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Robust detection and segmentation of cell nuclei in biomedical images based on a computational topology framework
Indexado
WoS WOS:000401383800007
Scopus SCOPUS_ID:85015105232
DOI 10.1016/J.MEDIA.2017.02.009
Año 2017
Tipo artículo de investigación

Citas Totales

Autores Afiliación Chile

Instituciones Chile

% Participación
Internacional

Autores
Afiliación Extranjera

Instituciones
Extranjeras


Abstract



The segmentation of cell nuclei is an important step towards the automated analysis of histological images. The presence of a large number of nuclei in whole-slide images necessitates methods that are computationally tractable in addition to being effective. In this work, a method is developed for the robust segmentation of cell nuclei in histological images based on the principles of persistent homology. More specifically, an abstract simplicial homology approach for image segmentation is established. Essentially, the approach deals with the persistence of disconnected sets in the image, thus identifying salient regions that express patterns of persistence, By introducing an image representation based on topological features, the task of segmentation is less dependent on variations of color or texture. This results in a novel approach that generalizes well and provides stable performance. The method conceptualizes regions of interest (cell nuclei) pertinent to their topological features in a successful manner. The time cost of the proposed approach is lower-bounded by an almost linear behavior and upper-bounded by O(n(2)) in a worst-case scenario. Time complexity matches a quasilinear behavior which is O(n(1+epsilon)) for epsilon < 1. Images acquired from histological sections of liver tissue are used as a case study to demonstrate the effectiveness of the approach. The histological landscape consists of hepatocytes and non-parenchymal cells. The accuracy of the proposed methodology is verified against an automated workflow created by the output of a conventional filter bank (validated by experts) and the supervised training of a random forest classifier. The results are obtained on a per-object basis. The proposed workflow successfully detected both hepatocyte and non-parenchymal cell nuclei with an accuracy of 84.6%, and hepatocyte cell nuclei only with an accuracy of 86.2%. A public histological dataset with supplied ground-truth data is also used for evaluating the performance of the proposed approach (accuracy: 94.5%). Further validations are carried out with a publicly available dataset and ground-truth data from the Gland Segmentation in Colon Histology Images Challenge (GIaS) contest. The proposed method is useful for obtaining unsupervised robust initial segmentations that can be further integrated in image/data processing and management pipelines. The development of a fully automated system supporting a human expert provides tangible benefits in the context of clinical decision-making. (C) 2017 Elsevier B.V. All rights reserved.

Revista



Revista ISSN
Medical Image Analysis 1361-8415

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Disciplinas de Investigación



WOS
Computer Science, Interdisciplinary Applications
Radiology, Nuclear Medicine & Medical Imaging
Computer Science, Artificial Intelligence
Engineering, Biomedical
Scopus
Radiology, Nuclear Medicine And Imaging
Computer Vision And Pattern Recognition
Computer Graphics And Computer Aided Design
Radiological And Ultrasound Technology
Health Informatics
SciELO
Sin Disciplinas

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Publicaciones WoS (Ediciones: ISSHP, ISTP, AHCI, SSCI, SCI), Scopus, SciELO Chile.

Colaboración Institucional



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Autores - Afiliación



Ord. Autor Género Institución - País
1 Rojas-Moraleda, Rodrigo Hombre German Canc Res Ctr - Alemania
Universidad Técnica Federico Santa María - Chile
German Cancer Research Center - Alemania
2 Xiong, Wei - Heidelberg Univ - Alemania
Universität Heidelberg - Alemania
Institut fur Theoretische Physik Heidelberg - Alemania
3 Halama, Niels Hombre Univ Heidelberg Hosp - Alemania
Universitätsklinikum Heidelberg - Alemania
German Cancer Research Center - Alemania
4 Breitkopf-Heinlein, Katja Mujer Heidelberg Univ - Alemania
Universität Heidelberg - Alemania
5 Dooley, Steven Hombre Heidelberg Univ - Alemania
Universität Heidelberg - Alemania
6 SALINAS-CARRASCO, LUIS ARMANDO Hombre Universidad Técnica Federico Santa María - Chile
7 Heermann, Dieter W. Hombre Heidelberg Univ - Alemania
Universität Heidelberg - Alemania
Institut fur Theoretische Physik Heidelberg - Alemania
8 Valous, Nektarios A. Hombre German Canc Res Ctr - Alemania
German Cancer Research Center - Alemania

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Financiamiento



Fuente
FONDECYT
China Scholarship Council
Fondo Nacional de Desarrollo Científico y Tecnológico
German Federal Ministry of Education and Research
China Scholarship Council (CSC)
Bundesministerium für Bildung und Forschung
Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica
Basal Project
AnilloProject
Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp)
German Federal Ministry of Education and Research: Virtual Liver Network grants
Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, University of Heidelberg
Human Genome Sciences

Muestra la fuente de financiamiento declarada en la publicación.

Agradecimientos



Agradecimiento
The authors are thankful to Ms. Katarina Abramovic for the technical assistance (immunohistochemistry). Experimental methods are supported by the German Federal Ministry of Education and Research: Virtual Liver Network grants 0315755 and 0315764 (SD). Dr. Luis Salinas acknowledges support from FONDECYT 1100805, Basal Project FB0821 CCTVal, and AnilloProject ACT119. Ms. Wei Xiong acknowledges the funding from the China Scholarship Council (CSC No. 2011604036) and support from the Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp).
The authors are thankful to Ms. Katarina Abramovic for the technical assistance (immunohistochemistry). Experimental methods are supported by the German Federal Ministry of Education and Research: Virtual Liver Network grants 0315755 and 0315764 (SD). Dr. Luis Salinas acknowledges support from FONDECYT 1100805, Basal Project FB0821 CCTVal, and AnilloProject ACT119. Ms. Wei Xiong acknowledges the funding from the China Scholarship Council (CSC No. 2011604036) and support from the Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp).

Muestra la fuente de financiamiento declarada en la publicación.