Journal Article
. 2009 Apr; 13(4):636-44.
doi: 10.1109/TITB.2009.2020159.

Virtual microscopy and grid-enabled decision support for large-scale analysis of imaged pathology specimens

Lin Yang 1 Wenjin Chen  Peter Meer  Gratian Salaru  Lauri A Goodell  Viktors Berstis  David J Foran  
Affiliations
  • PMID: 19369162
  •     11 References
  •     18 citations

Abstract

Breast cancer accounts for about 30% of all cancers and 15% of cancer deaths in women. Advances in computer-assisted analysis hold promise for classifying subtypes of disease and improving prognostic accuracy. We introduce a grid-enabled decision support system for performing automatic analysis of imaged breast tissue microarrays. To date, we have processed more than 1,00,000 digitized specimens (1200 x 1200 pixels each) on IBM's World Community Grid (WCG). As a part of the Help Defeat Cancer (HDC) project, we have analyzed that the data returned from WCG along with retrospective patient clinical profiles for a subset of 3744 breast tissue samples, and have reported the results in this paper. Texture-based features were extracted from the digitized specimens, and isometric feature mapping was applied to achieve nonlinear dimension reduction. Iterative prototyping and testing were performed to classify several major subtypes of breast cancer. Overall, the most reliable approach was gentle AdaBoost using an eight-node classification and regression tree as the weak learner. Using the proposed algorithm, a binary classification accuracy of 89% and the multiclass accuracy of 80% were achieved. Throughout the course of the experiments, only 30% of the dataset was used for training.

Neuroendocrine expression in metastatic prostate cancer: evaluation of high throughput tissue microarrays to detect heterogeneous protein expression.
N R Mucci, G Akdas, S Manely, M A Rubin.
Hum Pathol, 2000 May 23; 31(4). PMID: 10821485
Biopsy of a biopsy: validation of immunoprofiling in gastric cancer biopsy tissue microarrays.
C Gulmann, D Butler, +2 authors, M Leader.
Histopathology, 2002 Dec 21; 42(1). PMID: 12493028
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.
A global geometric framework for nonlinear dimensionality reduction.
J B Tenenbaum, V de Silva, J C Langford.
Science, 2000 Dec 23; 290(5500). PMID: 11125149
Highly Cited.
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
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.
A comparison of breast tissue classification techniques.
Arnau Oliver, Jordi Freixenet, Robert Martí, Reyer Zwiggelaar.
Med Image Comput Comput Assist Interv, 2007 Mar 16; 9(Pt 2). PMID: 17354855
Review.
Tissue microarrays for rapid linking of molecular changes to clinical endpoints.
J Torhorst, C Bucher, +9 authors, G Sauter.
Am J Pathol, 2001 Dec 06; 159(6). PMID: 11733374    Free PMC article.
Highly Cited.
Multiple Class Segmentation Using A Unified Framework over Mean-Shift Patches.
Lin Yang, Peter Meer, David J Foran.
Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit, 2007 Jul 16; 2007(4270254). PMID: 19295664    Free PMC article.
Reliability of tissue microarrays in detecting protein expression and gene amplification in breast cancer.
DaoHai Zhang, Manuel Salto-Tellez, +2 authors, Evelyn Siew-Chuan Koay.
Mod Pathol, 2003 Jan 16; 16(1). PMID: 12527717
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
Detection and classification of thyroid follicular lesions based on nuclear structure from histopathology images.
Wei Wang, John A Ozolek, Gustavo K Rohde.
Cytometry A, 2010 Jan 26; 77(5). PMID: 20099247    Free PMC article.
An optimal transportation approach for nuclear structure-based pathology.
Wei Wang, John A Ozolek, +3 authors, Gustavo K Rohde.
IEEE Trans Med Imaging, 2010 Oct 28; 30(3). PMID: 20977984    Free PMC article.
COMPUTER-AIDED GLEASON GRADING OF PROSTATE CANCER HISTOPATHOLOGICAL IMAGES USING TEXTON FORESTS.
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.
Interactive and automated application of virtual microscopy.
Klaus Kayser, Jürgen Görtler, Stephan Borkenfeld, Gian Kayser.
Diagn Pathol, 2011 Apr 22; 6 Suppl 1. PMID: 21489181    Free PMC article.
How to measure diagnosis-associated information in virtual slides.
Klaus Kayser, Jürgen Görtler, Stephan Borkenfeld, Gian Kayser.
Diagn Pathol, 2011 Apr 22; 6 Suppl 1. PMID: 21489204    Free PMC article.
Grid computing in image analysis.
Klaus Kayser, Jürgen Görtler, Stephan Borkenfeld, Gian Kayser.
Diagn Pathol, 2011 Apr 27; 6 Suppl 1. PMID: 21516880    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.
Automatic detection of melanoma progression by histological analysis of secondary sites.
Nikita V Orlov, Ashani T Weeraratna, +5 authors, Ilya G Goldberg.
Cytometry A, 2012 Apr 03; 81(5). PMID: 22467531    Free PMC article.
A linear optimal transportation framework for quantifying and visualizing variations in sets of images.
Wei Wang, Dejan Slepčev, +2 authors, Gustavo K Rohde.
Int J Comput Vis, 2013 Jun 05; 101(2). PMID: 23729991    Free PMC article.
Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data.
David A Gutman, Jake Cobb, +6 authors, Lee A D Cooper.
J Am Med Inform Assoc, 2013 Jul 31; 20(6). PMID: 23893318    Free PMC article.
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.
Detecting and visualizing cell phenotype differences from microscopy images using transport-based morphometry.
Saurav Basu, Soheil Kolouri, Gustavo K Rohde.
Proc Natl Acad Sci U S A, 2014 Feb 20; 111(9). PMID: 24550445    Free PMC article.
Influence of Texture and Colour in Breast TMA Classification.
M Milagro Fernández-Carrobles, Gloria Bueno, +3 authors, Lucía González-López.
PLoS One, 2015 Oct 30; 10(10). PMID: 26513238    Free PMC article.
Scalable analysis of Big pathology image data cohorts using efficient methods and high-performance computing strategies.
Tahsin Kurc, Xin Qi, +7 authors, David J Foran.
BMC Bioinformatics, 2015 Dec 03; 16. PMID: 26627175    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.
Multi-class texture analysis in colorectal cancer histology.
Jakob Nikolas Kather, Cleo-Aron Weis, +5 authors, Frank Gerrit Zöllner.
Sci Rep, 2016 Jun 17; 6. PMID: 27306927    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.
Review.
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.