Journal Article
. 2011 Dec; 59(3):754-65.
doi: 10.1109/TBME.2011.2179298.

Robust segmentation of overlapping cells in histopathology specimens using parallel seed detection and repulsive level set

Xin Qi 1 Fuyong Xing  David J Foran  Lin Yang  
Affiliations
  • PMID: 22167559
  •     28 References
  •     53 citations

Abstract

Automated image analysis of histopathology specimens could potentially provide support for early detection and improved characterization of breast cancer. Automated segmentation of the cells comprising imaged tissue microarrays (TMAs) is a prerequisite for any subsequent quantitative analysis. Unfortunately, crowding and overlapping of cells present significant challenges for most traditional segmentation algorithms. In this paper, we propose a novel algorithm that can reliably separate touching cells in hematoxylin-stained breast TMA specimens that have been acquired using a standard RGB camera. The algorithm is composed of two steps. It begins with a fast, reliable object center localization approach that utilizes single-path voting followed by mean-shift clustering. Next, the contour of each cell is obtained using a level set algorithm based on an interactive model. We compared the experimental results with those reported in the most current literature. Finally, performance was evaluated by comparing the pixel-wise accuracy provided by human experts with that produced by the new automated segmentation algorithm. The method was systematically tested on 234 image patches exhibiting dense overlap and containing more than 2200 cells. It was also tested on whole slide images including blood smears and TMAs containing thousands of cells. Since the voting step of the seed detection algorithm is well suited for parallelization, a parallel version of the algorithm was implemented using graphic processing units (GPU) that resulted in significant speedup over the C/C++ implementation.

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
High-throughput protein expression analysis using tissue microarray technology of a large well-characterised series identifies biologically distinct classes of breast cancer confirming recent cDNA expression analyses.
Dalia M Abd El-Rehim, Graham Ball, +6 authors, Ian O Ellis.
Int J Cancer, 2005 Apr 09; 116(3). PMID: 15818618
Highly Cited.
AUTOMATED CELL COUNTING AND CLUSTER SEGMENTATION USING CONCAVITY DETECTION AND ELLIPSE FITTING TECHNIQUES.
Sonal Kothari, Qaiser Chaudry, May D Wang.
Proc IEEE Int Symp Biomed Imaging, 2009 Jun 01; 2009. PMID: 28392889    Free PMC article.
Tissue microarray: a new technology for amplification of tissue resources.
D L Rimm, R L Camp, +3 authors, M Reiss.
Cancer J, 2001 Mar 28; 7(1). PMID: 11269645
Review.
Constraint factor graph cut-based active contour method for automated cellular image segmentation in RNAi screening.
C Chen, H Li, X Zhou, S T C Wong.
J Microsc, 2008 May 01; 230(Pt 2). PMID: 18445146    Free PMC article.
A caGRID-ENABLED, LEARNING BASED IMAGE SEGMENTATION METHOD FOR HISTOPATHOLOGY SPECIMENS.
David J Foran, Lin Yang, +5 authors, Joel H Saltz.
Proc IEEE Int Symp Biomed Imaging, 2009 Nov 26; 6. PMID: 19936299    Free PMC article.
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
3D cell nuclei segmentation based on gradient flow tracking.
Gang Li, Tianming Liu, +5 authors, Stephen T C Wong.
BMC Cell Biol, 2007 Sep 06; 8. PMID: 17784958    Free PMC article.
Digital slide and virtual microscopy based routine and telepathology evaluation of routine gastrointestinal biopsy specimens.
B Molnar, L Berczi, +4 authors, Z Tulassay.
J Clin Pathol, 2003 Jun 05; 56(6). PMID: 12783970    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.
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.
MicroRNA gene expression deregulation in human breast cancer.
Marilena V Iorio, Manuela Ferracin, +17 authors, Carlo M Croce.
Cancer Res, 2005 Aug 17; 65(16). PMID: 16103053
Highly Cited.
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
Tissue microarrays for high-throughput molecular profiling of tumor specimens.
J Kononen, L Bubendorf, +7 authors, O P Kallioniemi.
Nat Med, 1998 Jul 14; 4(7). PMID: 9662379
Highly Cited.
Tissue microarray technology for high-throughput molecular profiling of cancer.
O P Kallioniemi, U Wagner, J Kononen, G Sauter.
Hum Mol Genet, 2001 Mar 21; 10(7). PMID: 11257096
Highly Cited. Review.
A digital atlas of breast histopathology: an application of web based virtual microscopy.
M Lundin, J Lundin, H Helin, J Isola.
J Clin Pathol, 2004 Nov 26; 57(12). PMID: 15563669    Free PMC article.
Isoperimetric graph partitioning for image segmentation.
Leo Grady, Eric L Schwartz.
IEEE Trans Pattern Anal Mach Intell, 2006 Mar 11; 28(3). PMID: 16526432
Digital dynamic telepathology--the Virtual Microscope.
A Afework, M D Beynon, +8 authors, H Tsang.
Proc AMIA Symp, 1999 Feb 03;. PMID: 9929351    Free PMC article.
Algorithms for cytoplasm segmentation of fluorescence labelled cells.
Carolina Wählby, Joakim Lindblad, +2 authors, Lennart Björkesten.
Anal Cell Pathol, 2002 Nov 26; 24(2-3). PMID: 12446959    Free PMC article.
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.
Active contours without edges.
T F Chan, L A Vese.
IEEE Trans Image Process, 2008 Feb 06; 10(2). PMID: 18249617
Highly Cited.
Quantitative neurite outgrowth measurement based on image segmentation with topological dependence.
Weimiao Yu, Hwee Kuan Lee, +2 authors, Sohail Ahmed.
Cytometry A, 2008 Oct 28; 75(4). PMID: 18951464
A new strategy to obtain robust markers for blood vessels segmentation by using the watersheds method.
Roberto Rodríguez, Teresa E Alarcón, Oriana Pacheco.
Comput Biol Med, 2005 Aug 30; 35(8). PMID: 16124989
Assessment of interlaboratory variation in the immunohistochemical determination of estrogen receptor status using a breast cancer tissue microarray.
Robin L Parker, David G Huntsman, +4 authors, C Blake Gilks.
Am J Clin Pathol, 2002 Jul 02; 117(5). PMID: 12090420
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
A prototype for unsupervised analysis of tissue microarrays for cancer research and diagnostics.
Wenjin Chen, Michael Reiss, David J Foran.
IEEE Trans Inf Technol Biomed, 2004 Jun 26; 8(2). PMID: 15217253
Validation of tissue microarray technology in breast carcinoma.
R L Camp, L A Charette, D L Rimm.
Lab Invest, 2001 Jan 05; 80(12). PMID: 11140706
Highly Cited.
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
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.
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.
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.
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.
Digital reconstruction of the cell body in dense neural circuits using a spherical-coordinated variational model.
Tingwei Quan, Jing Li, +6 authors, Shaoqun Zeng.
Sci Rep, 2014 May 16; 4. PMID: 24829141    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.
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.
Content-based histopathology image retrieval using CometCloud.
Xin Qi, Daihou Wang, +8 authors, Lin Yang.
BMC Bioinformatics, 2014 Aug 27; 15. PMID: 25155691    Free PMC article.
Optimization of a cell counting algorithm for mobile point-of-care testing platforms.
DaeHan Ahn, Nam Sung Kim, +2 authors, Sang Hyuk Son.
Sensors (Basel), 2014 Sep 10; 14(8). PMID: 25195851    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.
Novel genotype-phenotype associations in human cancers enabled by advanced molecular platforms and computational analysis of whole slide images.
Lee A D Cooper, Jun Kong, +3 authors, Daniel J Brat.
Lab Invest, 2015 Jan 20; 95(4). PMID: 25599536    Free PMC article.
Review.
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.
Robust automatic breast cancer staging using a combination of functional genomics and image-omics.
Hai Su, Yong Shen, +4 authors, David J Foran.
Annu Int Conf IEEE Eng Med Biol Soc, 2016 Jan 07; 2015. PMID: 26737959    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.
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.
Hierarchical nucleus segmentation in digital pathology images.
Yi Gao, Vadim Ratner, +4 authors, Joel Saltz.
Proc SPIE Int Soc Opt Eng, 2016 Jul 05; 9791. PMID: 27375315    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.
Automated Segmentation of Nuclei in Breast Cancer Histopathology Images.
Maqlin Paramanandam, Michael O'Byrne, +4 authors, Vikram Pakrashi.
PLoS One, 2016 Sep 21; 11(9). PMID: 27649496    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.
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.
INTEGRATIVE ANALYSIS FOR LUNG ADENOCARCINOMA PREDICTS MORPHOLOGICAL FEATURES ASSOCIATED WITH GENETIC VARIATIONS.
Chao Wang, Hai Su, Lin Yang, Kun Huang.
Pac Symp Biocomput, 2016 Nov 30; 22. PMID: 27896964    Free PMC article.
UNSUPERVISED SHAPE PRIOR MODELING FOR CELL SEGMENTATION IN NEUROENDOCRINE TUMOR.
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.
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.
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.
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.
AUTOMATED LEVEL SET SEGMENTATION OF HISTOPATHOLOGIC CELLS WITH SPARSE SHAPE PRIOR SUPPORT AND DYNAMIC OCCLUSION CONSTRAINT.
Pengyue Zhang, Fusheng Wang, +3 authors, Jun Kong.
Proc IEEE Int Symp Biomed Imaging, 2017 Aug 07; 2017. PMID: 28781722    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.
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.
Histopathological Image Analysis: Path to Acceptance through Evaluation.
Metin N Gurcan.
Microsc Microanal, 2016 Jul 01; 22(Suppl 3). PMID: 28936115    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.
Quantifying Mesoscale Neuroanatomy Using X-Ray Microtomography.
Eva L Dyer, William Gray Roncal, +9 authors, Narayanan Kasthuri.
eNeuro, 2017 Nov 01; 4(5). PMID: 29085899    Free PMC article.
I-AbACUS: a Reliable Software Tool for the Semi-Automatic Analysis of Invasion and Migration Transwell Assays.
Marilisa Cortesi, Estelle Llamosas, +4 authors, Caroline E Ford.
Sci Rep, 2018 Mar 02; 8(1). PMID: 29491372    Free PMC article.
Measuring multiple parameters of CD8+ tumor-infiltrating lymphocytes in human cancers by image analysis.
Keith E Steele, Tze Heng Tan, +13 authors, Tobias Wiestler.
J Immunother Cancer, 2018 Mar 08; 6(1). PMID: 29510739    Free PMC article.
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.
IHC Color Histograms for Unsupervised Ki67 Proliferation Index Calculation.
Rokshana S Geread, Peter Morreale, +4 authors, April Khademi.
Front Bioeng Biotechnol, 2019 Oct 22; 7. PMID: 31632956    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.
Separating Touching Cells Using Pixel Replicated Elliptical Shape Models.
Mark Winter, Walter Mankowski, +3 authors, Andrew R Cohen.
IEEE Trans Med Imaging, 2018 Oct 09; 38(4). PMID: 30296216    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.
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.
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.
Fusion of whole and part features for the classification of histopathological image of breast tissue.
Chiranjibi Sitaula, Sunil Aryal.
Health Inf Sci Syst, 2020 Nov 13; 8(1). PMID: 33178434    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.
Review.
piNET-An Automated Proliferation Index Calculator Framework for Ki67 Breast Cancer Images.
Rokshana Stephny Geread, Abishika Sivanandarajah, +4 authors, April Khademi.
Cancers (Basel), 2020 Dec 31; 13(1). PMID: 33375043    Free PMC article.
A whole-slide image grading benchmark and tissue classification for cervical cancer precursor lesions with inter-observer variability.
Abdulkadir Albayrak, Asli Unlu Akhan, +6 authors, Lutfiye Durak-Ata.
Med Biol Eng Comput, 2021 Jul 11; 59(7-8). PMID: 34245400