Abstract
Microscopic image analysis technology helps solve the inadvertences of artificial traditional methods in disease, wastewater treatment, and environmental change monitoring analysis. Convolutional neural network (CNN) play an important role in microscopic image analysis. Image segmentation, in which U-Net is increasingly applied in microscopic image segmentation, is a crucial step in detection, tracking, monitoring, feature extraction, modelling, and analysis. This paper comprehensively reviews the development history of U-Net, analyses several research results of various segmentation methods since the emergence of U-Net, and conducts a comprehensive review of related papers. This paper summarised the improved methods of U-Net and then listed the existing significance of image segmentation techniques and their improvements introduced over the years. Finally, focusing on the different improvement strategies of U-Net in different papers, the related work of each application target is reviewed according to detailed technical categories to facilitate future research. Researchers can see the dynamics of the transmission of technological development and keep up with future trends in this interdisciplinary field.
Similar content being viewed by others
Data availability
This paper is a survey article, and there is no experimental work in it, so we did not use any data in this paper.
References
Wu Q, Merchant F, Castleman K (2010) Microscope image processing. Elsevier, Amsterdam
Zenhausern F, Boyle M, Wickramasinghe H (1994) Apertureless near-field optical microscope. Appl Phys Lett 65(13):1623–1625
Toledo-Crow R, Yang P, Chen Y, Vaez-Iravani M (1992) Near-field differential scanning optical microscope with atomic force regulation. Appl Phys Lett 60(24):2957–2959
Inouye Y, Kawata S (1994) Near-field scanning optical microscope with a metallic probe tip. Opt Lett 19(3):159–161
Williams D, Carter C (1996) The transmission electron microscope. Springer, Berlin, pp 3–17
Seiler H (1983) Secondary electron emission in the scanning electron microscope. J Appl Phys 54(11):R1–R18
Tersoff J, Hamann D (1985) Theory of the scanning tunneling microscope. Phys Rev B 31(2):805
Binnig G, Quate C, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56(9):930
Duncan M, Reintjes J, Manuccia T (1982) Scanning coherent anti-Stokes Raman microscope. Opt Lett 7(8):350–352
Adrian M, Dubochet J, Lepault J, McDowall A (1984) Cryo-electron microscopy of viruses. Nature 308(5954):32–36
Li C, Zhang J, Kulwa F, Qi S, Qi Z (2020) A SARS-CoV-2 microscopic image dataset with ground truth images and visual features. In Proc. of PRCV 2020, pp 244–255
Li C, Wang K, Xu N (2019) A survey for the applications of content-based microscopic image analysis in microorganism classification domains. Artif Intell Rev 51(4):577–646
Zhang J, Li C, Kosov S, Grzegorzek M, Shirahama K, Jiang T, Sun C, Li Z, Li H (2021) LCU-Net: a novel low-cost U-Net for environmental microorganism image segmentation. Pattern Recogn 115:107885
Li X, Li C, Rahaman M, Li X, Sun H, Zhang H, Zhang Y, Li X, Wu J, Yao Y (2022) A comprehensive review of computer-aided whole-slide image analysis: from datasets to feature extraction, segmentation, classification, and detection approaches. Art Intell Rev 55(6):4809–4878
Zhouand X, Li C, Rahaman M, Yao Y, Ai S, Sun C, Wang Q, Zhang Y, Li M, Li X (2020) A comprehensive review for breast histopathology image analysis using classical and deep neural networks. IEEE Access 8:90931–90956
Rahaman M, Li C, Wu X, Yao Y, Hu Z, Jiang T, Li X, Qi S (2020) A survey for cervical cytopathology image analysis using deep learning. IEEE Access 8:61687–61710
Hore S, Chakroborty S, Ashour A, Dey N, Ashour A, Sifaki-Pistolla D, Bhattacharya T, Chaudhuri S (2015) Finding contours of hippocampus brain cell using microscopic image analysis. J Adv Microsc Res 10(2):93–103
Øien S, Wragg D, Reinsch H, Svelle S, Bordiga S, Lamberti C, Lillerud K (2014) Detailed structure analysis of atomic positions and defects in zirconium metal-organic frameworks. Crystal Growth Des 14(11):5370–5372
Clelland W, Fens T (1991) Automated rock characterization with SEM/image-analysis techniques. SPE Form Eval 6(04):437–443
Pagliai M, Vignozzi N (2002) Image analysis and microscopic techniques to characterize soil pore system. In: Blahovec J, Kutilek M (eds) Physical methods in agriculture. Springer, Berlin, pp 13–38
Abell A, Willis K, Lange D (1999) Mercury intrusion porosimetry and image analysis of cement-based materials. J Colloid Interface Sci 211(1):39–44
Nilsson H (1995) Remote sensing and image analysis in plant pathology. Annu Rev Phytopathol 33(1):489–528
Nilsson N (2014) Principles of artificial intelligence. Morgan Kaufmann, Burlington
Litjens G, Kooi T, Bejnordi B, Setio A, Ciompi F, Ghafoorian M, Laak J, Ginneken B, Sánchez C (2017) A survey on deep learning in medical image analysis. Med Image Anal 42:60–88
Ronneberger O, Fischer P, Brox T (2015) U-net: Convolutional networks for biomedical image segmentation. In Proc. of ICMICCA 2015, pp 234–241
Long J, Shelhamer E, Darrell T (2015) Fully convolutional networks for semantic segmentation. In: Proc. of CVPR 2015, pp 3431–3440
Zhang J, Li C, Rahaman MM, Yao Y, Ma P, Zhang J, Zhao X, Jiang T, Grzegorzek M (2023) A comprehensive survey with quantitative comparison of image analysis methods for microorganism biovolume measurements. Arch Comput Methods Eng 30(1):639–673
Weiming Hu, Li Xintong, Li Chen, Li Rui, Jiang Tao, Sun Hongzan, Huang Xinyu, Grzegorzek Marcin, Li Xiaoyan (2023) A state-of-the-art survey of artificial neural networks for whole-slide image analysis: from popular convolutional neural networks to potential visual transformers. Comput Biol Med 161:107034
Ma Pingli, Li Chen, Rahaman Md Mamunur, Yao Yudong, Zhang Jiawei, Zou Shuojia, Zhao Xin, Grzegorzek Marcin (2023) A state-of-the-art survey of object detection techniques in microorganism image analysis: from classical methods to deep learning approaches. Artif Intell Rev 56(2):1627–1698
Zhang J, Li C, Rahaman MM, Yao Y, Ma P, Zhang J, Zhao X, Jiang T, Grzegorzek M (2022) A comprehensive review of image analysis methods for microorganism counting: from classical image processing to deep learning approaches. Art Intell Rev 55(4):2875–2944
Taghanaki S, Abhishek K, Cohen J, Cohen-Adad J, Hamarneh G (2020) Deep semantic segmentation of natural and medical images: a review. Art Intell Rev 54:137–178
Du G, Cao X, Liang J, Chen X, Zhan Y (2020) Medical image segmentation based on u-net: a review. J Imaging Sci Technol 64(2):20508
Colonna A, Scarpa F, Ruggeri A (2018) Segmentation of corneal nerves using a u-net-based convolutional neural network. In: Computational pathology and ophthalmic medical image analysis, pp 185–192
Seong S, Park H (2019) Automated identification of neural cells in the multi-photon images using deep-neural networks. arXiv: 1909.11269
Daniel M, Atzrodt L, Bucher F, Wacker K, Böhringer S, Reinhard T, Böhringer D (2019) Automated segmentation of the corneal endothelium in a large set of ‘real-world’specular microscopy images using the U-Net architecture. Sci Rep 9(1):1–7
Núñez-Fernández D, Ballan L, Jiménez-Avalos G, Coronel J, Zimic M(2020) Automatic semantic segmentation for prediction of tuberculosis using lens-free microscopy images. arXiv: 2007.02482
Ojeda-Pat A, Martin-Gonzalez A, Soberanis-Mukul R (2020) Convolutional Neural Network U-Net for Trypanosoma cruzi Segmentation. In: Proc. of ISICS 2020, pp 118–131
Chen Z, Liu X, Yang J, Little E, Zhou Y (2020) Deep learning-based method for SEM image segmentation in mineral characterization, an example from Duvernay Shale samples in Western Canada Sedimentary Basin. Comput. Geosci. 138:104450
Oktay A, Gurses A (2019) Automatic detection, localization and segmentation of nano-particles with deep learning in microscopy images. Micron 120:113–119
Farley S, Hodgkinson J, Gordon O, Turner J, Soltoggio A, Moriarty P, Hunsicker E (2020) Improving the segmentation of scanning probe microscope images using convolutional neural networks. Mach Learn Sci Technol 2(1):015015
Jaworek-Korjakowska J (2018) A deep learning approach to vascular structure segmentation in dermoscopy colour images. BioMed Res. Int. 2018:5049390–5049390
Meyer M, Costa P, Galdran A, Mendonça A, Campilho A (2017) A deep neural network for vessel segmentation of scanning laser ophthalmoscopy images. In: Proc. of ICIAR 2017, pp 507–515
Webb R, Hughes G, Pomerantzeff O (1980) Flying spot TV ophthalmoscope. Appl Opt 19(17):2991–2997
Zhang J, Dashtbozorg B, Bekkers E, Pluim J, Duits R, Romeny B (2016) Robust retinal vessel segmentation via locally adaptive derivative frames in orientation scores. IEEE Trans Med Imaging 35(12):2631–2644
Swiderska-Chadaj Z, Markiewicz T, Gallego J, Bueno G, Grala B, Lorent M (2018) Deep learning for damaged tissue detection and segmentation in Ki-7 brain tumor specimens based on the U-net model. Bulletin of the polish academy of sciences. Tech Sci 66(6):849–856
learning dense volumetric segmentation from sparse annotation (2016) Özgün Çiçek, A. Abdulkadir, S. Lienkamp, T. Brox, and O. Ronneberger. 3D U-Net. In: Proceeding of ICMICCAI 2016, pp 424–432
Fang Z, Yue W, Zhitao X, Lei G, Jun W, Yanbei L, Wen W (2019) Nanoparticle segmentation based on U-Net convolutional neural network. Laser Optoelectron. Progr 56(6):061005
Fu C, Lee S, Ho D, Han S, Salama P, Dunn K, Delp E (2018) Three dimensional fluorescence microscopy image synthesis and segmentation. In: Proceeding of CVPR 2018, pp 2221–2229
Eschweiler D, Spina T, Choudhury R, Meyerowitz E, Cunha A, Stegmaier J (2019) CNN-based preprocessing to optimize watershed-based cell segmentation in 3D confocal microscopy images. In: Proceeding of ISBI 2019, pp 223–227
Willis L, Refahi Y, Wightman R, Landrein B, José Teles, Huang K, Meyerowitz E, Henrik Jönsson (2016) Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche. Proc Natl Acad Sci 113(51):E8238–E8246
Fernandez R, Das P, Mirabet V, Moscardi E, Traas J, Verdeil J, Malandain G, Godin C (2010) Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nat Methods 7(7):547
Mosaliganti K, Noche R, Xiong F, Swinburne I, Megason S (2012) ACME: automated cell morphology extractor for comprehensive reconstruction of cell membranes. PLoS Comput Biol 8(12):e1002780
Heinrich L, Funke J, Pape C, Nunez-Iglesias J, Saalfeld S (2018) Synaptic cleft segmentation in non-isotropic volume electron microscopy of the complete drosophila brain. In: Proceeding of ICMICCAI 2018, pp 317–325
Wang H, Zhang D, Song Y, Liu S, Wang Y, Feng D, Peng H, Cai W (2019) Segmenting neuronal structure in 3D optical microscope images via knowledge distillation with teacher-student network. In: Proceeding of ISBI 2019, pp 228–231
Zhang M, Li X, Xu M, Li Q (2017) Image segmentation and classification for sickle cell disease using deformable u-net. arXiv: 1710.08149
Zhang M, Li X, Xu X, Li Q (2018) RBC semantic segmentation for sickle cell disease based on deformable U-Net. In: Proceeding of ICMICCAI 2018, pp 695–702
Xu X, Papageorgiou D, Abidi S, Dao M, Zhao H, Karniadakis G (2017) A deep convolutional neural network for classification of red blood cells in sickle cell anemia. PLoS Comput Biol 13(10):e1005746
Qin X, Wu C, Chang H, Lu H, Zhang X (2020) Match feature U-Net: dynamic receptive field networks for biomedical image segmentation. Symmetry 12(8):1230
Rad R, Saeedi P, Au J, Havelock J (2018) Blastomere cell counting and centroid localization in microscopic images of human embryo. In: Proceeding of MMSP 2018, pp 1–6
Rad R, Saeedi P, Au J, Havelock J (2020) Trophectoderm segmentation in human embryo images via inceptioned U-Net. Med Image Anal 62:101612
Szegedy C, Liu W, Jia Y, Sermanet P, Reed S, Anguelov D, Erhan D, Vanhoucke V, Rabinovich A (2015) Going deeper with convolutions. In Proceeding of CVPR 2015:1–9
Saeedi P, Yee D, Au J, Havelock J (2017) Automatic identification of human blastocyst components via texture. IEEE Trans Biomed Eng 64(12):2968–2978
Matuszewski D, Sintorn I (2018) Minimal annotation training for segmentation of microscopy images. In: Proceeding of ISBI 2018, pp 387–390
Kylberg G, Uppström M, HEDLUND K, Borgefors G, SINTORN I (2012) Segmentation of virus particle candidates in transmission electron microscopy images. J Microsc 245(2):140–147
Mocan I, Itu R, Ciurte A, Danescu R, Buiga R (2018) Automatic Detection of Tumor Cells in Microscopic Images of Unstained Blood using Convolutional Neural Networks. In: Proceeding of ICCP 2018, pp 319–324
Xu Z, Sobhani F, Moro C, Zhang Q (2019) Us-net for robust and efficient nuclei instance segmentation. In: Proceeding of ISBI 2019, pp 44–47
Li W, Qian X, Ji J (2017) Noise-tolerant deep learning for histopathological image segmentation. In: Proc. of ICIP 2017, pp 3075–3079
Fabijańska A (2018) Segmentation of corneal endothelium images using a U-Net-based convolutional neural network. Artif Intell Med 88:1–13
Kumar C, TN M, Narasimhadhan A (2020) Cell Segmentation by Modified U-Net Architecture for Biomedical Images. In: Proceeding of CONECCT 2020, pp 1–6
Bermúdez-Chacón R, Márquez-Neila P, Salzmann M, Fua P (2018) A domain-adaptive two-stream U-Net for electron microscopy image segmentation. In: Proceeding of ISBI 2018, pp 400–404
Jha D, Riegler M, Johansen D, Halvorsen P, Johansen H (2020) Doubleu-net: A deep convolutional neural network for medical image segmentation. In: Proceeding of CBMS 2020, pp 558–564
Zhuang J (2018) Laddernet: Multi-path networks based on u-net for medical image segmentation. arXiv: 1810.07810
Simonyan K, Zisserman A (2014) Very deep convolutional networks for large-scale image recognition. arXiv: 1409.1556
Bernal J, Sánchez F, Fernández-Esparrach G, Gil D, Rodríguez C, Vilariño F (2015) WM-DOVA maps for accurate polyp highlighting in colonoscopy: Validation vs. saliency maps from physicians. Comput Med Imaging Graph 43:99–111
Torr A, Basaran D, Sero J, Rittscher J, Sailem H (2020) DeepSplit: Segmentation of Microscopy Images Using Multi-Task Convolutional Networks. In: Annual conference on medical image understanding and analysis, pp 155–167
Bozkurt A, Kose K, Alessi-Fox C, Gill M, Dy J, Brooks D, Rajadhyaksha M (2018) A multiresolution convolutional neural network with partial label training for annotating reflectance confocal microscopy images of skin. In: Proceeding of ICMICCAI 2018, pp 292–299
Zhao B, Chen X, Li Z, Yu Z, Yao S, Yan L, Wang Y, Liu Z, Liang C, Han C (2020) Triple U-net: Hematoxylin-aware nuclei segmentation with progressive dense feature aggregation. Med Image Anal 65:101786
Huang G, Liu Z, Maaten L, Weinberger K (2017) Densely connected convolutional networks. In: Proceeding of CVPR 2017, pp 4700–4708
Vahadane Abhishek, Atheeth B, Majumdar Shantanu (2021) Dual encoder attention u-net for nuclei segmentation. In: 2021 43rd annual international conference of the IEEE engineering in medicine & biology society (EMBC), IEEE, pp 3205–3208
Dang Vu Quoc, Simon Graham, Tahsin Kurc, Nhat To Minh Nguyen, Muhammad Shaban, Talha Qaiser, Alemi Koohbanani Navid, Ali Khurram Syed, Jayashree Kalpathy-Cramer, Tianhao Zhao et al (2019) Methods for segmentation and classification of digital microscopy tissue images. Front Bioeng Biotechnol 7:53
Oktay O, Schlemper J, Folgoc L, Lee M, Heinrich M, Misawa K, Mori K, McDonagh S, Hammerla N, Kainz B (2018) Attention u-net: Learning where to look for the pancreas. arXiv: 1804.03999
Lian S, Luo Z, Zhong Z, Lin X, Su S, Li S (2018) Attention guided U-Net for accurate iris segmentation. J Vis Commun Image Represent 56:296–304
Proença H, Filipe S, Santos R, Oliveira J, Alexandre L (2009) The UBIRIS. v2: a database of visible wavelength iris images captured on-the-move and at-a-distance. IEEE Trans Pattern Anal Mach Intell 32(8):1529–1535
Lv Y, Ma H, Li J, Liu S (2020) Attention guided U-Net with atrous convolution for accurate retinal vessels segmentation. IEEE Access 8:32826–32839
Bansal N, Dutta M (2013) Retina vessels detection algorithm for biomedical symptoms diagnosis. Int J Comput Appl, 71(20)
Guo Y, Budak Ü, Vespa L, Khorasani E, Şengür A (2018) A retinal vessel detection approach using convolution neural network with reinforcement sample learning strategy. Measurement 125:586–591
Thangaraj S, Periyasamy V, Balaji R (2018) Retinal vessel segmentation using neural network. IET Image Proc 12(5):669–678
Mou L, Zhao Y, Chen L, Cheng J, Gu Z, Hao H, Qi H, Zheng Y, Frangi A, Liu J (2019) CS-Net: channel and spatial attention network for curvilinear structure segmentation. In: Proceeding of ICMICCAI 2019, pp 721–730
Li R, Li M, Li J, Zhou Y (2019) Connection sensitive attention u-net for accurate retinal vessel segmentation. arXiv:1903.05558
Jiang Y, Wang F, Gao J, Cao S (2020) Multi-path recurrent u-net segmentation of retinal fundus image. Appl Sci 10(11):3777
Zhang H, Zhu H, Ling X (2020) Polar coordinate sampling-based segmentation of overlapping cervical cells using attention U-Net and random walk. Neurocomputing 383:212–223
Zhu N, Liu C, Singer Z, Danino T, Laine A, Guo J (2020) Segmentation with residual attention u-net and an edge-enhancement approach preserves cell shape features. arXiv:2001.05548
Sivaswamy J, Krishnadas S, Chakravarty A, Joshi G, Tabish A (2015) A comprehensive retinal image dataset for the assessment of glaucoma from the optic nerve head analysis. JSM Biomed Imaging Data Papers 2(1):1004
He K, Zhang X, Ren S, Sun J (2016) Deep residual learning for image recognition. In: Proceeding CVPR 2016, pp 770–778
Xiancheng W, Wei L, Bingyi M, He J, Jiang Z, Xu W, Ji Z, Hong G, Zhaomeng S (2018) Retina blood vessel segmentation using a U-net based convolutional neural network. In: Procedia Computer Science, pp 1–11
Leng J, Liu Y, Zhang T, Quan P, Cui Z (2018) Context-aware u-net for biomedical image segmentation. In: Proceeding of BIBM 2018, pp 2535–2538
Chidester B, Ton T, Tran M, Ma J, Do M (2019) Enhanced rotation-equivariant u-net for nuclear segmentation. In: Proceeding of CVPRW 2019
Zhang J, Li C, Kosov S, Grzegorzek M, Shirahama K, Jiang T, Sun C, Li Zihan, Li H (2021) LCU-Net: A novel low-cost U-Net for environmental microorganism image segmentation. Pattern Recogn 115:107885
Petit Olivi, Thome N, Rambour C, Themyr L, Collins T, Soler L (2021) U-net transformer: Self and cross attention for medical image segmentation. In: Machine Learning in medical imaging: 12th international workshop, MLMI 2021, held in conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings vol 12, Springer, pp 267–276.
Huang G, Chen D, Li T, Wu F, Maaten L, Weinberger K (2017) Multi-scale dense convolutional networks for efficient prediction. arXiv: 1703.09844, 2
Jégou S, Drozdzal M, Vazquez D, Romero A, Bengio Y (2017) The one hundred layers tiramisu: Fully convolutional densenets for semantic segmentation. In: Proceeding of CVPR 2017, pp 11–19
Cheng Y, Ma M, Zhang L, Jin C, Ma L, Zhou Y (2020) Retinal blood vessel segmentation based on Densely Connected U-Net. Math Biosci Eng 17:3088–3108
He K, Zhang X, Ren S, Sun J (2015) Delving deep into rectifiers: Surpassing human-level performance on imagenet classification. In: Proceeding of ICCV 2015, pp 1026–1034
Owen C, Rudnicka A, Mullen R, Barman S, Monekosso D, Whincup P, Ng J, Paterson C (2009) Measuring retinal vessel tortuosity in 10-year-old children: validation of the computer-assisted image analysis of the retina (CAIAR) program. Investig Ophthalmol Visual Sci 50(5):2004–2010
Wang C, Zhao Z, Ren Q, Xu Y, Yu Y (2019) Dense U-net based on patch-based learning for retinal vessel segmentation. Entropy 21(2):168
Samanta P, Raipuria G, Singhal N (2021) Context Aggregation Network For Semantic Labeling In Histopathology Images. In: Proceeding of ISBI 2021, pp 673–676
Li J, Yang S, Huang X, Da Q, Yang X, Hu Z, Duan Q, Wang C, Li H (2019) Signet ring cell detection with a semi-supervised learning framework. In: Proceeding of ICIPMI 2019, pp 842–854
Sirinukunwattana K, Pluim J, Chen H, Qi X, Heng P, Guo Y, Wang L, Matuszewski B, Bruni E, Sanchez U (2017) Gland segmentation in colon histology images: the glas challenge contest. Med Image Anal 35:489–502
Zhang J, Jin Y, Xu J, Xu X, Zhang Y (2018) Mdu-net: Multi-scale densely connected u-net for biomedical image segmentation. arXiv:1812.00352
Liu Y, Treible W, Kolagunda A, Nedo A, Saponaro P, Caplan J, Kambhamettu C (2018) Densely connected stacked u-network for filament segmentation in microscopy images. In: Proceeding of ECCV 2018
Wu C, Xie Y, Shao L, Yang J, Ai D, Song H, Wang Y, Huang Y (2019) Automatic boundary segmentation of vascular doppler optical coherence tomography images based on cascaded U-net architecture. OSA Contin 2(3):677–689
Zhou Z, RSiddiquee M, Tajbakhsh N, Liang J (2018) Unet++: A nested u-net architecture for medical image segmentation. In: Deep learning in medical image analysis and multimodal learning for clinical decision support, pp 3–11
Zhou Z, Siddiquee M, Tajbakhsh N, Liang J (2019) Unet++: Redesigning skip connections to exploit multiscale features in image segmentation. IEEE Trans Med Imaging 39(6):1856–1867
Wang H, Li Y, Luo Z (2020) An Improved Breast Cancer Nuclei Segmentation Method Based on UNet++. In: Proceeding of ICCAI 2020, pp 193–197
Janowczyk A, Madabhushi A (2016) Deep learning for digital pathology image analysis: a comprehensive tutorial with selected use cases. J Pathol Inform 7:29
Tsunomura M, Shishikura M, Ishii T, Takahashi R, Tsumura N (2020) Segmentation of microscopic image of colorants using u-net based deep convolutional networks for material appearance design. In: International conference on image and signal processing, pp 197–204
Xu X, Tan T, Xu F (2018) An improved U-net architecture for simultaneous arteriole and venule segmentation in fundus image. In: Proceeding of ACMIUA 2018, pp 333–340
Liang X, Wang B (2020) Wheat powdery mildew spore images segmentation based on U-Net. J Phys Conf Series 1631:012074
Patel G, Tekchandani H, Verma S (2019) Cellular segmentation of bright-field absorbance images using residual u-net. In: Proceeding of ICAC 2019, pp 1–5
Gómez de Mariscal E, Maška M, Kotrbová A, Pospíchalová V, Matula P, Muñoz-Barrutia A (2019) Deep-learning-based segmentation of small extracellular vesicles in transmission electron microscopy images. Sci Rep 9(1):1–10
Quan T, Hildebrand D, Jeong W (2016) Fusionnet: A deep fully residual convolutional neural network for image segmentation in connectomics. arXiv:1612.05360
Arganda-Carreras I, Turaga S, Berger D, Cireşan D, Giusti A, Gambardella L, Schmidhuber J, Laptev D, Dwivedi S, Buhmann J (2015) Crowdsourcing the creation of image segmentation algorithms for connectomics. Front Neuroanat 9:142
Mehta S, Mercan E, Bartlett J, Weaver D, Elmore JG, Shapiro L (2018) Y-Net: joint segmentation and classification for diagnosis of breast biopsy images. In: Proceeding of ICMICCAI 2018, pp 893–901
Ke R, Bugeau A, Papadakis N, Schuetz P, Schönlieb C (2019) A multi-task U-net for segmentation with lazy labels. arXiv preprint arXiv:1906.12177
Wang Zekun, Zou Yanni, Liu Peter X (2021) Hybrid dilation and attention residual U-Net for medical image segmentation. Comput Biol Med 134:104449
Zunair Hasib, Hamza A Ben (2021) Sharp U-Net: Depthwise convolutional network for biomedical image segmentation. Comput Biol Med 136:104699
Yang Zhenzhen, Pengfei Xu, Yang Yongpeng, Bao Bing-Kun (2021) A densely connected network based on U-Net for medical image segmentation. ACM Trans Multimed Comput Commun Appl 17(3):1–14
Ibtehaz N, Rahman M (2020) MultiResUNet: Rethinking the U-Net architecture for multimodal biomedical image segmentation. Neural Netw 121:74–87
Coelho LP, Shariff A, Murphy RF (2009) Nuclear segmentation in microscope cell images: a hand-segmented dataset and comparison of algorithms. In: Proceeding of ISBI 2009, pp 518–521
Lou A, Guan S, Loew M (2021) DC-UNet: rethinking the U-Net architecture with dual channel efficient CNN for medical image segmentation. In: medical imaging 2021: image processing, vol 11596, pp 115962T
Gadosey P, Li Y, Adjei E, Zhang T, Liu Z, Yamak P, Essaf F (2020) Sd-unet: stripping down u-net for segmentation of biomedical images on platforms with low computational budgets. Diagnostics 10(2):110
Arbelle A, Raviv T (2019) Microscopy cell segmentation via convolutional LSTM networks. In: Proceedimg of ISBI 2019, pp 1008–1012
Abdallah H, Formosa B, Liyanaarachchi A, Saigh M, Silvers S, Arslanturk S, Taatjes D, Larsson L, Jena B, Gatti D (2020) Res-CR-Net, a residual network with a novel architecture optimized for the semantic segmentation of microscopy images. Mach Learn Sci Technol 1(4):045004
Kumar N, Verma R, Sharma S, Bhargava S, Vahadane A, Sethi A (2017) A dataset and a technique for generalized nuclear segmentation for computational pathology. IEEE Trans Med Imaging 36(7):1550–1560
Chakravarty A, Sivaswamy J (2018) RACE-net: a recurrent neural network for biomedical image segmentation. IEEE J Biomed Health Inform 23(3):1151–1162
Alom M, Hasan M, Yakopcic C, Taha T, Asari V (2018) Recurrent residual convolutional neural network based on u-net (r2u-net) for medical image segmentation. arXiv:1802.06955
Alom M, Yakopcic C, Hasan M, Taha T, Asari V (2019) Recurrent residual U-Net for medical image segmentation. J Med Imaging 6(1):014006
Alom M, Yakopcic C, Taha T, Asari V (2018) Nuclei segmentation with recurrent residual convolutional neural networks based U-Net (R2U-Net). In: Proceeding of NAECON 2018, pp 228–233
Zahangir A, Yakopcic C, Taha T, Asari V (2018) microscopic nuclei classification, segmentation and detection with improved deep convolutional neural network (DCNN) approaches. arXiv e-prints, pages arXiv–1811
Yang Q, Xu Z, Liao C, Cai J, Huang Y, Chen H, Tao X, Huang Z, Chen J, Dong J (2020) Epithelium segmentation and automated Gleason grading of prostate cancer via deep learning in label-free multiphoton microscopic images. J Biophotonics 13(2):e201900203
Krizhevsky A, Sutskever I, Hinton G (2012) Imagenet classification with deep convolutional neural networks. Adv Neural Inf Process Syst 25:1097–1105
Szegedy C, Ioffe S, Vanhoucke V, Alemi A (2017) Inception-v4, inception-resnet and the impact of residual connections on learning. In: Proceeding of AAAI, vol 31, pp 2017
Gu Z, Cheng J, Fu H, Zhou K, Hao H, Zhao Y, Zhang T, Gao S, Liu J (2019) Ce-net: Context encoder network for 2d medical image segmentation. IEEE Trans Med Imaging 38(10):2281–2292
Zhang Z, Yin F, Liu J, Wong W, Tan N, Lee B, Cheng J, Wong T (2010) Origa-light: an online retinal fundus image database for glaucoma analysis and research. In: Proceeding of AICEMB 2010, pp 3065–3068
Zhang Z, Wu C, Coleman S, Kerr D (2020) DENSE-INception U-net for medical image segmentation. Comput Methods Progr Biomed 192:105395
Huang Y, Li X, Yan C, Liu L, Dai H (2020) MIRD-Net for Medical Image Segmentation. In: Pacific-Asia conference on knowledge discovery and data mining, pp 207–219
Trimeche I, Rossant F, Bloch I, Pâques M (2020) Fully automatic CNN-based segmentation of retinal bifurcations in 2D adaptive optics ophthalmoscopy images. In: Proceeding of IPTA 2020, pp 1–6
Chen A, Li C, Zou S, Rahaman Md M, Yao Y, Chen H, Yang H, Zhao P, Weiming H, Liu W et al (2022) SVIA dataset: a new dataset of microscopic videos and images for computer-aided sperm analysis. Biocybern Biomed Eng 42(1):204–214
Zhao P, Li C, Rahaman Md M, Hao X, Ma P, Yang H, Sun H, Jiang T, Ning X, Grzegorzek M (2022) Emds-6: environmental microorganism image dataset sixth version for image denoising, segmentation, feature extraction, classification, and detection method evaluation. Front Microbiol 13:829027
Yang H, Li C, Zhao X, Cai B, Zhang J, Ma P, Zhao P, Chen A, Jiang T, Sun H et al (2023) EMDS-7: environmental microorganism image dataset seventh version for multiple object detection evaluation. Front Microbiol 14:1084312
Weiming H, Li C, Rahaman Md M, Chen H, Liu W, Yao Y, Sun H, Grzegorzek M, Li X, 2023) EBHI: a new enteroscope biopsy histopathological H &E image dataset for image classification evaluation. Phys Med 107:102534
Shi L, Li X, Weiming H, Chen H, Chen J, Fan Z, Gao M, Jing Y, Guotao L, Ma D et al (2023) EBHI-Seg: a novel enteroscope biopsy histopathological hematoxylin and eosin image dataset for image segmentation tasks. Front Med 10:1114673
Weiming H, Li C, Li X, Rahaman Md M, Ma J, Zhang Y, Chen H, Liu W, Sun C, Yao Y et al (2022) GasHisSDB: a new gastric histopathology image dataset for computer aided diagnosis of gastric cancer. Comput Biol Med 142:105207
Piantadosi G, Sansone M, Sansone C (2018) Breast segmentation in mri via u-net deep convolutional neural networks. In: Proceeding of ICPR 2018, pp 3917–3922
Wang F, Jiang R, Zheng L, Meng C, Biswal B (2019) 3d u-net based brain tumor segmentation and survival days prediction. In: Proceeding of MICCAI-BW 2019, pp 131–141
Lee B, Yamanakkanavar N, Choi J (2020) Automatic segmentation of brain MRI using a novel patch-wise U-net deep architecture. PLoS ONE 15(8):e0236493
Rundo L, Han C, Nagano Y, Zhang J, Hataya R, Militello C, Tangherloni A, Nobile M, Ferretti C, Besozzi D (2019) USE-Net: incorporating squeeze-and-excitation blocks into U-net for prostate zonal segmentation of multi-institutional MRI datasets. Neurocomputing 365:31–43
Kermi A, Mahmoudi I, Khadir M (2018) Deep convolutional neural networks using U-Net for automatic brain tumor segmentation in multimodal MRI volumes. In: Proceeding of MICCAI-BW 2018, pp 37–48
Chen Y, Cao Z, Cao C, Yang J, Zhang J (2018) A modified U-Net for brain Mr image segmentation. In: Proceeding of ICCCS 2018, pp 233–242
Song T, Meng F, Rodriguez-Paton A, Li P, Zheng P, Wang X (2019) U-next: a novel convolution neural network with an aggregation u-net architecture for gallstone segmentation in CT images. IEEE Access 7:166823–166832
Roth H, Oda H, Zhou X, Shimizu N, Yang Y, Hayashi Y, Oda M, Fujiwara M, Misawa K, Mori K (2018) An application of cascaded 3D fully convolutional networks for medical image segmentation. Comput Med Imaging Graph 66:90–99
Roth H, Shen C, Oda H, Oda M, Hayashi Y, Misawa K, Mori K (2018) Deep learning and its application to medical image segmentation. Med Imaging Technol 36(2):63–71
Chen Y, Lin Y, Wang C, Lee C, Lee W, Wang T, Chen C (2019) Coronary artery segmentation in cardiac CT angiography using 3D multi-channel U-net. arXiv:1907.12246
Saeedizadeh N, Minaee S, Kafieh R, Yazdani S, Sonka M (2021) COVID TV-Unet: Segmenting COVID-19 chest CT images using connectivity imposed Unet. Comput Methods Progr Biomed Update 1:100007
Weng Y, Zhou T, Li Y, Qiu X (2019) Nas-unet: neural architecture search for medical image segmentation. IEEE Access 7:44247–44257
Almajalid R, Shan J, Du Y, Zhang M (2018) Development of a deep-learning-based method for breast ultrasound image segmentation. In: Proceeding of ICMLA 2018, pp 1103–1108
Wang Y, Wei C, Wang Z, Lu Q, Wang C (2018) A more streamlined u-net for nerve segmentation in ultrasound images. In: Proceeding of CAC 2018, pp 101–104
Li X, Hong Y, Kong D, Zhang X (2019) Automatic segmentation of levator hiatus from ultrasound images using U-net with dense connections. Phys Med Biol 64(7):075015
Yang J, Faraji M, Basu A (2019) Robust segmentation of arterial walls in intravascular ultrasound images using Dual Path U-Net. Ultrasonics 96:24–33
Amiri M, Brooks R, Behboodi B, Rivaz H (2020) Two-stage ultrasound image segmentation using U-Net and test time augmentation. Int J Comput Assist Radiol Surg 15(6):981–988
Amiri M, Brooks R, Rivaz H (2019) Fine tuning u-net for ultrasound image segmentation: Which layers? In: Domain adaptation and representation transfer and medical image learning with less labels and imperfect data, pp 235–242
Wu J, Liu W, Li C, Jiang T, Shariful IM, Sun H, Li X, Li X, Huang X, Grzegorzek M (2022) A state-of-the-art survey of u-net in microscopic image analysis: from simple usage to structure mortification. arXiv:2202.06465
Acknowledgements
This work is supported by the “National Natural Science Foundation of China” (No. 82220108007). We thank Miss. Zixian Li and Mr. Guoxian Li for their important discussion in this work. We thank B.A. Qi Qiu and B.A. Yingying Hou for their professional English proofreading in this paper. Chen Li and Hongzan Sun have the same contributions as corresponding authors in this paper. A preprint has previously been published in arXiv. [172].
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflicts of interest in this paper.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Wu, J., Liu, W., Li, C. et al. A state-of-the-art survey of U-Net in microscopic image analysis: from simple usage to structure mortification. Neural Comput & Applic 36, 3317–3346 (2024). https://doi.org/10.1007/s00521-023-09284-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00521-023-09284-4