title: Scalable analysis of Big pathology image data cohorts using efficient methods and high-performance computing strategies.
abstract: BACKGROUND
  We describe a suite of tools and methods that form a core set of capabilities for researchers and clinical investigators to evaluate multiple analytical pipelines and quantify sensitivity and variability of the results while conducting large-scale studies in investigative pathology and oncology. The overarching objective of the current investigation is to address the challenges of large data sizes and high computational demands.
  
  
  RESULTS
  The proposed tools and methods take advantage of state-of-the-art parallel machines and efficient content-based image searching strategies. The content based image retrieval (CBIR) algorithms can quickly detect and retrieve image patches similar to a query patch using a hierarchical analysis approach. The analysis component based on high performance computing can carry out consensus clustering on 500,000 data points using a large shared memory system.
  
  
  CONCLUSIONS
  Our work demonstrates efficient CBIR algorithms and high performance computing can be leveraged for efficient analysis of large microscopy images to meet the challenges of clinically salient applications in pathology. These technologies enable researchers and clinical investigators to make more effective use of the rich informational content contained within digitized microscopy specimens.
authors.affiliation: Department of Biomedical Informatics, Stony Brook University, Stony Brook, USA. tahsin.kurc@stonybrook.edu.
authors.forename: Tahsin
authors.initials: T
authors.lastname: Kurc
authors.affiliation: Department of Pathology & Laboratory Medicine, Rutgers -- Robert Wood Johnson Medical School, New Brunswick, USA. qixi@rutgers.edu.|Rutgers Cancer Institute of New Jersey, New Brunswick, USA. qixi@rutgers.edu.
authors.forename: Xin
authors.initials: X
authors.lastname: Qi
authors.affiliation: Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, USA. daihou.wang@rutgers.edu.
authors.forename: Daihou
authors.initials: D
authors.lastname: Wang
authors.affiliation: Department of Biomedical Informatics, Stony Brook University, Stony Brook, USA. fusheng.wang@stonybrook.edu.|Department of Computer Science, Stony Brook University, Stony Brook, USA. fusheng.wang@stonybrook.edu.
authors.forename: Fusheng
authors.initials: F
authors.lastname: Wang
authors.affiliation: Department of Biomedical Informatics, Stony Brook University, Stony Brook, USA. teodoro@unb.br.|Department of Computer Science, University of Brasilia, Brasília, Brazil. teodoro@unb.br.
authors.forename: George
authors.initials: G
authors.lastname: Teodoro
authors.affiliation: Department of Biomedical Informatics, Emory University, Atlanta, USA. lee.cooper@emory.edu.
authors.forename: Lee
authors.initials: L
authors.lastname: Cooper
authors.affiliation: Department of Biomedical Informatics, Emory University, Atlanta, USA. mnalisn@emory.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Nalisnik
authors.affiliation: Department of Biomedical Engineering, University of Florida, Gainesville, USA. lin.yang@bme.ufl.edu.
authors.forename: Lin
authors.initials: L
authors.lastname: Yang
authors.affiliation: Department of Biomedical Informatics, Stony Brook University, Stony Brook, USA. joel.saltz@stonybrookmedicine.edu.
authors.forename: Joel
authors.initials: J
authors.lastname: Saltz
authors.affiliation: Department of Pathology & Laboratory Medicine, Rutgers -- Robert Wood Johnson Medical School, New Brunswick, USA. foran@cinj.rutgers.edu.|Rutgers Cancer Institute of New Jersey, New Brunswick, USA. foran@cinj.rutgers.edu.
authors.forename: David J
authors.initials: DJ
authors.lastname: Foran
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D003952:Diagnostic Imaging / Q000379:methods*; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D016247:Information Storage and Retrieval; D008297:Male; D060787:Neoplasm Grading; D010363:Pattern Recognition, Automated; D011471:Prostatic Neoplasms / Q000473:pathology*; D046888:Tissue Array Analysis / Q000295:instrumentation*