A comprehensive framework for classification of nuclei in digital microscopy imaging: An application to diffuse gliomas

Jun Kong*, Lee Cooper, Fusheng Wang, Candace Chisolm, Carlos Moreno, Tahsin Kurc, Patrick Widener, Daniel Brat, Joel Saltz

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

11 Scopus citations

Abstract

In this paper, we present a comprehensive framework to support classification of nuclei in digital microscopy images of diffuse gliomas. This system integrates multiple modules designed for convenient human annotations, standard-based data management, efficient data query and analysis. In our study, 2770 nuclei of six types are annotated by neuropathologists from 29 whole-slide images of glioma biopsies. After machine-based nuclei segmentation for whole-slide images, a set of features describing nuclear shape, texture and cytoplasmic staining is calculated to describe each nucleus. These features along with nuclear boundaries are represented by a standardized data model and saved in the spatial relational database in our framework. Features derived from nuclei classified by neuropathologists are retrieved from the database through efficient spatial queries and used to train distinct classifiers. The best average classification accuracy is 87.43% for 100 independent five-fold cross validations. This suggests that the derived nuclear and cytoplasmic features can achieve promising classification results for six nuclear classes commonly presented in gliomas. Our framework is generic, and can be easily adapted for other related applications.

Original languageEnglish (US)
Title of host publication2011 8th IEEE International Symposium on Biomedical Imaging
Subtitle of host publicationFrom Nano to Macro, ISBI'11
Pages2128-2131
Number of pages4
DOIs
StatePublished - 2011
Event2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11 - Chicago, IL, United States
Duration: Mar 30 2011Apr 2 2011

Publication series

NameProceedings - International Symposium on Biomedical Imaging
ISSN (Print)1945-7928
ISSN (Electronic)1945-8452

Conference

Conference2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11
CountryUnited States
CityChicago, IL
Period3/30/114/2/11

Keywords

  • diffuse glioma
  • feature selection
  • metadata model
  • microscopy image analysis
  • Nuclei classification

ASJC Scopus subject areas

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

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