A prototype for unsupervised analysis of tissue microarrays for cancer research and diagnostics

IEEE Trans Inf Technol Biomed. 2004 Jun;8(2):89-96. doi: 10.1109/titb.2004.828891.


The tissue microarray (TMA) technique enables researchers to extract small cylinders of tissue from histological sections and arrange them in a matrix configuration on a recipient paraffin block such that hundreds can be analyzed simultaneously. TMA offers several advantages over traditional specimen preparation by maximizing limited tissue resources and providing a highly efficient means for visualizing molecular targets. By enabling researchers to reliably determine the protein expression profile for specific types of cancer, it may be possible to elucidate the mechanism by which healthy tissues are transformed into malignancies. Currently, the primary methods used to evaluate arrays involve the interactive review of TMA samples while they are viewed under a microscope, subjectively evaluated, and scored by a technician. This process is extremely slow, tedious, and prone to error. In order to facilitate large-scale, multi-institutional studies, a more automated and reliable means for analyzing TMAs is needed. We report here a web-based prototype which features automated imaging, registration, and distributed archiving of TMAs in multiuser network environments. The system utilizes a principal color decomposition approach to identify and characterize the predominant staining signatures of specimens in color space. This strategy was shown to be reliable for detecting and quantifying the immunohistochemical expression levels for TMAs.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.
  • Validation Study

MeSH terms

  • Adolescent
  • Adult
  • Biomarkers, Tumor / analysis*
  • Biomarkers, Tumor / metabolism
  • Breast Neoplasms / diagnosis*
  • Breast Neoplasms / metabolism
  • Breast Neoplasms / pathology
  • Colorimetry / instrumentation
  • Colorimetry / methods
  • Culture Techniques / instrumentation
  • Culture Techniques / methods
  • Equipment Design
  • Equipment Failure Analysis
  • Feasibility Studies
  • Female
  • Histocytochemistry / instrumentation*
  • Histocytochemistry / methods
  • Humans
  • Image Interpretation, Computer-Assisted / instrumentation
  • Image Interpretation, Computer-Assisted / methods*
  • Immunohistochemistry / instrumentation*
  • Immunohistochemistry / methods
  • Internet
  • Micromanipulation / instrumentation*
  • Micromanipulation / methods
  • Microscopy / instrumentation
  • Microscopy / methods
  • Neoplasm Proteins / analysis
  • Neoplasm Proteins / metabolism
  • Pilot Projects
  • Protein Array Analysis / methods*
  • Reproducibility of Results
  • Robotics / instrumentation*
  • Sensitivity and Specificity
  • Software
  • Systems Integration
  • Telemedicine / instrumentation
  • Telemedicine / methods


  • Biomarkers, Tumor
  • Neoplasm Proteins