Journal Article
. 2009 Nov; 57(4):841-52.
doi: 10.1109/TBME.2009.2035102.

Improved automatic detection and segmentation of cell nuclei in histopathology images

Yousef Al-Kofahi 1 Wiem Lassoued  William Lee  Badrinath Roysam  
  • PMID: 19884070
  •     153 citations


Automatic segmentation of cell nuclei is an essential step in image cytometry and histometry. Despite substantial progress, there is a need to improve accuracy, speed, level of automation, and adaptability to new applications. This paper presents a robust and accurate novel method for segmenting cell nuclei using a combination of ideas. The image foreground is extracted automatically using a graph-cuts-based binarization. Next, nuclear seed points are detected by a novel method combining multiscale Laplacian-of-Gaussian filtering constrained by distance-map-based adaptive scale selection. These points are used to perform an initial segmentation that is refined using a second graph-cuts-based algorithm incorporating the method of alpha expansions and graph coloring to reduce computational complexity. Nuclear segmentation results were manually validated over 25 representative images (15 in vitro images and 10 in vivo images, containing more than 7400 nuclei) drawn from diverse cancer histopathology studies, and four types of segmentation errors were investigated. The overall accuracy of the proposed segmentation algorithm exceeded 86%. The accuracy was found to exceed 94% when only over- and undersegmentation errors were considered. The confounding image characteristics that led to most detection/segmentation errors were high cell density, high degree of clustering, poor image contrast and noisy background, damaged/irregular nuclei, and poor edge information. We present an efficient semiautomated approach to editing automated segmentation results that requires two mouse clicks per operation.

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.
Cell-based quantification of molecular biomarkers in histopathology specimens.
Yousef Al-Kofahi, Wiem Lassoued, +6 authors, Badrinath Roysam.
Histopathology, 2011 Jul 21; 59(1). PMID: 21771025    Free PMC article.
Machine vision-based localization of nucleic and cytoplasmic injection sites on low-contrast adherent cells.
Hadi Esmaeilsabzali, Kelly Sakaki, +2 authors, Edward J Park.
Med Biol Eng Comput, 2011 Sep 29; 50(1). PMID: 21947866
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.
Statistical 4D graphs for multi-organ abdominal segmentation from multiphase CT.
Marius George Linguraru, John A Pura, Vivek Pamulapati, Ronald M Summers.
Med Image Anal, 2012 Mar 02; 16(4). PMID: 22377657    Free PMC article.
A fast, automatic segmentation algorithm for locating and delineating touching cell boundaries in imaged histopathology.
X Qi, F Xing, D J Foran, L Yang.
Methods Inf Med, 2012 Apr 25; 51(3). PMID: 22526139    Free PMC article.
NetMets: software for quantifying and visualizing errors in biological network segmentation.
David Mayerich, Chris Bjornsson, Jonathan Taylor, Badrinath Roysam.
BMC Bioinformatics, 2012 May 25; 13 Suppl 8. PMID: 22607549    Free PMC article.
Improved synapse detection for mGRASP-assisted brain connectivity mapping.
Linqing Feng, Ting Zhao, Jinhyun Kim.
Bioinformatics, 2012 Jun 13; 28(12). PMID: 22689768    Free PMC article.
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.
Learning histopathological patterns.
Andreas Kårsnäs, Anders L Dahl, Rasmus Larsen.
J Pathol Inform, 2011 Jan 01; 2. PMID: 22811956    Free PMC article.
Pathology Imaging Informatics for Clinical Practice and Investigative and Translational Research.
Evita T Sadimin, David J Foran.
N Am J Med Sci (Boston), 2012 Aug 03; 5(2). PMID: 22855694    Free PMC article.
Ranked retrieval of segmented nuclei for objective assessment of cancer gene repositioning.
William J Cukierski, Kaustav Nandy, +4 authors, Stephen J Lockett.
BMC Bioinformatics, 2012 Sep 14; 13. PMID: 22971117    Free PMC article.
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.
Preexisting epithelial diversity in normal human livers: a tissue-tethered cytometric analysis in portal/periportal epithelial cells.
Kumiko Isse, Andrew Lesniak, +7 authors, Anthony J Demetris.
Hepatology, 2012 Nov 15; 57(4). PMID: 23150208    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.
The study of muscle remodeling in Drosophila metamorphosis using in vivo microscopy and bioimage informatics.
Rambabu Chinta, Joo Huang Tan, Martin Wasser.
BMC Bioinformatics, 2013 Jan 11; 13 Suppl 17. PMID: 23282138    Free PMC article.
A computational approach to detect gap junction plaques and associate them with cells in fluorescent images.
Joshua S Goldberg, Tegy J Vadakkan, Karen K Hirschi, Mary E Dickinson.
J Histochem Cytochem, 2013 Jan 18; 61(4). PMID: 23324867    Free PMC article.
Non-parametric and integrated framework for segmenting and counting neuroblastic cells within neuroblastoma tumor images.
Siamak Tafavogh, Karla Felix Navarro, Daniel R Catchpoole, Paul J Kennedy.
Med Biol Eng Comput, 2013 Jan 30; 51(6). PMID: 23359256
An entropy-based automated cell nuclei segmentation and quantification: application in analysis of wound healing process.
Varun Oswal, Ashwin Belle, Robert Diegelmann, Kayvan Najarian.
Comput Math Methods Med, 2013 Mar 28; 2013. PMID: 23533544    Free PMC article.
NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model.
Tingwei Quan, Ting Zheng, +7 authors, Shaoqun Zeng.
Sci Rep, 2013 Apr 03; 3. PMID: 23546385    Free PMC article.
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.
Chapter 17: bioimage informatics for systems pharmacology.
Fuhai Li, Zheng Yin, +2 authors, Stephen T C Wong.
PLoS Comput Biol, 2013 May 02; 9(4). PMID: 23633943    Free PMC article.
Automated and accurate detection of soma location and surface morphology in large-scale 3D neuron images.
Cheng Yan, Anan Li, +3 authors, Hui Gong.
PLoS One, 2013 May 03; 8(4). PMID: 23638117    Free PMC article.
Reduced Oct4 expression directs a robust pluripotent state with distinct signaling activity and increased enhancer occupancy by Oct4 and Nanog.
Violetta Karwacki-Neisius, Jonathan Göke, +11 authors, Ian Chambers.
Cell Stem Cell, 2013 May 07; 12(5). PMID: 23642364    Free PMC article.
Highly Cited.
Stain guided mean-shift filtering in automatic detection of human tissue nuclei.
Yu Zhou, Derek Magee, Darren Treanor, Andrew Bulpitt.
J Pathol Inform, 2013 Jun 15; 4(Suppl). PMID: 23766942    Free PMC article.
Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE).
Sharif Chowdhury, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S Ribeiro.
BMC Bioinformatics, 2013 Dec 07; 14 Suppl 10. PMID: 24267594    Free PMC article.
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.
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.
Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks.
Johannes Stegmaier, Jens C Otte, +5 authors, Ralf Mikut.
PLoS One, 2014 Mar 04; 9(2). PMID: 24587204    Free PMC article.
An active learning approach for rapid characterization of endothelial cells in human tumors.
Raghav K Padmanabhan, Vinay H Somasundar, +14 authors, William M F Lee.
PLoS One, 2014 Mar 08; 9(3). PMID: 24603893    Free PMC article.
Wnt-responsive cancer stem cells are located close to distorted blood vessels and not in hypoxic regions in a p53-null mouse model of human breast cancer.
Tegy J Vadakkan, John D Landua, +7 authors, Mei Zhang.
Stem Cells Transl Med, 2014 May 07; 3(7). PMID: 24797826    Free PMC article.
Large-scale automated image analysis for computational profiling of brain tissue surrounding implanted neuroprosthetic devices using Python.
Nicolas Rey-Villamizar, Vinay Somasundar, +6 authors, Badri Roysam.
Front Neuroinform, 2014 May 09; 8. PMID: 24808857    Free PMC article.
Current automated 3D cell detection methods are not a suitable replacement for manual stereologic cell counting.
Christoph Schmitz, Brian S Eastwood, +3 authors, Patrick R Hof.
Front Neuroanat, 2014 May 23; 8. PMID: 24847213    Free PMC article.
A semi-automated technique for labeling and counting of apoptosing retinal cells.
Mukhtar Bizrah, Steve C Dakin, +7 authors, M Francesca Cordeiro.
BMC Bioinformatics, 2014 Jun 07; 15. PMID: 24902592    Free PMC article.
Cancer diagnosis by nuclear morphometry using spatial information .
Hu Huang, Akif Burak Tosun, +4 authors, Gustavo K Rohde.
Pattern Recognit Lett, 2014 Jun 10; 42. PMID: 24910485    Free PMC article.
Drosophila Eye Nuclei Segmentation Based on Graph Cut and Convex Shape Prior.
Jin Qi, B Wang, +4 authors, L A Nunes Amaral.
Int Conf Signal Process Proc, 2014 Aug 05;. PMID: 25089515    Free PMC article.
Cellular quantitative analysis of neuroblastoma tumor and splitting overlapping cells.
Siamak Tafavogh, Daniel R Catchpoole, Paul J Kennedy.
BMC Bioinformatics, 2014 Aug 12; 15. PMID: 25109603    Free PMC article.
An automated three-dimensional detection and segmentation method for touching cells by integrating concave points clustering and random walker algorithm.
Yong He, Yunlong Meng, +5 authors, Anan Li.
PLoS One, 2014 Aug 12; 9(8). PMID: 25111442    Free PMC article.
Anima: modular workflow system for comprehensive image data analysis.
Ville Rantanen, Miko Valori, Sampsa Hautaniemi.
Front Bioeng Biotechnol, 2014 Aug 16; 2. PMID: 25126541    Free PMC article.
Automated grading of renal cell carcinoma using whole slide imaging.
Fang-Cheng Yeh, Anil V Parwani, Liron Pantanowitz, Chien Ho.
J Pathol Inform, 2014 Sep 06; 5(1). PMID: 25191622    Free PMC article.
Novel image markers for non-small cell lung cancer classification and survival prediction.
Hongyuan Wang, Fuyong Xing, +2 authors, Lin Yang.
BMC Bioinformatics, 2014 Sep 23; 15. PMID: 25240495    Free PMC article.
Effective identification and localization of immature precursors in bone marrow biopsy.
Guitao Cao, Ling Li, +4 authors, Xuehua Liu.
Med Biol Eng Comput, 2014 Nov 29; 53(3). PMID: 25430420
Digital immunohistochemistry wizard: image analysis-assisted stereology tool to produce reference data set for calibration and quality control.
Benoît Plancoulaine, Aida Laurinaviciene, +4 authors, Arvydas Laurinavicius.
Diagn Pathol, 2015 Jan 08; 9 Suppl 1. PMID: 25565221    Free PMC article.
An advanced image analysis tool for the quantification and characterization of breast cancer in microscopy images.
Theodosios Goudas, Ilias Maglogiannis.
J Med Syst, 2015 Feb 15; 39(3). PMID: 25681102
Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors.
Murad Megjhani, Nicolas Rey-Villamizar, +7 authors, Badrinath Roysam.
Bioinformatics, 2015 Feb 24; 31(13). PMID: 25701570    Free PMC article.
Automated detection of soma location and morphology in neuronal network cultures.
Burcin Ozcan, Pooran Negi, +2 authors, Demetrio Labate.
PLoS One, 2015 Apr 09; 10(4). PMID: 25853656    Free PMC article.
Graph-regularized 3D shape reconstruction from highly anisotropic and noisy images.
Christian Widmer, Stephanie Heinrich, +3 authors, Gunnar Rätsch.
Signal Image Video Process, 2015 Apr 14; 8(1 Suppl). PMID: 25866587    Free PMC article.
In vivo cell-cycle profiling in xenograft tumors by quantitative intravital microscopy.
Deepak R Chittajallu, Stefan Florian, +5 authors, Timothy J Mitchison.
Nat Methods, 2015 Apr 14; 12(6). PMID: 25867850    Free PMC article.
Histological image segmentation using fast mean shift clustering method.
Geming Wu, Xinyan Zhao, Shuqian Luo, Hongli Shi.
Biomed Eng Online, 2015 Apr 18; 14. PMID: 25884695    Free PMC article.
A computational approach to detect and segment cytoplasm in muscle fiber images.
Yanen Guo, Xiaoyin Xu, +3 authors, Shunren Xia.
Microsc Res Tech, 2015 Apr 23; 78(6). PMID: 25900156    Free PMC article.
Rapid 3-D delineation of cell nuclei for high-content screening platforms.
Arkadiusz Gertych, Zhaoxuan Ma, +2 authors, Beatrice S Knudsen.
Comput Biol Med, 2015 May 20; 69. PMID: 25982066    Free PMC article.
Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition.
B Mathew, A Schmitz, +4 authors, S C Fischer.
BMC Bioinformatics, 2015 Jun 08; 16. PMID: 26049713    Free PMC article.
Automated profiling of individual cell-cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING).
Amine Merouane, Nicolas Rey-Villamizar, +7 authors, Badrinath Roysam.
Bioinformatics, 2015 Jun 11; 31(19). PMID: 26059718    Free PMC article.
iCut: an Integrative Cut Algorithm Enables Accurate Segmentation of Touching Cells.
Yong He, Hui Gong, +7 authors, Shangbin Chen.
Sci Rep, 2015 Jul 15; 5. PMID: 26168908    Free PMC article.
Stacked Sparse Autoencoder (SSAE) for Nuclei Detection on Breast Cancer Histopathology Images.
Jun Xu, Lei Xiang, +4 authors, Anant Madabhushi.
IEEE Trans Med Imaging, 2015 Jul 25; 35(1). PMID: 26208307    Free PMC article.
Highly Cited.
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.
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.
Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images.
Michael Chiang, Sam Hallman, +7 authors, Olivier Cinquin.
BMC Bioinformatics, 2015 Nov 27; 16. PMID: 26607933    Free PMC article.
A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture.
Hernán Morales-Navarrete, Fabián Segovia-Miranda, +7 authors, Yannis Kalaidzidis.
Elife, 2015 Dec 18; 4. PMID: 26673893    Free PMC article.
Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review.
Fuyong Xing, Lin Yang.
IEEE Rev Biomed Eng, 2016 Jan 08; 9. PMID: 26742143    Free PMC article.
Highly Cited. Review.
Position-dependent plasticity of distinct progenitor types in the primitive streak.
Filip J Wymeersch, Yali Huang, +4 authors, Valerie Wilson.
Elife, 2016 Jan 19; 5. PMID: 26780186    Free PMC article.
Highly Cited.
Robust Cell Detection of Histopathological Brain Tumor Images Using Sparse Reconstruction and Adaptive Dictionary Selection.
Hai Su, Fuyong Xing, Lin Yang.
IEEE Trans Med Imaging, 2016 Jan 27; 35(6). PMID: 26812706    Free PMC article.
Detection and Classification of Cancer from Microscopic Biopsy Images Using Clinically Significant and Biologically Interpretable Features.
Rajesh Kumar, Rajeev Srivastava, Subodh Srivastava.
J Med Eng, 2015 Jan 01; 2015. PMID: 27006938    Free PMC article.
A methodological pipeline for serial-section imaging and tissue realignment for whole-brain functional and connectivity assessment.
Lilia Mesina, Aaron A Wilber, +4 authors, Bruce L McNaughton.
J Neurosci Methods, 2016 Apr 05; 266. PMID: 27039972    Free PMC article.
A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images.
Yaser Afshar, Ivo F Sbalzarini.
PLoS One, 2016 Apr 06; 11(4). PMID: 27046144    Free PMC article.
Quantitative Assessment of Retinopathy Using Multi-parameter Image Analysis.
Zahra Ghanian, Kevin Staniszewski, +5 authors, Mahsa Ranji.
J Med Signals Sens, 2016 May 18; 6(2). PMID: 27186534    Free PMC article.
Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space.
Yu Toyoshima, Terumasa Tokunaga, +7 authors, Yuichi Iino.
PLoS Comput Biol, 2016 Jun 09; 12(6). PMID: 27271939    Free PMC article.
Object Segmentation and Ground Truth in 3D Embryonic Imaging.
Bhavna Rajasekaran, Koichiro Uriu, +2 authors, Andrew C Oates.
PLoS One, 2016 Jun 23; 11(6). PMID: 27332860    Free PMC article.
The link between diffusion MRI and tumor heterogeneity: Mapping cell eccentricity and density by diffusional variance decomposition (DIVIDE).
Filip Szczepankiewicz, Danielle van Westen, +5 authors, Markus Nilsson.
Neuroimage, 2016 Jul 28; 142. PMID: 27450666    Free PMC article.
Highly Cited.
TissueWikiMobile: an Integrative Protein Expression Image Browser for Pathological Knowledge Sharing and Annotation on a Mobile Device.
Chihwen Cheng, Todd H Stokes, Sovandy Hang, May D Wang.
IEEE Int Conf Bioinform Biomed Workshops, 2010 Dec 01; 2010. PMID: 27532057    Free PMC article.
Tomographic brain imaging with nucleolar detail and automatic cell counting.
Simone E Hieber, Christos Bikis, +5 authors, Bert Müller.
Sci Rep, 2016 Sep 02; 6. PMID: 27581254    Free PMC article.
Large-scale localization of touching somas from 3D images using density-peak clustering.
Shenghua Cheng, Tingwei Quan, Xiaomao Liu, Shaoqun Zeng.
BMC Bioinformatics, 2016 Sep 16; 17(1). PMID: 27628179    Free PMC article.
Multi-Pass Adaptive Voting for Nuclei Detection in Histopathological Images.
Cheng Lu, Hongming Xu, +3 authors, Anant Madabhushi.
Sci Rep, 2016 Oct 04; 6. PMID: 27694950    Free PMC article.
Self-organization of human embryonic stem cells on micropatterns.
Alessia Deglincerti, Fred Etoc, +8 authors, Aryeh Warmflash.
Nat Protoc, 2016 Oct 14; 11(11). PMID: 27735934    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.
Transfer Shape Modeling Towards High-throughput Microscopy Image Segmentation.
Fuyong Xing, Xiaoshuang Shi, +3 authors, Lin Yang.
Med Image Comput Comput Assist Interv, 2016 Dec 08; 9902. PMID: 27924318    Free PMC article.
Binge alcohol alters exercise-driven neuroplasticity.
Emily A Barton, Yanbin Lu, +4 authors, J Leigh Leasure.
Neuroscience, 2016 Dec 10; 343. PMID: 27932309    Free PMC article.
Glioma Grading Using Cell Nuclei Morphologic Features in Digital Pathology Images.
Syed M S Reza, Khan M Iftekharuddin.
Proc SPIE Int Soc Opt Eng, 2016 Dec 13; 9785. PMID: 27942094    Free PMC article.
Detection of Multiple Innervation Zones from Multi-Channel Surface EMG Recordings with Low Signal-to-Noise Ratio Using Graph-Cut Segmentation.
Hamid Reza Marateb, Morteza Farahi, +2 authors, Dario Farina.
PLoS One, 2016 Dec 16; 11(12). PMID: 27978535    Free PMC article.
Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers.
Daniel M Spagnolo, Rekha Gyanchandani, +10 authors, S Chakra Chennubhotla.
J Pathol Inform, 2016 Dec 21; 7. PMID: 27994939    Free PMC article.
Detecting and segmenting cell nuclei in two-dimensional microscopy images.
Chi Liu, Fei Shang, John A Ozolek, Gustavo K Rohde.
J Pathol Inform, 2017 Jan 10; 7. PMID: 28066682    Free PMC article.
Computer-based image analysis in breast pathology.
Ziba Gandomkar, Patrick C Brennan, Claudia Mello-Thoms.
J Pathol Inform, 2017 Jan 10; 7. PMID: 28066683    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.
Three-Dimensional Segmentation of the Ex-Vivo Anterior Lamina Cribrosa From Second-Harmonic Imaging Microscopy.
Sundaresh Ram, Forest Danford, +2 authors, Jonathan P Vande Geest.
IEEE Trans Biomed Eng, 2017 Mar 03; 65(7). PMID: 28252388    Free PMC article.
Spatial Statistics for Segmenting Histological Structures in H&E Stained Tissue Images.
Luong Nguyen, Akif Burak Tosun, +3 authors, S Chakra Chennubhotla.
IEEE Trans Med Imaging, 2017 Mar 23; 36(7). PMID: 28328502    Free PMC article.
Morphologically constrained spectral unmixing by dictionary learning for multiplex fluorescence microscopy.
Murad Megjhani, Pedro Correa de Sampaio, +2 authors, Badrinath Roysam.
Bioinformatics, 2017 Mar 24; 33(14). PMID: 28334208    Free PMC article.
Robust cell tracking in epithelial tissues through identification of maximum common subgraphs.
Jochen Kursawe, Rémi Bardenet, +2 authors, Alexander G Fletcher.
J R Soc Interface, 2016 Jan 01; 13(124). PMID: 28334699    Free PMC article.
An alternative reference space for H&E color normalization.
Mark D Zarella, Chan Yeoh, David E Breen, Fernando U Garcia.
PLoS One, 2017 Mar 30; 12(3). PMID: 28355298    Free PMC article.
Robust Cell Segmentation for Histological Images of Glioblastoma.
Jun Kong, Pengyue Zhang, +3 authors, Fusheng Wang.
Proc IEEE Int Symp Biomed Imaging, 2017 Apr 11; 2016. PMID: 28392891    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.
Automatic extraction of cell nuclei from H&E-stained histopathological images.
Faliu Yi, Junzhou Huang, +2 authors, Guanghua Xiao.
J Med Imaging (Bellingham), 2017 Jun 28; 4(2). PMID: 28653017    Free PMC article.
Spatial pattern analysis of nuclear migration in remodelled muscles during Drosophila metamorphosis.
Kuleesha, Lin Feng, Martin Wasser.
BMC Bioinformatics, 2017 Jul 12; 18(1). PMID: 28693471    Free PMC article.
Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy.
Yongxin Zhao, Octavian Bucur, +11 authors, Edward S Boyden.
Nat Biotechnol, 2017 Jul 18; 35(8). PMID: 28714966    Free PMC article.
Automated Functional Analysis of Astrocytes from Chronic Time-Lapse Calcium Imaging Data.
Yinxue Wang, Guilai Shi, +6 authors, Guoqiang Yu.
Front Neuroinform, 2017 Aug 05; 11. PMID: 28769780    Free PMC article.
A Quantitative Analysis of the Distribution of CRH Neurons in Whole Mouse Brain.
Jie Peng, Ben Long, +6 authors, Anan Li.
Front Neuroanat, 2017 Aug 10; 11. PMID: 28790896    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.
Efficient processing of fluorescence images using directional multiscale representations.
D Labate, F Laezza, +2 authors, M Papadakis.
Math Model Nat Phenom, 2014 Jan 01; 9(5). PMID: 28804225    Free PMC article.
Maximized Inter-Class Weighted Mean for Fast and Accurate Mitosis Cells Detection in Breast Cancer Histopathology Images.
Ramin Nateghi, Habibollah Danyali, Mohammad Sadegh Helfroush.
J Med Syst, 2017 Aug 16; 41(9). PMID: 28808813
Segmentation and classification of two-channel C. elegans nucleus-labeled fluorescence images.
Mengdi Zhao, Jie An, +6 authors, Louis Tao.
BMC Bioinformatics, 2017 Sep 17; 18(1). PMID: 28915791    Free PMC article.
Touching Soma Segmentation Based on the Rayburst Sampling Algorithm.
Tianyu Hu, Qiufeng Xu, Wei Lv, Qian Liu.
Neuroinformatics, 2017 Sep 25; 15(4). PMID: 28940176    Free PMC article.
Automatic cellularity assessment from post-treated breast surgical specimens.
Mohammad Peikari, Sherine Salama, Sharon Nofech-Mozes, Anne L Martel.
Cytometry A, 2017 Oct 05; 91(11). PMID: 28976721    Free PMC article.
Cell Detection Using Extremal Regions in a Semisupervised Learning Framework.
Nisha Ramesh, Ting Liu, Tolga Tasdizen.
J Healthc Eng, 2017 Oct 27; 2017. PMID: 29065596    Free PMC article.
A platform for stereological quantitative analysis of the brain-wide distribution of type-specific neurons.
Chen Zhang, Cheng Yan, +4 authors, Jing Yuan.
Sci Rep, 2017 Nov 01; 7(1). PMID: 29085023    Free PMC article.
Fuzzy-based propagation of prior knowledge to improve large-scale image analysis pipelines.
Johannes Stegmaier, Ralf Mikut.
PLoS One, 2017 Nov 03; 12(11). PMID: 29095927    Free PMC article.
Image analysis of neural stem cell division patterns in the zebrafish brain.
Valerio Lupperger, Felix Buggenthin, Prisca Chapouton, Carsten Marr.
Cytometry A, 2017 Nov 11; 93(3). PMID: 29125897    Free PMC article.
Correlation Filters for Detection of Cellular Nuclei in Histopathology Images.
Asif Ahmad, Amina Asif, +2 authors, Fayyaz Ul Amir Afsar Minhas.
J Med Syst, 2017 Nov 23; 42(1). PMID: 29164340
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.
Robust Cell Detection for Large-Scale 3D Microscopy Using GPU-Accelerated Iterative Voting.
Leila Saadatifard, Louise C Abbott, +2 authors, David Mayerich.
Front Neuroanat, 2018 May 15; 12. PMID: 29755325    Free PMC article.
Multi-tissue and multi-scale approach for nuclei segmentation in H&E stained images.
Massimo Salvi, Filippo Molinari.
Biomed Eng Online, 2018 Jun 22; 17(1). PMID: 29925379    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.
Identifying the morphologic basis for radiomic features in distinguishing different Gleason grades of prostate cancer on MRI: Preliminary findings.
Gregory Penzias, Asha Singanamalli, +13 authors, Anant Madabhushi.
PLoS One, 2018 Sep 01; 13(8). PMID: 30169514    Free PMC article.
A deep learning-based algorithm for 2-D cell segmentation in microscopy images.
Yousef Al-Kofahi, Alla Zaltsman, +2 authors, Mirabela Rusu.
BMC Bioinformatics, 2018 Oct 05; 19(1). PMID: 30285608    Free PMC article.
Investigating the Relevance of Graph Cut Parameter on Interactive and Automatic Cell Segmentation.
Kazeem Oyeyemi Oyebode, Shengzhi Du, Barend Jacobus van Wyk, Karim Djouani.
Comput Math Methods Med, 2018 Oct 23; 2018. PMID: 30344617    Free PMC article.
Comparative Study on Automated Cell Nuclei Segmentation Methods for Cytology Pleural Effusion Images.
Khin Yadanar Win, Somsak Choomchuay, Kazuhiko Hamamoto, Manasanan Raveesunthornkiat.
J Healthc Eng, 2018 Oct 23; 2018. PMID: 30344991    Free PMC article.
Artificial intelligence in digital pathology - new tools for diagnosis and precision oncology.
Kaustav Bera, Kurt A Schalper, +2 authors, Anant Madabhushi.
Nat Rev Clin Oncol, 2019 Aug 11; 16(11). PMID: 31399699    Free PMC article.
Highly Cited. Review.
TDP-43 cytoplasmic inclusion formation is disrupted in C9orf72-associated amyotrophic lateral sclerosis/frontotemporal lobar degeneration.
Samuel M Lee, Seneshaw Asress, +7 authors, Jonathan D Glass.
Brain Commun, 2019 Oct 22; 1(1). PMID: 31633109    Free PMC article.
Automated Individualization of Size-Varying and Touching Neurons in Macaque Cerebral Microscopic Images.
Zhenzhen You, Yaël Balbastre, +6 authors, Thierry Delzescaux.
Front Neuroanat, 2020 Jan 11; 13. PMID: 31920567    Free PMC article.
Effective nuclei segmentation with sparse shape prior and dynamic occlusion constraint for glioblastoma pathology images.
Pengyue Zhang, Fusheng Wang, +4 authors, Jun Kong.
J Med Imaging (Bellingham), 2019 Mar 21; 6(1). PMID: 30891467    Free PMC article.
Segmentation of Heavily Clustered Nuclei from Histopathological Images.
Mahmoud Abdolhoseini, Murielle G Kluge, Frederick R Walker, Sarah J Johnson.
Sci Rep, 2019 Mar 16; 9(1). PMID: 30872619    Free PMC article.
Multiplexed (18-Plex) Measurement of Signaling Targets and Cytotoxic T Cells in Trastuzumab-Treated Patients using Imaging Mass Cytometry.
Daniel E Carvajal-Hausdorf, Jonathan Patsenker, +10 authors, David L Rimm.
Clin Cancer Res, 2019 Feb 24; 25(10). PMID: 30796036    Free PMC article.
Three-dimensional GPU-accelerated active contours for automated localization of cells in large images.
Mahsa Lotfollahi, Sebastian Berisha, +3 authors, David Mayerich.
PLoS One, 2019 Jun 08; 14(6). PMID: 31173591    Free PMC article.
Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures.
Guillaume Blin, Daina Sadurska, +3 authors, Sally Lowell.
PLoS Biol, 2019 Aug 10; 17(8). PMID: 31398189    Free PMC article.
DeepSynth: Three-dimensional nuclear segmentation of biological images using neural networks trained with synthetic data.
Kenneth W Dunn, Chichen Fu, +4 authors, Edward J Delp.
Sci Rep, 2019 Dec 05; 9(1). PMID: 31797882    Free PMC article.
Deep learning pathological microscopic features in endemic nasopharyngeal cancer: Prognostic value and protentional role for individual induction chemotherapy.
Kuiyuan Liu, Weixiong Xia, +4 authors, Xing Lv.
Cancer Med, 2019 Dec 21; 9(4). PMID: 31860791    Free PMC article.
Introduction to digital pathology and computer-aided pathology.
Soojeong Nam, Yosep Chong, +5 authors, Heounjeong Go.
J Pathol Transl Med, 2020 Feb 13; 54(2). PMID: 32045965    Free PMC article.
Nucleus segmentation of cervical cytology images based on multi-scale fuzzy clustering algorithm.
Jinjie Huang, Tao Wang, Dequan Zheng, Yongjun He.
Bioengineered, 2020 Apr 14; 11(1). PMID: 32279589    Free PMC article.
Spatial models of cell distribution in human lumbar dorsal root ganglia.
Zachariah J Sperry, Robert D Graham, +2 authors, Tim M Bruns.
J Comp Neurol, 2019 Dec 25; 528(10). PMID: 31872433    Free PMC article.
Computer-Assisted Nuclear Atypia Scoring of Breast Cancer: a Preliminary Study.
Ziba Gandomkar, Patrick C Brennan, Claudia Mello-Thoms.
J Digit Imaging, 2019 Feb 06; 32(5). PMID: 30719586    Free PMC article.
Identification of topological features in renal tumor microenvironment associated with patient survival.
Jun Cheng, Xiaokui Mo, +3 authors, Kun Huang.
Bioinformatics, 2017 Nov 15; 34(6). PMID: 29136101    Free PMC article.
Artificial intelligence in digital breast pathology: Techniques and applications.
Asmaa Ibrahim, Paul Gamble, +4 authors, Emad A Rakha.
Breast, 2020 Jan 15; 49. PMID: 31935669    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.
Deep-learning-based accurate hepatic steatosis quantification for histological assessment of liver biopsies.
Mousumi Roy, Fusheng Wang, +6 authors, Jun Kong.
Lab Invest, 2020 Jul 15; 100(10). PMID: 32661341    Free PMC article.
Machine Learning Models for Multiparametric Glioma Grading With Quantitative Result Interpretations.
Xiuying Wang, Dingqian Wang, +7 authors, Yingchao Liu.
Front Neurosci, 2019 Jan 29; 12. PMID: 30686996    Free PMC article.
Convolutional neural network initialized active contour model with adaptive ellipse fitting for nuclear segmentation on breast histopathological images.
Jun Xu, Lei Gong, +4 authors, Anant Madabhushi.
J Med Imaging (Bellingham), 2019 Mar 07; 6(1). PMID: 30840729    Free PMC article.
Introduction to Digital Image Analysis in Whole-slide Imaging: A White Paper from the Digital Pathology Association.
Famke Aeffner, Mark D Zarella, +11 authors, Douglas Bowman.
J Pathol Inform, 2019 Apr 16; 10. PMID: 30984469    Free PMC article.
Highly Cited. Review.
Deep Learning for Semantic Segmentation vs. Classification in Computational Pathology: Application to Mitosis Analysis in Breast Cancer Grading.
Gabriel Jiménez, Daniel Racoceanu.
Front Bioeng Biotechnol, 2019 Jul 10; 7. PMID: 31281813    Free PMC article.
Multi-Organ Gland Segmentation Using Deep Learning.
Thomas Binder, El Mehdi Tantaoui, +3 authors, Maria Gabrani.
Front Med (Lausanne), 2019 Aug 21; 6. PMID: 31428614    Free PMC article.
Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images.
Błażej Ruszczycki, Katarzyna Karolina Pels, +12 authors, Grzegorz Marek Wilczyński.
Front Neuroanat, 2019 Sep 05; 13. PMID: 31481881    Free PMC article.
Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion.
Nikolaus Korfhage, Markus Mühling, +3 authors, Bernd Freisleben.
PLoS Comput Biol, 2020 Sep 09; 16(9). PMID: 32898132    Free PMC article.
Multi-aspect testing and ranking inference to quantify dimorphism in the cytoarchitecture of cerebellum of male, female and intersex individuals: a model applied to bovine brains.
L Corain, E Grisan, +3 authors, A Peruffo.
Brain Struct Funct, 2020 Sep 30; 225(9). PMID: 32989472    Free PMC article.
Automatic segmentation and supervised learning-based selection of nuclei in cancer tissue images.
Kaustav Nandy, Prabhakar R Gudla, +3 authors, Stephen J Lockett.
Cytometry A, 2012 Aug 18; 81(9). PMID: 22899462    Free PMC article.
A novel computational method for automatic segmentation, quantification and comparative analysis of immunohistochemically labeled tissue sections.
Elena Casiraghi, Veronica Huber, +6 authors, Barbara Vergani.
BMC Bioinformatics, 2018 Oct 28; 19(Suppl 10). PMID: 30367588    Free PMC article.
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.
A deep learning algorithm for one-step contour aware nuclei segmentation of histopathology images.
Yuxin Cui, Guiying Zhang, +2 authors, Jianjun Hu.
Med Biol Eng Comput, 2019 Jul 28; 57(9). PMID: 31346949
Accurate Neuronal Soma Segmentation Using 3D Multi-Task Learning U-Shaped Fully Convolutional Neural Networks.
Tianyu Hu, Xiaofeng Xu, Shangbin Chen, Qian Liu.
Front Neuroanat, 2021 Feb 09; 14. PMID: 33551758    Free PMC article.
Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks.
Dragan Maric, Jahandar Jahanipour, +6 authors, Badrinath Roysam.
Nat Commun, 2021 Mar 12; 12(1). PMID: 33692351    Free PMC article.
Applications of Topological Data Analysis in Oncology.
Anuraag Bukkuri, Noemi Andor, Isabel K Darcy.
Front Artif Intell, 2021 May 01; 4. PMID: 33928240    Free PMC article.
Automatic wavelet-based 3D nuclei segmentation and analysis for multicellular embryo quantification.
Tzu-Ching Wu, Xu Wang, +2 authors, David M Umulis.
Sci Rep, 2021 May 12; 11(1). PMID: 33972575    Free PMC article.