. 2016 Jan; 9:234-63.
doi: 10.1109/RBME.2016.2515127.

Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review

Fuyong Xing  Lin Yang  
  • PMID: 26742143
  •     180 References
  •     69 citations


Digital pathology and microscopy image analysis is widely used for comprehensive studies of cell morphology or tissue structure. Manual assessment is labor intensive and prone to interobserver variations. Computer-aided methods, which can significantly improve the objectivity and reproducibility, have attracted a great deal of interest in recent literature. Among the pipeline of building a computer-aided diagnosis system, nucleus or cell detection and segmentation play a very important role to describe the molecular morphological information. In the past few decades, many efforts have been devoted to automated nucleus/cell detection and segmentation. In this review, we provide a comprehensive summary of the recent state-of-the-art nucleus/cell segmentation approaches on different types of microscopy images including bright-field, phase-contrast, differential interference contrast, fluorescence, and electron microscopies. In addition, we discuss the challenges for the current methods and the potential future work of nucleus/cell detection and segmentation.

Segmentation of confocal microscope images of cell nuclei in thick tissue sections.
C Ortiz de Solórzano, E García Rodriguez, +4 authors, S J Lockett.
J Microsc, 1999 Apr 13; 193(Pt 3). PMID: 10199001
An automated machine vision system for the histological grading of cervical intraepithelial neoplasia (CIN).
S J Keenan, J Diamond, +4 authors, P W Hamilton.
J Pathol, 2000 Oct 31; 192(3). PMID: 11054719
Segmentation of nuclei and cells using membrane related protein markers.
C O De Solorzano, R Malladi, S A Lelièvre, S J Lockett.
J Microsc, 2001 Mar 10; 201(Pt 3). PMID: 11240857
Quantification of histochemical staining by color deconvolution.
A C Ruifrok, D A Johnston.
Anal Quant Cytol Histol, 2001 Sep 04; 23(4). PMID: 11531144
Highly Cited.
Segmentation and tracking of migrating cells in videomicroscopy with parametric active contours: a tool for cell-based drug testing.
Christophe Zimmer, Elisabeth Labruyère, +2 authors, Jean-Christophe Olivo-Marin.
IEEE Trans Med Imaging, 2003 Feb 15; 21(10). PMID: 12585703
Harmonic cut and regularized centroid transform for localization of subcellular structures.
Qing Yang, Bahram Parvin.
IEEE Trans Biomed Eng, 2003 May 02; 50(4). PMID: 12723058
A hybrid 3D watershed algorithm incorporating gradient cues and object models for automatic segmentation of nuclei in confocal image stacks.
Gang Lin, Umesh Adiga, +3 authors, Badrinath Roysam.
Cytometry A, 2003 Oct 21; 56(1). PMID: 14566936
Blood cells with fetal haemoglobin (F-cells) detected by immunohistochemistry as indicators of solid tumours.
M Wolk, J E Martin, R Constantin.
J Clin Pathol, 2004 Jun 29; 57(7). PMID: 15220368    Free PMC article.
Combining intensity, edge and shape information for 2D and 3D segmentation of cell nuclei in tissue sections.
C Wählby, I-M Sintorn, +2 authors, E Bengtsson.
J Microsc, 2004 Jul 03; 215(Pt 1). PMID: 15230877
Hierarchical, model-based merging of multiple fragments for improved three-dimensional segmentation of nuclei.
Gang Lin, Monica K Chawla, +3 authors, Badrinath Roysam.
Cytometry A, 2004 Dec 08; 63(1). PMID: 15584021
An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision.
Yuri Boykov, Vladimir Kolmogorov.
IEEE Trans Pattern Anal Mach Intell, 2005 Mar 04; 26(9). PMID: 15742889
Highly Cited.
Intravital leukocyte detection using the gradient inverse coefficient of variation.
Gang Dong, Nilanjan Ray, Scott T Acton.
IEEE Trans Med Imaging, 2005 Jul 14; 24(7). PMID: 16011321
Unsupervised segmentation based on robust estimation and color active contour models.
Lin Yang, Peter Meer, David J Foran.
IEEE Trans Inf Technol Biomed, 2005 Sep 20; 9(3). PMID: 16167702
Automated evaluation of Her-2/neu status in breast tissue from fluorescent in situ hybridization images.
Francesco Raimondo, Marios A Gavrielides, +3 authors, Ioannis Kostopoulos.
IEEE Trans Image Process, 2005 Sep 30; 14(9). PMID: 16190465
Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces.
Alexandre Dufour, Vasily Shinin, +3 authors, Christophe Zimmer.
IEEE Trans Image Process, 2005 Sep 30; 14(9). PMID: 16190474
Coupled parametric active contours.
Christophe Zimmer, J C Olivo-Marin.
IEEE Trans Pattern Anal Mach Intell, 2005 Nov 16; 27(11). PMID: 16285382
A new detection algorithm (NDA) based on fuzzy cellular neural networks for white blood cell detection.
Wang Shitong, Wang Min.
IEEE Trans Inf Technol Biomed, 2006 Feb 01; 10(1). PMID: 16445244
Development of fetal haemoglobin-blood cells (F cells) within colorectal tumour tissues.
M Wolk, J E Martin, C Reinus.
J Clin Pathol, 2006 Feb 14; 59(6). PMID: 16469830    Free PMC article.
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen.
Jason Moffat, Dorre A Grueneberg, +16 authors, David E Root.
Cell, 2006 Mar 28; 124(6). PMID: 16564017
Highly Cited.
Automated segmentation, classification, and tracking of cancer cell nuclei in time-lapse microscopy.
Xiaowei Chen, Xiaobo Zhou, Stephen T C Wong.
IEEE Trans Biomed Eng, 2006 Apr 11; 53(4). PMID: 16602586
Towards automated cellular image segmentation for RNAi genome-wide screening.
Xiaobo Zhou, K Y Liu, +2 authors, Stephen T C Wong.
Med Image Comput Comput Assist Interv, 2006 May 12; 8(Pt 1). PMID: 16685930
Supervised learning-based cell image segmentation for p53 immunohistochemistry.
K Z Mao, Peng Zhao, Puay-Hoon Tan.
IEEE Trans Biomed Eng, 2006 Jun 10; 53(6). PMID: 16761842
Repulsive force based snake model to segment and track neuronal axons in 3D microscopy image stacks.
Hongmin Cai, Xiaoyin Xu, +3 authors, Stephen T C Wong.
Neuroimage, 2006 Jul 25; 32(4). PMID: 16861006
On weighting clustering.
Richard Nock, Frank Nielsen.
IEEE Trans Pattern Anal Mach Intell, 2006 Aug 05; 28(8). PMID: 16886859
High-throughput analysis of multispectral images of breast cancer tissue.
Umesh Adiga, Ravikanth Malladi, Rodrigo Fernandez-Gonzalez, Carlos Ortiz de Solorzano.
IEEE Trans Image Process, 2006 Aug 12; 15(8). PMID: 16900681
Automated tool for the detection of cell nuclei in digital microscopic images: application to retinal images.
Jiyun Byun, Mark R Verardo, +3 authors, Steven K Fisher.
Mol Vis, 2006 Sep 01; 12. PMID: 16943767
Automated tracking of gene expression in individual cells and cell compartments.
Hailin Shen, Glyn Nelson, +7 authors, Douglas B Kell.
J R Soc Interface, 2006 Oct 04; 3(11). PMID: 17015304    Free PMC article.
Random walks for image segmentation.
Leo Grady.
IEEE Trans Pattern Anal Mach Intell, 2006 Oct 27; 28(11). PMID: 17063682
Highly Cited.
CellProfiler: image analysis software for identifying and quantifying cell phenotypes.
Anne E Carpenter, Thouis R Jones, +9 authors, David M Sabatini.
Genome Biol, 2006 Nov 02; 7(10). PMID: 17076895    Free PMC article.
Highly Cited.
Cell segmentation using coupled level sets and graph-vertex coloring.
Sumit K Nath, Kannappan Palaniappan, Filiz Bunyak.
Med Image Comput Comput Assist Interv, 2007 Mar 16; 9(Pt 1). PMID: 17354879    Free PMC article.
Iterative voting for inference of structural saliency and characterization of subcellular events.
Bahram Parvin, Qing Yang, +3 authors, Mary Helen Barcellos-Hoff.
IEEE Trans Image Process, 2007 Mar 16; 16(3). PMID: 17357723
A multi-model approach to simultaneous segmentation and classification of heterogeneous populations of cell nuclei in 3D confocal microscope images.
Gang Lin, Monica K Chawla, +5 authors, Badrinath Roysam.
Cytometry A, 2007 Jul 27; 71(9). PMID: 17654650
Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy.
Meng Wang, Xiaobo Zhou, +3 authors, Stephen T C Wong.
Bioinformatics, 2007 Nov 09; 24(1). PMID: 17989093
High throughput analysis of breast cancer specimens on the grid.
Lin Yang, Wenjin Chen, +3 authors, David J Foran.
Med Image Comput Comput Assist Interv, 2007 Dec 07; 10(Pt 1). PMID: 18051110    Free PMC article.
Image registration based on boundary mapping.
C Davatzikos, J L Prince, R N Bryan.
IEEE Trans Med Imaging, 1996 Jan 01; 15(1). PMID: 18215894
An adaptive resource-allocating network for automated detection, segmentation, and classification of breast cancer nuclei topic area: image processing and recognition.
Kyoung-Mi Lee, W N Street.
IEEE Trans Neural Netw, 2008 Feb 02; 14(3). PMID: 18238048
Active contours without edges.
T F Chan, L A Vese.
IEEE Trans Image Process, 2008 Feb 06; 10(2). PMID: 18249617
Highly Cited.
Spatially adaptive wavelet thresholding with context modeling for image denoising.
S G Chang, B Yu, M Vetterli.
IEEE Trans Image Process, 2008 Feb 12; 9(9). PMID: 18262990
Automatic segmentation of high-throughput RNAi fluorescent cellular images.
P Yan, X Zhou, M Shah, S T C Wong.
IEEE Trans Inf Technol Biomed, 2008 Feb 14; 12(1). PMID: 18270043    Free PMC article.
Snakes, shapes, and gradient vector flow.
C Xu, J L Prince.
IEEE Trans Image Process, 2008 Feb 16; 7(3). PMID: 18276256
Highly Cited.
MAC: magnetostatic active contour model.
Xianghua Xie, Majid Mirmehdi.
IEEE Trans Pattern Anal Mach Intell, 2008 Feb 16; 30(4). PMID: 18276969
An automated method for cell detection in zebrafish.
Tianming Liu, Gang Li, +6 authors, Stephen T C Wong.
Neuroinformatics, 2008 Feb 22; 6(1). PMID: 18288618
Morphological grayscale reconstruction in image analysis: applications and efficient algorithms.
L Vincent.
IEEE Trans Image Process, 1993 Jan 01; 2(2). PMID: 18296207
Highly Cited.
Segmentation of touching cell nuclei using gradient flow tracking.
G Li, T Liu, +7 authors, S T C Wong.
J Microsc, 2008 Jul 22; 231(Pt 1). PMID: 18638189
Cell population tracking and lineage construction with spatiotemporal context.
Kang Li, Eric D Miller, +3 authors, Phil G Campbell.
Med Image Anal, 2008 Jul 29; 12(5). PMID: 18656418    Free PMC article.
Spatio-temporal cell cycle phase analysis using level sets and fast marching methods.
Dirk Padfield, Jens Rittscher, Nick Thomas, Badrinath Roysam.
Med Image Anal, 2008 Aug 30; 13(1). PMID: 18752984
Automatic image analysis of histopathology specimens using concave vertex graph.
Lin Yang, Oncel Tuzel, Peter Meer, David J Foran.
Med Image Comput Comput Assist Interv, 2008 Nov 05; 11(Pt 1). PMID: 18979823    Free PMC article.
Robust face recognition via sparse representation.
John Wright, Allen Y Yang, +2 authors, Yi Ma.
IEEE Trans Pattern Anal Mach Intell, 2008 Dec 27; 31(2). PMID: 19110489
Highly Cited.
A unified framework for automated 3-d segmentation of surface-stained living cells and a comprehensive segmentation evaluation.
Erlend Hodneland, Nickolay V Bukoreshtliev, +4 authors, Hans-Hermann Gerdes.
IEEE Trans Med Imaging, 2009 Jan 10; 28(5). PMID: 19131295
Automated quantitative assessment of HER-2/neu immunohistochemical expression in breast cancer.
Hela Masmoudi, Stephen M Hewitt, +2 authors, Marios A Gavrielides.
IEEE Trans Med Imaging, 2009 Jan 24; 28(6). PMID: 19164073    Free PMC article.
PathMiner: a Web-based tool for computer-assisted diagnostics in pathology.
Lin Yang, Oncel Tuzel, +4 authors, David J Foran.
IEEE Trans Inf Technol Biomed, 2009 Jan 28; 13(3). PMID: 19171530    Free PMC article.
Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning.
Thouis R Jones, Anne E Carpenter, +8 authors, David M Sabatini.
Proc Natl Acad Sci U S A, 2009 Feb 04; 106(6). PMID: 19188593    Free PMC article.
Highly Cited.
A novel cell segmentation method and cell phase identification using Markov model.
Xiaobo Zhou, Fuhai Li, Jun Yan, Stephen T C Wong.
IEEE Trans Inf Technol Biomed, 2009 Mar 11; 13(2). PMID: 19272857    Free PMC article.
Segmentation of clustered nuclei with shape markers and marking function.
Jierong Cheng, Jagath C Rajapakse.
IEEE Trans Biomed Eng, 2009 Mar 11; 56(3). PMID: 19272880
Virtual microscopy and grid-enabled decision support for large-scale analysis of imaged pathology specimens.
Lin Yang, Wenjin Chen, +4 authors, David J Foran.
IEEE Trans Inf Technol Biomed, 2009 Apr 17; 13(4). PMID: 19369162    Free PMC article.
Multiple nuclei tracking using integer programming for quantitative cancer cell cycle analysis.
Fuhai Li, Xiaobo Zhou, Jinwen Ma, Stephen T C Wong.
IEEE Trans Med Imaging, 2009 Aug 01; 29(1). PMID: 19643704    Free PMC article.
A 3D digital atlas of C. elegans and its application to single-cell analyses.
Fuhui Long, Hanchuan Peng, +2 authors, Eugene Myers.
Nat Methods, 2009 Aug 18; 6(9). PMID: 19684595    Free PMC article.
Digital pathology in Europe: coordinating patient care and research efforts.
Marcial Garcia Rojo, Vytenis Punys, +3 authors, Bernd Blobel.
Stud Health Technol Inform, 2009 Sep 12; 150. PMID: 19745463
Segmentation of heterogeneous blob objects through voting and level set formulation.
Hang Chang, Qing Yang, Bahram Parvin.
Pattern Recognit Lett, 2007 Jan 01; 28(13). PMID: 19774202    Free PMC article.
TurboPixels: fast superpixels using geometric flows.
Alex Levinshtein, Adrian Stere, +3 authors, Kaleem Siddiqi.
IEEE Trans Pattern Anal Mach Intell, 2009 Oct 17; 31(12). PMID: 19834148
Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy.
Quanli Wang, Jarad Niemi, +2 authors, Mike West.
Cytometry A, 2009 Oct 22; 77(1). PMID: 19845017    Free PMC article.
A biosegmentation benchmark for evaluation of bioimage analysis methods.
Elisa Drelie Gelasca, Boguslaw Obara, +2 authors, Bs Manjunath.
BMC Bioinformatics, 2009 Nov 03; 10. PMID: 19878606    Free PMC article.
Improved automatic detection and segmentation of cell nuclei in histopathology images.
Yousef Al-Kofahi, Wiem Lassoued, William Lee, Badrinath Roysam.
IEEE Trans Biomed Eng, 2009 Nov 04; 57(4). PMID: 19884070
Highly Cited.
Classification of hematologic malignancies using texton signatures.
Oncel Tuzel, Lin Yang, Peter Meer, David J Foran.
Pattern Anal Appl, 2007 Oct 01; 10(4). PMID: 19890460    Free PMC article.
Cells segmentation from 3-D confocal images of early zebrafish embryogenesis.
Cecilia Zanella, Matteo Campana, +6 authors, Alessandro Sarti.
IEEE Trans Image Process, 2009 Dec 04; 19(3). PMID: 19955038
Evolving generalized Voronoi diagrams for accurate cellular image segmentation.
Weimiao Yu, Hwee Kuan Lee, +2 authors, Sohail Ahmed.
Cytometry A, 2010 Feb 20; 77(4). PMID: 20169588
Expectation-maximization-driven geodesic active contour with overlap resolution (EMaGACOR): application to lymphocyte segmentation on breast cancer histopathology.
Hussain Fatakdawala, Jun Xu, +5 authors, Anant Madabhushi.
IEEE Trans Biomed Eng, 2010 Feb 23; 57(7). PMID: 20172780
Advanced level-set-based cell tracking in time-lapse fluorescence microscopy.
Oleh Dzyubachyk, Wiggert A van Cappellen, +2 authors, Erik Meijering.
IEEE Trans Med Imaging, 2010 Mar 05; 29(3). PMID: 20199920
Cell segmentation using front vector flow guided active contours.
Fuhai Li, Xiaobo Zhou, Hong Zhao, Stephen T C Wong.
Med Image Comput Comput Assist Interv, 2009 Jan 01; 12(Pt 2). PMID: 20426162    Free PMC article.
Detection of spatially correlated objects in 3D images using appearance models and coupled active contours.
Kishore Mosaliganti, Arnaud Gelas, +3 authors, Sean Megason.
Med Image Comput Comput Assist Interv, 2009 Jan 01; 12(Pt 2). PMID: 20426166    Free PMC article.
A better lens on disease.
Mike May.
Sci Am, 2010 May 07; 302(5). PMID: 20443381
Cell nuclei and cytoplasm joint segmentation using the sliding band filter.
Pedro Quelhas, Monica Marcuzzo, Ana Maria Mendonça, Aurélio Campilho.
IEEE Trans Med Imaging, 2010 Jun 08; 29(8). PMID: 20525532
Huiming Peng, Xiaobo Zhou, +2 authors, Stephen T C Wong.
Proc IEEE Int Symp Biomed Imaging, 2010 Jun 30; 2009. PMID: 20585412    Free PMC article.
Computer-aided detection of centroblasts for follicular lymphoma grading using adaptive likelihood-based cell segmentation.
Olcay Sertel, Gerard Lozanski, Arwa Shana'ah, Metin N Gurcan.
IEEE Trans Biomed Eng, 2010 Jul 03; 57(10). PMID: 20595077    Free PMC article.
Luís Pedro Coelho, Aabid Shariff, Robert F Murphy.
Proc IEEE Int Symp Biomed Imaging, 2009 Jan 01; 5193098. PMID: 20628545    Free PMC article.
Unsupervised segmentation of overlapped nuclei using Bayesian classification.
Chanho Jung, Changick Kim, Seoung Wan Chae, Sukjoong Oh.
IEEE Trans Biomed Eng, 2010 Jul 27; 57(12). PMID: 20656648
Segmenting clustered nuclei using H-minima transform-based marker extraction and contour parameterization.
Chanho Jung, Changick Kim.
IEEE Trans Biomed Eng, 2010 Jul 27; 57(10). PMID: 20656653
Histopathological image analysis: a review.
Metin N Gurcan, Laura E Boucheron, +3 authors, B Yener.
IEEE Rev Biomed Eng, 2009 Jan 01; 2. PMID: 20671804    Free PMC article.
Highly Cited. Review.
CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging.
Michael Held, Michael H A Schmitz, +6 authors, Daniel W Gerlich.
Nat Methods, 2010 Aug 10; 7(9). PMID: 20693996
Highly Cited.
Contour detection and hierarchical image segmentation.
Pablo Arbeláez, Michael Maire, Charless Fowlkes, Jitendra Malik.
IEEE Trans Pattern Anal Mach Intell, 2010 Aug 25; 33(5). PMID: 20733228
Distance regularized level set evolution and its application to image segmentation.
Chunming Li, Chenyang Xu, Changfeng Gui, Martin D Fox.
IEEE Trans Image Process, 2010 Aug 31; 19(12). PMID: 20801742
Highly Cited.
Coupled minimum-cost flow cell tracking for high-throughput quantitative analysis.
Dirk Padfield, Jens Rittscher, Badrinath Roysam.
Med Image Anal, 2010 Sep 25; 15(4). PMID: 20864383
Fast random walker with priors using precomputation for interactive medical image segmentation.
Shawn Andrews, Ghassan Hamarneh, Ahmed Saad.
Med Image Comput Comput Assist Interv, 2010 Oct 01; 13(Pt 3). PMID: 20879377
Automated detection of cell nuclei in pap smear images using morphological reconstruction and clustering.
Marina E Plissiti, Christophoros Nikou, Antonia Charchanti.
IEEE Trans Inf Technol Biomed, 2010 Oct 19; 15(2). PMID: 20952343
3-D active meshes: fast discrete deformable models for cell tracking in 3-D time-lapse microscopy.
Alexandre Dufour, Roman Thibeaux, +2 authors, Jean-Christophe Olivo-Marin.
IEEE Trans Image Process, 2011 Jan 05; 20(7). PMID: 21193379
Parmeshwar Khurd, Claus Bahlmann, +4 authors, John V Frangioni.
Proc IEEE Int Symp Biomed Imaging, 2011 Jan 12; 14-17 April 2010. PMID: 21221421    Free PMC article.
Tracking biological cells in time-lapse microscopy: an adaptive technique combining motion and topological features.
M Ali Akber Dewan, M Omair Ahmad, M N S Swamy.
IEEE Trans Biomed Eng, 2011 Feb 01; 58(6). PMID: 21278009
Hough forests for object detection, tracking, and action recognition.
Juergen Gall, Angela Yao, +2 authors, Victor Lempitsky.
IEEE Trans Pattern Anal Mach Intell, 2011 Apr 06; 33(11). PMID: 21464503
Computational pathology: challenges and promises for tissue analysis.
Thomas J Fuchs, Joachim M Buhmann.
Comput Med Imaging Graph, 2011 Apr 13; 35(7-8). PMID: 21481567
Partitioning histopathological images: an integrated framework for supervised color-texture segmentation and cell splitting.
Hui Kong, Metin Gurcan, Kamel Belkacem-Boussaid.
IEEE Trans Med Imaging, 2011 Apr 14; 30(9). PMID: 21486712    Free PMC article.
ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology.
David J Foran, Lin Yang, +8 authors, Joel H Saltz.
J Am Med Inform Assoc, 2011 May 25; 18(4). PMID: 21606133    Free PMC article.
Pop out many small structures from a very large microscopic image.
Elena Bernardis, Stella X Yu.
Med Image Anal, 2011 Aug 16; 15(5). PMID: 21839666
Simultaneous recognition and segmentation of cells: application in C.elegans.
Lei Qu, Fuhui Long, +3 authors, Hanchuan Peng.
Bioinformatics, 2011 Aug 19; 27(20). PMID: 21849395    Free PMC article.
A computational approach to edge detection.
J Canny.
IEEE Trans Pattern Anal Mach Intell, 1986 Jun 01; 8(6). PMID: 21869365
Highly Cited.
Discriminative segmentation of microscopic cellular images.
Li Cheng, Ning Ye, Weimiao Yu, Andre Cheah.
Med Image Comput Comput Assist Interv, 2011 Oct 19; 14(Pt 1). PMID: 22003672
Robust segmentation of overlapping cells in histopathology specimens using parallel seed detection and repulsive level set.
Xin Qi, Fuyong Xing, David J Foran, Lin Yang.
IEEE Trans Biomed Eng, 2011 Dec 15; 59(3). PMID: 22167559    Free PMC article.
Segmentation of cervical cell nuclei in high-resolution microscopic images: A new algorithm and a web-based software framework.
Christoph Bergmeir, Miguel García Silvente, José Manuel Benítez.
Comput Methods Programs Biomed, 2012 Feb 07; 107(3). PMID: 22306072
Embedding topic discovery in conditional random fields model for segmenting nuclei using multispectral data.
Xuqing Wu, Mojgan Amrikachi, Shishir K Shah.
IEEE Trans Biomed Eng, 2012 Mar 01; 59(6). PMID: 22374343
A state-of-the-art review on segmentation algorithms in intravascular ultrasound (IVUS) images.
Amin Katouzian, Elsa D Angelini, +3 authors, Andrew F Laine.
IEEE Trans Inf Technol Biomed, 2012 Mar 06; 16(5). PMID: 22389156
An integrated region-, boundary-, shape-based active contour for multiple object overlap resolution in histological imagery.
Sahirzeeshan Ali, Anant Madabhushi.
IEEE Trans Med Imaging, 2012 Apr 14; 31(7). PMID: 22498689
A parallel solution for high resolution histological image analysis.
G Bueno, R González, +5 authors, J Salido.
Comput Methods Programs Biomed, 2012 Apr 24; 108(1). PMID: 22522064
A new framework for particle detection in low-SNR fluorescence live-cell images and its application for improved particle tracking.
Lei Yang, Zhen Qiu, Alan H Greenaway, Weiping Lu.
IEEE Trans Biomed Eng, 2012 May 04; 59(7). PMID: 22552546
SLIC superpixels compared to state-of-the-art superpixel methods.
Radhakrishna Achanta, Appu Shaji, +3 authors, Sabine Süsstrunk.
IEEE Trans Pattern Anal Mach Intell, 2012 May 30; 34(11). PMID: 22641706
Highly Cited.
Mapping infected cell phenotype.
U Adiga, B L Bell, +4 authors, T J Lamkin.
IEEE Trans Biomed Eng, 2012 Jun 20; 59(8). PMID: 22711766
A call for bioimaging software usability.
Anne E Carpenter, Lee Kamentsky, Kevin W Eliceiri.
Nat Methods, 2012 Jun 30; 9(7). PMID: 22743771    Free PMC article.
Biological imaging software tools.
Kevin W Eliceiri, Michael R Berthold, +12 authors, Anne E Carpenter.
Nat Methods, 2012 Jun 30; 9(7). PMID: 22743775    Free PMC article.
Highly Cited.
Overlapping cell nuclei segmentation using a spatially adaptive active physical model.
Marina E Plissiti, Christophoros Nikou.
IEEE Trans Image Process, 2012 Jul 04; 21(11). PMID: 22752135
Detection and segmentation of cell nuclei in virtual microscopy images: a minimum-model approach.
Stephan Wienert, Daniel Heim, +6 authors, Frederick Klauschen.
Sci Rep, 2012 Jul 13; 2. PMID: 22787560    Free PMC article.
Efficient globally optimal segmentation of cells in fluorescence microscopy images using level sets and convex energy functionals.
Jan-Philip Bergeest, Karl Rohr.
Med Image Anal, 2012 Jul 17; 16(7). PMID: 22795525
Segmentation, Inference and Classification of Partially Overlapping Nanoparticles.
Chiwoo Park, Jianhua Z Huang, Jim X Ji, Yu Ding.
IEEE Trans Pattern Anal Mach Intell, 2012 Aug 01; 35(3). PMID: 22848127
Semiautomatic white blood cell segmentation based on multiscale analysis.
L B Dorini, R Minetto, N J Leite.
IEEE J Biomed Health Inform, 2012 Aug 03; 17(1). PMID: 22855228
State of the art and trends for digital pathology.
Marcial García Rojo.
Stud Health Technol Inform, 2012 Aug 29; 179. PMID: 22925782
Digital image analysis in breast cancer: an example of an automated methodology and the effects of image compression.
Carlos López, Marylène Lejeune, +7 authors, Joaquín Jaén.
Stud Health Technol Inform, 2012 Aug 29; 179. PMID: 22925796
Emerging trends: grid technology in pathology.
Gloria Bueno, Marcial García-Rojo, +4 authors, Jesús García-González.
Stud Health Technol Inform, 2012 Aug 29; 179. PMID: 22925801
NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri.
Nat Methods, 2012 Aug 30; 9(7). PMID: 22930834    Free PMC article.
Highly Cited.
Multireference level set for the characterization of nuclear morphology in glioblastoma multiforme.
Hang Chang, Ju Han, Paul T Spellman, Bahram Parvin.
IEEE Trans Biomed Eng, 2012 Sep 19; 59(12). PMID: 22987497    Free PMC article.
Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association.
Hang Chang, Ju Han, +4 authors, Bahram Parvin.
IEEE Trans Med Imaging, 2012 Dec 12; 32(4). PMID: 23221815    Free PMC article.
Learning to detect cells using non-overlapping extremal regions.
Carlos Arteta, Victor Lempitsky, J Alison Noble, Andrew Zisserman.
Med Image Comput Comput Assist Interv, 2013 Jan 05; 15(Pt 1). PMID: 23285570
Hierarchical partial matching and segmentation of interacting cells.
Zheng Wu, Danna Gurari, Joyce Y Wong, Margrit Betke.
Med Image Comput Comput Assist Interv, 2013 Jan 05; 15(Pt 1). PMID: 23285575
Segmentation and shape tracking of whole fluorescent cells based on the Chan-Vese model.
Martin Maška, Ondřej Daněk, +3 authors, Carlos Ortiz-de-Solorzano.
IEEE Trans Med Imaging, 2013 Feb 02; 32(6). PMID: 23372077
Attributed relational graphs for cell nucleus segmentation in fluorescence microscopy images.
Salim Arslan, Tulin Ersahin, Rengul Cetin-Atalay, Cigdem Gunduz-Demir.
IEEE Trans Med Imaging, 2013 Apr 04; 32(6). PMID: 23549886
A flexible and robust approach for segmenting cell nuclei from 2D microscopy images using supervised learning and template matching.
Cheng Chen, Wei Wang, John A Ozolek, Gustavo K Rohde.
Cytometry A, 2013 Apr 10; 83(5). PMID: 23568787    Free PMC article.
A generalized Laplacian of Gaussian filter for blob detection and its applications.
Hui Kong, Hatice Cinar Akakin, Sanjay E Sarma.
IEEE Trans Cybern, 2013 Jun 13; 43(6). PMID: 23757570
Learning hierarchical features for scene labeling.
Clément Farabet, Camille Couprie, Laurent Najman, Yann Lecun.
IEEE Trans Pattern Anal Mach Intell, 2013 Jun 22; 35(8). PMID: 23787344
Highly Cited.
Automatic cell segmentation and nuclear-to-cytoplasmic ratio analysis for third harmonic generated microscopy medical images.
Gwo Giun Lee, Huan-Hsiang Lin, +5 authors, Chun-Fu Chen.
IEEE Trans Biomed Circuits Syst, 2013 Jul 16; 7(2). PMID: 23853298
Mitosis detection in breast cancer histological images An ICPR 2012 contest.
Ludovic Roux, Daniel Racoceanu, +7 authors, Metin N Gurcan.
J Pathol Inform, 2013 Jul 17; 4. PMID: 23858383    Free PMC article.
Computer-Aided Breast Cancer Diagnosis Based on the Analysis of Cytological Images of Fine Needle Biopsies.
Pawel Filipczuk, Thomas Fevens, Adam Krzyzak, Roman Monczak.
IEEE Trans Med Imaging, 2013 Aug 06; 32(12). PMID: 23912498
Pathology imaging informatics for quantitative analysis of whole-slide images.
Sonal Kothari, John H Phan, Todd H Stokes, May D Wang.
J Am Med Inform Assoc, 2013 Aug 21; 20(6). PMID: 23959844    Free PMC article.
Highly Cited. Review.
Automatic Cell Detection in Bright-Field Microscope Images Using SIFT, Random Forests, and Hierarchical Clustering.
Firas Mualla, Simon Scholl, +2 authors, Joachim Hornegger.
IEEE Trans Med Imaging, 2013 Sep 05; 32(12). PMID: 24001988
Charisma: an integrated approach to automatic H&E-stained skeletal muscle cell segmentation using supervised learning and novel robust clump splitting.
Thomas Janssens, Laura Antanas, +3 authors, Fabian Güiza Grandas.
Med Image Anal, 2013 Sep 10; 17(8). PMID: 24012925
Parallel content-based sub-image retrieval using hierarchical searching.
Lin Yang, Xin Qi, +3 authors, David J Foran.
Bioinformatics, 2013 Nov 12; 30(7). PMID: 24215030    Free PMC article.
DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data.
Violeta N Kovacheva, Adnan M Khan, +2 authors, Nasir M Rajpoot.
Bioinformatics, 2013 Nov 26; 30(3). PMID: 24273247
Semi-automatic segmentation and classification of Pap smear cells.
Yung-Fu Chen, Po-Chi Huang, +6 authors, John Y Chiang.
IEEE J Biomed Health Inform, 2014 Jan 10; 18(1). PMID: 24403407
An integrated framework for automatic Ki-67 scoring in pancreatic neuroendocrine tumor.
Fuyong Xing, Hai Su, Lin Yang.
Med Image Comput Comput Assist Interv, 2014 Feb 08; 16(Pt 1). PMID: 24505696    Free PMC article.
Automated nucleus and cytoplasm segmentation of overlapping cervical cells.
Zhi Lu, Gustavo Carneiro, Andrew P Bradley.
Med Image Comput Comput Assist Interv, 2014 Feb 08; 16(Pt 1). PMID: 24505698
Robust selection-based sparse shape model for lung cancer image segmentation.
Fuyong Xing, Lin Yang.
Med Image Comput Comput Assist Interv, 2014 Feb 08; 16(Pt 3). PMID: 24505787    Free PMC article.
A benchmark for comparison of cell tracking algorithms.
Martin Maška, Vladimír Ulman, +27 authors, Carlos Ortiz-de-Solorzano.
Bioinformatics, 2014 Feb 15; 30(11). PMID: 24526711    Free PMC article.
Highly Cited.
Automatic Ki-67 counting using robust cell detection and online dictionary learning.
Fuyong Xing, Hai Su, Janna Neltner, Lin Yang.
IEEE Trans Biomed Eng, 2014 Feb 22; 61(3). PMID: 24557687
Mitosis detection in breast cancer histology images with deep neural networks.
Dan C Cireşan, Alessandro Giusti, Luca M Gambardella, Jürgen Schmidhuber.
Med Image Comput Comput Assist Interv, 2014 Mar 01; 16(Pt 2). PMID: 24579167
Highly Cited.
A novel framework for cellular tracking and mitosis detection in dense phase contrast microscopy images.
Ketheesan Thirusittampalam, M Julius Hossain, Ovidiu Ghita, Paul F Whelan.
IEEE J Biomed Health Inform, 2014 Mar 05; 17(3). PMID: 24592465
Toward automatic mitotic cell detection and segmentation in multispectral histopathological images.
Cheng Lu, Mrinal Mandal.
IEEE J Biomed Health Inform, 2014 Mar 13; 18(2). PMID: 24608059
Breast cancer histopathology image analysis: a review.
Mitko Veta, Josien P W Pluim, Paul J van Diest, Max A Viergever.
IEEE Trans Biomed Eng, 2014 Apr 25; 61(5). PMID: 24759275
Methods for nuclei detection, segmentation, and classification in digital histopathology: a review-current status and future potential.
Humayun Irshad, Antoine Veillard, Ludovic Roux, Daniel Racoceanu.
IEEE Rev Biomed Eng, 2014 May 08; 7. PMID: 24802905
Highly Cited. Review.
Accurate diagnosis of thyroid follicular lesions from nuclear morphology using supervised learning.
John A Ozolek, Akif Burak Tosun, +5 authors, Gustavo K Rohde.
Med Image Anal, 2014 May 20; 18(5). PMID: 24835183    Free PMC article.
A nonlinear mapping approach to stain normalization in digital histopathology images using image-specific color deconvolution.
Adnan Mujahid Khan, Nasir Rajpoot, Darren Treanor, Derek Magee.
IEEE Trans Biomed Eng, 2014 May 23; 61(6). PMID: 24845283
A system for counting fetal and maternal red blood cells.
Ji Ge, Zheng Gong, +5 authors, Yu Sun.
IEEE Trans Biomed Eng, 2014 Jun 01; 61(12). PMID: 24879644
A robust algorithm for segmenting and tracking clustered cells in time-lapse fluorescent microscopy.
Wojciech Tarnawski, Vartan Kurtcuoglu, +7 authors, Aldo Ferrari.
IEEE J Biomed Health Inform, 2014 Jul 24; 17(4). PMID: 25055315
Representing and decomposing neural potential signals.
Jose C Principe, Austin J Brockmeier.
Curr Opin Neurobiol, 2014 Aug 13; 31. PMID: 25113153
Active contour-based cell segmentation during freezing and its application in cryopreservation.
Pengxiang Wu, Jingru Yi, +3 authors, Dayong Gao.
IEEE Trans Biomed Eng, 2014 Aug 28; 62(1). PMID: 25163052
An efficient technique for nuclei segmentation based on ellipse descriptor analysis and improved seed detection algorithm.
Hongming Xu, Cheng Lu, Mrinal Mandal.
IEEE J Biomed Health Inform, 2014 Sep 06; 18(5). PMID: 25192578
Small blob identification in medical images using regional features from optimum scale.
Min Zhang, Teresa Wu, Kevin M Bennett.
IEEE Trans Biomed Eng, 2014 Sep 30; 62(4). PMID: 25265624
Towards large-scale histopathological image analysis: hashing-based image retrieval.
Xiaofan Zhang, Wei Liu, +2 authors, Shaoting Zhang.
IEEE Trans Med Imaging, 2014 Oct 15; 34(2). PMID: 25314696
Cell detection and segmentation using correlation clustering.
Chong Zhang, Julian Yarkony, Fred A Hamprecht.
Med Image Comput Comput Assist Interv, 2014 Oct 22; 17(Pt 1). PMID: 25333095
Optree: a learning-based adaptive watershed algorithm for neuron segmentation.
Mustafa Gökhan Uzunbaş, Chao Chen, Dimitris Metaxas.
Med Image Comput Comput Assist Interv, 2014 Oct 22; 17(Pt 1). PMID: 25333106
A new 2.5D representation for lymph node detection using random sets of deep convolutional neural network observations.
Holger R Roth, Le Lu, +6 authors, Ronald M Summers.
Med Image Comput Comput Assist Interv, 2014 Oct 22; 17(Pt 1). PMID: 25333158    Free PMC article.
A method for automatic segmentation of nuclei in phase-contrast images based on intensity, convexity and texture.
M Ali Akber Dewan, M Omair Ahmad, M N S Swamy.
IEEE Trans Biomed Circuits Syst, 2014 Nov 13; 8(5). PMID: 25388879
Mining histopathological images via composite hashing and online learning.
Xiaofan Zhang, Lin Yang, +2 authors, Shaoting Zhang.
Med Image Comput Comput Assist Interv, 2014 Dec 09; 17(Pt 2). PMID: 25485414
Cell words: modelling the visual appearance of cells in histopathology images.
Korsuk Sirinukunwattana, Adnan M Khan, Nasir M Rajpoot.
Comput Med Imaging Graph, 2014 Dec 17; 42. PMID: 25498246
Localisation of luminal epithelium edge in digital histopathology images of IHC stained slides of endometrial biopsies.
Guannan Li, Victor Sanchez, +2 authors, Nasir Rajpoot.
Comput Med Imaging Graph, 2014 Dec 23; 42. PMID: 25529641
Assessment of algorithms for mitosis detection in breast cancer histopathology images.
Mitko Veta, Paul J van Diest, +26 authors, Josien P W Pluim.
Med Image Anal, 2014 Dec 31; 20(1). PMID: 25547073
An improved joint optimization of multiple level set functions for the segmentation of overlapping cervical cells.
Zhi Lu, Gustavo Carneiro, Andrew P Bradley.
IEEE Trans Image Process, 2015 Jan 15; 24(4). PMID: 25585419
Cell Detection From Redundant Candidate Regions Under Nonoverlapping Constraints.
Ryoma Bise, Yoichi Sato.
IEEE Trans Med Imaging, 2015 Jan 17; 34(7). PMID: 25594964
Accurate Segmentation of Cervical Cytoplasm and Nuclei Based on Multiscale Convolutional Network and Graph Partitioning.
Youyi Song, Ling Zhang, +3 authors, Tianfu Wang.
IEEE Trans Biomed Eng, 2015 May 13; 62(10). PMID: 25966470
Detecting overlapping instances in microscopy images using extremal region trees.
Carlos Arteta, Victor Lempitsky, J Alison Noble, Andrew Zisserman.
Med Image Anal, 2015 May 20; 27. PMID: 25980675
Deep learning.
Yann LeCun, Yoshua Bengio, Geoffrey Hinton.
Nature, 2015 May 29; 521(7553). PMID: 26017442
Highly Cited. Review.
Weighted Hashing with Multiple Cues for Cell-Level Analysis of Histopathological Images.
Xiaofan Zhang, Hai Su, Lin Yang, Shaoting Zhang.
Inf Process Med Imaging, 2015 Jul 30; 24. PMID: 26221682
Evaluation of cytokeratin-19 in breast cancer tissue samples: a comparison of automatic and manual evaluations of scanned tissue microarray cylinders.
Cristina Callau, Marylène Lejeune, +7 authors, Carlos López.
Biomed Eng Online, 2015 Sep 04; 14 Suppl 2. PMID: 26329009    Free PMC article.
Automatic Myonuclear Detection in Isolated Single Muscle Fibers Using Robust Ellipse Fitting and Sparse Representation.
Hai Su, Fuyong Xing, +2 authors, Lin Yang.
IEEE/ACM Trans Comput Biol Bioinform, 2014 Jul 01; 11(4). PMID: 26356342    Free PMC article.
Jun Kong, Fusheng Wang, +4 authors, Daniel J Brat.
Proc IEEE Int Symp Biomed Imaging, 2015 Sep 26; 2015. PMID: 26405506    Free PMC article.
An Automatic Learning-Based Framework for Robust Nucleus Segmentation.
Fuyong Xing, Yuanpu Xie, Lin Yang.
IEEE Trans Med Imaging, 2015 Sep 29; 35(2). PMID: 26415167
High-throughput histopathological image analysis via robust cell segmentation and hashing.
Xiaofan Zhang, Fuyong Xing, +2 authors, Shaoting Zhang.
Med Image Anal, 2015 Nov 26; 26(1). PMID: 26599156    Free PMC article.
Automatic batch-invariant color segmentation of histological cancer images.
Sonal Kothari, John H Phan, +5 authors, May D Wang.
Proc IEEE Int Symp Biomed Imaging, 2011 Mar 01; 2011. PMID: 27532016    Free PMC article.
Robust Cell Detection and Segmentation in Histopathological Images Using Sparse Reconstruction and Stacked Denoising Autoencoders.
Hai Su, Fuyong Xing, +3 authors, Lin Yang.
Med Image Comput Comput Assist Interv, 2016 Nov 01; 9351. PMID: 27796013    Free PMC article.
Fuyong Xing, Lin Yang.
Proc IEEE Int Symp Biomed Imaging, 2015 Apr 01; 2015. PMID: 27924189    Free PMC article.
Fast Cell Segmentation Using Scalable Sparse Manifold Learning and Affine Transform-approximated Active Contour.
Fuyong Xing, Lin Yang.
Med Image Comput Comput Assist Interv, 2015 Oct 01; 9351. PMID: 27924317    Free PMC article.
Deep Voting: A Robust Approach Toward Nucleus Localization in Microscopy Images.
Yuanpu Xie, Xiangfei Kong, +3 authors, Lin Yang.
Med Image Comput Comput Assist Interv, 2015 Oct 01; 9351. PMID: 28083567    Free PMC article.
Beyond Classification: Structured Regression for Robust Cell Detection Using Convolutional Neural Network.
Yuanpu Xie, Fuyong Xing, +2 authors, Lin Yang.
Med Image Comput Comput Assist Interv, 2015 Oct 01; 9351. PMID: 28090601    Free PMC article.
Yin Zhou, Hang Chang, Kenneth E Barner, Bahram Parvin.
Proc IEEE Int Symp Biomed Imaging, 2015 Apr 01; 2015. PMID: 28101301    Free PMC article.
Sonal Kothari, Qaiser Chaudry, May D Wang.
Proc IEEE Int Symp Biomed Imaging, 2009 Jun 01; 2009. PMID: 28392889    Free PMC article.
A geometric snake model for segmentation of medical imagery.
A Yezzi, S Kichenassamy, +2 authors, A Tannenbaum.
IEEE Trans Med Imaging, 1997 Apr 01; 16(2). PMID: 9101329
Limits of Applicability of the Voronoi Tessellation Determined by Centers of Cell Nuclei to Epithelium Morphology.
Sara Kaliman, Christina Jayachandran, Florian Rehfeldt, Ana-Sunčana Smith.
Front Physiol, 2016 Dec 10; 7. PMID: 27932987    Free PMC article.
AIIMDs: An Integrated Framework of Automatic Idiopathic Inflammatory Myopathy Diagnosis for Muscle.
Manish Sapkota, Fujun Liu, +3 authors, Lin Yang.
IEEE J Biomed Health Inform, 2017 Apr 20; 22(3). PMID: 28422672    Free PMC article.
Segmentation of White Blood Cells From Microscopic Images Using a Novel Combination of K-Means Clustering and Modified Watershed Algorithm.
Narjes Ghane, Alireza Vard, Ardeshir Talebi, Pardis Nematollahy.
J Med Signals Sens, 2017 May 30; 7(2). PMID: 28553582    Free PMC article.
Detection of Nuclei in H&E Stained Sections Using Convolutional Neural Networks.
Mina Khoshdeli, Richard Cong, Bahram Parvin.
IEEE EMBS Int Conf Biomed Health Inform, 2017 Jun 06; 2017. PMID: 28580455    Free PMC article.
Efficient and robust cell detection: A structured regression approach.
Yuanpu Xie, Fuyong Xing, +3 authors, Lin Yang.
Med Image Anal, 2017 Aug 12; 44. PMID: 28797548    Free PMC article.
A Methodology for Texture Feature-based Quality Assessment in Nucleus Segmentation of Histopathology Image.
Si Wen, Tahsin M Kurc, +3 authors, Wei Zhu.
J Pathol Inform, 2017 Oct 03; 8. PMID: 28966837    Free PMC article.
Acquisition of cell migration defines NK cell differentiation from hematopoietic stem cell precursors.
Barclay J Lee, Emily M Mace.
Mol Biol Cell, 2017 Oct 13; 28(25). PMID: 29021341    Free PMC article.
Systems pathology by multiplexed immunohistochemistry and whole-slide digital image analysis.
Sami Blom, Lassi Paavolainen, +7 authors, Teijo Pellinen.
Sci Rep, 2017 Nov 16; 7(1). PMID: 29138507    Free PMC article.
Highly Cited.
Machine Learning for Nuclear Mechano-Morphometric Biomarkers in Cancer Diagnosis.
Adityanarayanan Radhakrishnan, Karthik Damodaran, +2 authors, G V Shivashankar.
Sci Rep, 2017 Dec 22; 7(1). PMID: 29263424    Free PMC article.
Fluorescence anisotropy imaging in drug discovery.
Claudio Vinegoni, Paolo Fumene Feruglio, +2 authors, Ralph Weissleder.
Adv Drug Deliv Rev, 2018 Feb 08; 151-152. PMID: 29410158    Free PMC article.
Feature-Based Representation Improves Color Decomposition and Nuclear Detection Using a Convolutional Neural Network.
Mina Khoshdeli, Bahram Parvin.
IEEE Trans Biomed Eng, 2018 Feb 21; 65(3). PMID: 29461964    Free PMC article.
Deep Learning Nuclei Detection in Digitized Histology Images by Superpixels.
Sudhir Sornapudi, Ronald Joe Stanley, +6 authors, Shelliane R Frazier.
J Pathol Inform, 2018 Apr 06; 9. PMID: 29619277    Free PMC article.
Comparison of Different Classifiers with Active Learning to Support Quality Control in Nucleus Segmentation in Pathology Images.
Si Wen, Tahsin M Kurc, +7 authors, Wei Zhu.
AMIA Jt Summits Transl Sci Proc, 2018 Jun 12; 2017. PMID: 29888078    Free PMC article.
Fusion of encoder-decoder deep networks improves delineation of multiple nuclear phenotypes.
Mina Khoshdeli, Garrett Winkelmaier, Bahram Parvin.
BMC Bioinformatics, 2018 Aug 09; 19(1). PMID: 30086715    Free PMC article.
Automated fluorescence intensity and gradient analysis enables detection of rare fluorescent mutant cells deep within the tissue of RaDR mice.
Dushan N Wadduwage, Jennifer Kay, +5 authors, Peter T C So.
Sci Rep, 2018 Aug 16; 8(1). PMID: 30108260    Free PMC article.
Relationship between the Ki67 index and its area based approximation in breast cancer.
Muhammad Khalid Khan Niazi, Caglar Senaras, +3 authors, Metin N Gurcan.
BMC Cancer, 2018 Sep 05; 18(1). PMID: 30176814    Free PMC article.
Machine Learning Methods for Histopathological Image Analysis.
Daisuke Komura, Shumpei Ishikawa.
Comput Struct Biotechnol J, 2018 Oct 03; 16. PMID: 30275936    Free PMC article.
Highly Cited. Review.
Automated Cell Tracking Using Motion Prediction-Based Matching and Event Handling.
Fatima Boukari, Sokratis Makrogiannis.
IEEE/ACM Trans Comput Biol Bioinform, 2018 Oct 20; 17(3). PMID: 30334766    Free PMC article.
Cone Photoreceptor Cell Segmentation and Diameter Measurement on Adaptive Optics Images Using Circularly Constrained Active Contour Model.
Jianfei Liu, HaeWon Jung, Alfredo Dubra, Johnny Tam.
Invest Ophthalmol Vis Sci, 2018 Oct 30; 59(11). PMID: 30372733    Free PMC article.
Open access image repositories: high-quality data to enable machine learning research.
F Prior, J Almeida, +4 authors, J Saltz.
Clin Radiol, 2019 May 02; 75(1). PMID: 31040006    Free PMC article.
Deep fusion of contextual and object-based representations for delineation of multiple nuclear phenotypes.
Mina Khoshdeli, Garrett Winkelmaier, Bahram Parvin.
Bioinformatics, 2019 May 29; 35(22). PMID: 31135022    Free PMC article.
Automated detection and quantification of breast cancer brain metastases in an animal model using democratized machine learning tools.
Dina Sikpa, Jérémie P Fouquet, +3 authors, Martin Lepage.
Sci Rep, 2019 Nov 24; 9(1). PMID: 31758004    Free PMC article.
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl.
Juan C Caicedo, Allen Goodman, +10 authors, Anne E Carpenter.
Nat Methods, 2019 Oct 23; 16(12). PMID: 31636459    Free PMC article.
ki67 nuclei detection and ki67-index estimation: a novel automatic approach based on human vision modeling.
Barbara Rita Barricelli, Elena Casiraghi, +4 authors, Barbara Vergani.
BMC Bioinformatics, 2019 Dec 29; 20(1). PMID: 31881821    Free PMC article.
Immune profiles in acute myeloid leukemia bone marrow associate with patient age, T-cell receptor clonality, and survival.
Oscar Brück, Olli Dufva, +14 authors, Satu Mustjoki.
Blood Adv, 2020 Jan 23; 4(2). PMID: 31968078    Free PMC article.
Joint Region and Nucleus Segmentation for Characterization of Tumor Infiltrating Lymphocytes in Breast Cancer.
Mohamed Amgad, Anindya Sarkar, +8 authors, Michael Barnes.
Proc SPIE Int Soc Opt Eng, 2020 Jan 31; 10956. PMID: 31997849    Free PMC article.
Deep Convolutional Hashing for Low-Dimensional Binary Embedding of Histopathological Images.
Manish Sapkota, Xiaoshuang Shi, Fuyong Xing, Lin Yang.
IEEE J Biomed Health Inform, 2018 Jul 12; 23(2). PMID: 29993648    Free PMC article.
Immune cell constitution in bone marrow microenvironment predicts outcome in adult ALL.
Helena Hohtari, Oscar Brück, +7 authors, Satu Mustjoki.
Leukemia, 2019 Jan 13; 33(7). PMID: 30635636    Free PMC article.
Segmentation and Classification in Digital Pathology for Glioma Research: Challenges and Deep Learning Approaches.
Tahsin Kurc, Spyridon Bakas, +21 authors, Keyvan Farahani.
Front Neurosci, 2020 Mar 11; 14. PMID: 32153349    Free PMC article.
A deep learning-based framework for lung cancer survival analysis with biomarker interpretation.
Lei Cui, Hansheng Li, +5 authors, Jun Feng.
BMC Bioinformatics, 2020 Mar 19; 21(1). PMID: 32183709    Free PMC article.
Automated Decision Support System for Detection of Leukemia from Peripheral Blood Smear Images.
Roopa B Hegde, Keerthana Prasad, +2 authors, I Sandhya.
J Digit Imaging, 2019 Nov 16; 33(2). PMID: 31728805    Free PMC article.
Deep Reinforcement Learning for Data Association in Cell Tracking.
Junjie Wang, Xiaohong Su, Lingling Zhao, Jun Zhang.
Front Bioeng Biotechnol, 2020 Apr 25; 8. PMID: 32328484    Free PMC article.
Analysis of Cellular Feature Differences of Astrocytomas with Distinct Mutational Profiles Using Digitized Histopathology Images.
Mousumi Roy, Fusheng Wang, +3 authors, Jun Kong.
Annu Int Conf IEEE Eng Med Biol Soc, 2018 Nov 18; 2018. PMID: 30441386    Free PMC article.
Optimizing parameter sensitivity analysis of large-scale microscopy image analysis workflows with multilevel computation reuse.
Willian Barreiros, Jeremias Moreira, +4 authors, George Teodoro.
Concurr Comput, 2020 Jul 17; 32(2). PMID: 32669980    Free PMC article.
An annotated fluorescence image dataset for training nuclear segmentation methods.
Florian Kromp, Eva Bozsaky, +11 authors, Sabine Taschner-Mandl.
Sci Data, 2020 Aug 13; 7(1). PMID: 32782410    Free PMC article.
Few-shot hypercolumn-based mitochondria segmentation in cardiac and outer hair cells in focused ion beam-scanning electron microscopy (FIB-SEM) data.
Julia Dietlmeier, Kevin McGuinness, +3 authors, Noel E O'Connor.
Pattern Recognit Lett, 2020 Aug 31; 128. PMID: 32863491    Free PMC article.
An automatic nuclei segmentation method based on deep convolutional neural networks for histopathology images.
Hwejin Jung, Bilal Lodhi, Jaewoo Kang.
BMC Biomed Eng, 2020 Sep 10; 1. PMID: 32903361    Free PMC article.
Sphere estimation network: three-dimensional nuclei detection of fluorescence microscopy images.
David Joon Ho, Daniel Mas Montserrat, +3 authors, Edward J Delp.
J Med Imaging (Bellingham), 2020 Sep 10; 7(4). PMID: 32904135    Free PMC article.
Interactive thyroid whole slide image diagnostic system using deep representation.
Pingjun Chen, Xiaoshuang Shi, +3 authors, Paul D Gader.
Comput Methods Programs Biomed, 2020 Jul 08; 195. PMID: 32634647    Free PMC article.
Twenty Years of Digital Pathology: An Overview of the Road Travelled, What is on the Horizon, and the Emergence of Vendor-Neutral Archives.
Liron Pantanowitz, Ashish Sharma, +3 authors, Joel Saltz.
J Pathol Inform, 2019 Jan 05; 9. PMID: 30607307    Free PMC article.
Sparse Autoencoder for Unsupervised Nucleus Detection and Representation in Histopathology Images.
Le Hou, Vu Nguyen, +8 authors, Joel H Saltz.
Pattern Recognit, 2019 Jan 12; 86. PMID: 30631215    Free PMC article.
Methods for Segmentation and Classification of Digital Microscopy Tissue Images.
Quoc Dang Vu, Simon Graham, +12 authors, Keyvan Farahani.
Front Bioeng Biotechnol, 2019 Apr 20; 7. PMID: 31001524    Free PMC article.
Segmentation of Total Cell Area in Brightfield Microscopy Images.
Martin Čepa.
Methods Protoc, 2019 Jun 06; 1(4). PMID: 31164583    Free PMC article.
Volumetric Segmentation of Cell Cycle Markers in Confocal Images Using Machine Learning and Deep Learning.
Faraz Ahmad Khan, Ute Voß, Michael P Pound, Andrew P French.
Front Plant Sci, 2020 Sep 29; 11. PMID: 32983190    Free PMC article.
Artificial intelligence (AI) and big data in cancer and precision oncology.
Zodwa Dlamini, Flavia Zita Francies, Rodney Hull, Rahaba Marima.
Comput Struct Biotechnol J, 2020 Oct 01; 18. PMID: 32994889    Free PMC article.
A bird's-eye view of deep learning in bioimage analysis.
Erik Meijering.
Comput Struct Biotechnol J, 2020 Oct 01; 18. PMID: 32994890    Free PMC article.
Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells.
Erod Keaton Baybay, Eric Esposito, Silke Hauf.
Sci Rep, 2020 Oct 08; 10(1). PMID: 33024177    Free PMC article.
Identification of Retinal Ganglion Cells from β-III Stained Fluorescent Microscopic Images.
He Gai, Yi Wang, Leanne L H Chan, Bernard Chiu.
J Digit Imaging, 2020 Jul 25; 33(5). PMID: 32705432    Free PMC article.
A versatile toolbox for semi-automatic cell-by-cell object-based colocalization analysis.
Anders Lunde, Joel C Glover.
Sci Rep, 2020 Nov 06; 10(1). PMID: 33149236    Free PMC article.
Digital Staining of High-Definition Fourier Transform Infrared (FT-IR) Images Using Deep Learning.
Mahsa Lotfollahi, Sebastian Berisha, Davar Daeinejad, David Mayerich.
Appl Spectrosc, 2019 Jan 19; 73(5). PMID: 30657342    Free PMC article.
Machine learning approaches for pathologic diagnosis.
Daisuke Komura, Shumpei Ishikawa.
Virchows Arch, 2019 Jun 22; 475(2). PMID: 31222375
Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison.
Tomas Vicar, Jan Balvan, +4 authors, Jaromir Gumulec.
BMC Bioinformatics, 2019 Jun 30; 20(1). PMID: 31253078    Free PMC article.
Towards pixel-to-pixel deep nucleus detection in microscopy images.
Fuyong Xing, Yuanpu Xie, +3 authors, Lin Yang.
BMC Bioinformatics, 2019 Sep 16; 20(1). PMID: 31521104    Free PMC article.
Changes in CT Radiomic Features Associated with Lymphocyte Distribution Predict Overall Survival and Response to Immunotherapy in Non-Small Cell Lung Cancer.
Mohammadhadi Khorrami, Prateek Prasanna, +10 authors, Anant Madabhushi.
Cancer Immunol Res, 2019 Nov 14; 8(1). PMID: 31719058    Free PMC article.
Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0.
Tristan Dubos, Axel Poulet, +9 authors, Sophie Desset.
Nucleus, 2020 Nov 07; 11(1). PMID: 33153359    Free PMC article.
Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation.
Jianfeng Cao, Guoye Guan, +5 authors, Hong Yan.
Nat Commun, 2020 Dec 09; 11(1). PMID: 33288755    Free PMC article.
Deep learning networks reflect cytoarchitectonic features used in brain mapping.
Kai Kiwitz, Christian Schiffer, +2 authors, Katrin Amunts.
Sci Rep, 2020 Dec 18; 10(1). PMID: 33328511    Free PMC article.
Leveraging multimodal microscopy to optimize deep learning models for cell segmentation.
William D Cameron, Alex M Bennett, +2 authors, Jonathan V Rocheleau.
APL Bioeng, 2021 Jan 09; 5(1). PMID: 33415313    Free PMC article.
Practical fluorescence reconstruction microscopy for large samples and low-magnification imaging.
Julienne LaChance, Daniel J Cohen.
PLoS Comput Biol, 2020 Dec 29; 16(12). PMID: 33362219    Free PMC article.
Bioimage Analysis and Cell Motility.
Aleix Boquet-Pujadas, Jean-Christophe Olivo-Marin, Nancy Guillén.
Patterns (N Y), 2021 Jan 30; 2(1). PMID: 33511365    Free PMC article.
Deeply-supervised density regression for automatic cell counting in microscopy images.
Shenghua He, Kyaw Thu Minn, +2 authors, Hua Li.
Med Image Anal, 2020 Dec 08; 68. PMID: 33285481    Free PMC article.
Split and Merge Watershed: a two-step method for cell segmentation in fluorescence microscopy images.
Margarita Gamarra, Eduardo Zurek, +2 authors, Homero San-Juan-Vergara.
Biomed Signal Process Control, 2019 Aug 01; 53. PMID: 33719364    Free PMC article.
Automated gleason grading on prostate biopsy slides by statistical representations of homology profile.
Chaoyang Yan, Kazuaki Nakane, +6 authors, Jun Xu.
Comput Methods Programs Biomed, 2020 May 30; 194. PMID: 32470903    Free PMC article.
Tumor-Associated Stromal Cellular Density as a Predictor of Recurrence and Mortality in Breast Cancer: Results from Ethnically Diverse Study Populations.
Mustapha Abubakar, Jing Zhang, +10 authors, Xiaohong Rose Yang.
Cancer Epidemiol Biomarkers Prev, 2021 May 07; 30(7). PMID: 33952648    Free PMC article.
Pixelwise H-score: A novel digital image analysis-based metric to quantify membrane biomarker expression from immunohistochemistry images.
Sripad Ram, Pamela Vizcarra, +6 authors, Eric L Powell.
PLoS One, 2021 Sep 28; 16(9). PMID: 34570796    Free PMC article.
A machine learning approach for single cell interphase cell cycle staging.
Hemaxi Narotamo, Maria Sofia Fernandes, +4 authors, João Miguel Sanches.
Sci Rep, 2021 Oct 01; 11(1). PMID: 34588507    Free PMC article.
Artificial Intelligence and Cellular Segmentation in Tissue Microscopy Images.
Madeleine S Durkee, Rebecca Abraham, Marcus R Clark, Maryellen L Giger.
Am J Pathol, 2021 Jun 16; 191(10). PMID: 34129842    Free PMC article.
Viability fingerprint of glioblastoma cell lines: roles of mitotic, proliferative, and epigenetic targets.
Darja Lavogina, Tõnis Laasfeld, +2 authors, Jana Jaal.
Sci Rep, 2021 Oct 15; 11(1). PMID: 34645858    Free PMC article.
Bidirectional Mapping-Based Domain Adaptation for Nucleus Detection in Cross-Modality Microscopy Images.
Fuyong Xing, Toby C Cornish, Tellen D Bennett, Debashis Ghosh.
IEEE Trans Med Imaging, 2020 Dec 08; 40(10). PMID: 33284750    Free PMC article.