang Tianzhu · 2023
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Field-dependent deep learning enables high-throughput whole-cell 3d super-resolution imaging
Shuang Fu, Wei Shi, Tingdan Luo, Yingchuan He, Lulu Zhou, Jie Yang, Zhichao Yang, Jiadong Liu, Xiaotian Liu, Zhiyong Guo, et al · 2023
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Localization uncertainty estimation for anchor-free object detection
Youngwan Lee, Joong-Won Hwang, Hyung-Il Kim, Kimin Yun, Yongjin Kwon, Yuseok Bae, and Sung Ju Hwang · 2023
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Conic challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting
Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Martin Weigert, Uwe Schmidt, Wenhua Zhang, Jun Zhang, Sen Yang, Jinxi Xiang, Xiyue Wang, Josef Lorenz Rumberger, Elias Baumann, Peter Hirsch, Lihao Liu, Chenyang Hong, Angelica I. Aviles-Rivero, Ayushi Jain, Heeyoung Ahn, Yiyu Hong, Hussam Azzuni, Min Xu, Mohammad Yaqub, Marie-Claire Blache, Benoît Piégu, Bertrand Vernay, Tim Scherr, Moritz Böhland, Katharina Löffler, Jiachen Li, Weiqin Ying, Chixin Wang, David Snead, Shan E. Ahmed Raza, Fayyaz Minhas, and Nasir M. Rajpoot · 2024
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Segment anything in medical images
Jun Ma, Yuting He, Feifei Li, Lin Han, Chenyu You, and Bo Wang · 2024
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Metrics reloaded: recommendations for image analysis validation
Lena Maier-Hein, Annika Reinke, Evangelia Christodoulou, Ben Glocker, Patrick Godau, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, et al · 2024
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