Open Access Highly Accessed Research article

Real-time interactive data mining for chemical imaging information: application to automated histopathology

David Mayerich1, Michael Walsh2, Matthew Schulmerich13 and Rohit Bhargava13456*

Author Affiliations

1 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, USA

2 Departmet of Pathology, University of Illinois at Chicago, Chicago, IL, USA

3 Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL, USA

4 Department of Mechanical Science and Engineering, University of Illinois at Urbana–Champaign, Urbana, IL, USA

5 Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL, USA

6 University of Illinois Cancer Center, Urbana, IL, USA

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BMC Bioinformatics 2013, 14:156  doi:10.1186/1471-2105-14-156

Published: 8 May 2013

Abstract

Background

Vibrational spectroscopic imaging is now used in several fields to acquire molecular information from microscopically heterogeneous systems. Recent advances have led to promising applications in tissue analysis for cancer research, where chemical information can be used to identify cell types and disease. However, recorded spectra are affected by the morphology of the tissue sample, making identification of chemical structures difficult.

Results

Extracting features that can be used to classify tissue is a cumbersome manual process which limits this technology from wide applicability. In this paper, we describe a method for interactive data mining of spectral features using GPU-based manipulation of the spectral distribution.

Conclusions

This allows researchers to quickly identify chemical features corresponding to cell type. These features are then applied to tissue samples in order to visualize the chemical composition of the tissue without the use of chemical stains.