Enhancement of m-FISH Images using Spectral Unmixing

Authors: Martin De Biasio, Raimund Leitner, Franz G. Wuertz, Sergey Verzakov, Pierre J. Elbischger

Abstract:

Breast carcinoma is the most common form of cancer in women. Multicolour fluorescent in-situ hybridisation (m-FISH) is a common method for staging breast carcinoma. The interpretation of m-FISH images is complicated due to two effects: (i) Spectral overlap in the emission spectra of fluorochrome marked DNA probes and (ii) tissue autofluorescence. In this paper hyper-spectral images of m-FISH samples are used and spectral unmixing is applied to produce false colour images with higher contrast and better information content than standard RGB images. The spectral unmixing is realised by combinations of: Orthogonal Projection Analysis (OPA), Alterating Least Squares (ALS), Simple-to-use Interactive Self-Modeling Mixture Analysis (SIMPLISMA) and VARIMAX. These are applied on the data to reduce tissue autofluorescence and resolve the spectral overlap in the emission spectra. The results show that spectral unmixing methods reduce the intensity caused by tissue autofluorescence by up to 78% and enhance image contrast by algorithmically reducing the overlap of the emission spectra.

Keywords: breast carcinoma, hyperspectral imaging, m-FISH, spectral unmixing

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1062124

References:

[1] N. Harbeck, W. Eiermann, J. Engel, I. Funke, A. Lebeau, W. Parmanetter and M. Untch Prognosefaktoren beim prim¨aren Mammakarzinom, Tumorzentrum Muenchen: Manual Mammakarzinome: Empfehlungen zur Diagnostik, Therapie und Nachsorge, 8. Aufl., Zuckerschwedt, Muenchen, Bern, Wien, New York, pages 39-43, 2001
[2] R. Lupu, M. Cardillo, L. Harris, M. Hijazi and K. Rosenberg Interaction between erbB-receptors and heregulin in breast cancer tumor progression and drug resistance, Sem Cancer Biol, Vol 6, pages 135-145, 1995
[3] D.M. Barnes, J. Bartkova, R.S. Camplejohn, W.J. Gullick, P.J. Smith P.J and R.R. Millis Overexpression of the c-erbB-2 oncogene: Why does this occur more frequently in ductal carcinoma in situ than in invasive mammary carcinoma and is this of prognostic significance?, Eur J Cancer, Vol 28, pages 644-648, 1992
[4] E. Liu, A. Thor, M. He, M. Barcos, B.M. Ljung and C. Benz The HER2 (c-erbB-2) oncogene is frequently amplified in in situ carcinomas of the breast, Oncogene, Vol 7, pages 1027-1032, 1992
[5] N.E. Hynes and D.F. Stern The biology of erbB-2/neu/HER-2 and its role in cancer, Biochim Biophys Acta, Vol 198, pages 165-184, 1994
[6] G.D. Lewis, I. Figari, B. Fendly, W.L. Wong, P. Carter, C. Gorman and H.M. Shepard Differential responses of human tumor cell lines to antip185HER2 monoclonal antibodies, Cancer Immunol Immunother, Vol 37, pages 255-263, 1993
[7] A. Munoz-Barrutia, J. Garcia-Munoz, B. Ucar, I. Fernandez-Garcia and C. Ortiz-de-Solorzano Semi-supervised linear spectral unmixing using a hierarchical Bayesian model for hyperspectral imagery , IRIT/ENSEEIHT/TeSA, 2 rue Camichel, BP 7122, 31071 Toulouse cedex 7, France, 2007
[8] E. Hyytinen, T. Visakorpi, A. Kallioniemi, O.P. Kallioniemi and J. Isola Improved technique for analysis of formalin-fixed, paraffin-embedded tumors by fluorescence in situ hybridization, Cytometry, Vol 16, pages 93-99, 1994
[9] J. Chang-Claude, H. Becher, U. Hamann and T. Schroeder-Kurtz Risikoabsch¨atzung fuer das familiaere Auftreten von Brustkrebs, Zentralblatt fuer Gynaekologie 117, pages 432-434, 1995
[10] S. Herzog Evaluation der HER-2/neu-Genamplifikation an Tumorabklatschpr ¨aparaten von Mammakarzinomen mittels FISH und deren Wertigkeit im Vergleich zur immunhistochemischen membranassoziierten Proteinueberexpression, Universit¨ats-Frauenklinik mit Poliklinik Tuebingen, Allgemeine Geburtshilfe und Frauenheilkunde, Germany, pages 22- 25, 2005
[11] PathVysion HER-2/neu DNA Probe Kit Package Insert, Vysis Inc.
[12] F. Raimondo, MA Gavrielides, G. Karayannopoulou, K. Lyroudia, I. Pitas and I. Kostopoulos Automated evaluation of Her-2/neu status in breast tissue from fluorescent in situ hybridization images, IEEE Trans Image Processing 14(9), pages 1288-99, Sep. 2005
[13] N. Dobigeon, J. Tourneret and Ch. Chang Blind Spectral Unmixing of m-FISH Images by Non-negative Matrix Factorization, Engineering in Medicine and Biology Society, 2007, EMBS 2007, 29th Annual International Conference of the IEEE, Page(s):6247 - 6250, Volume, Issue, 22-26 Aug. 2007
[14] F. C. Snachez, J. Toft, B. van den Bogaert and D. L. Massart Orthogonal Projection Approach Applied to Peak Purity Asessment, Anla. Chem. 68, 1,pages 79-85, 1996
[15] W. Windig and J. Guilment, Interactive Self-Modeling Mixture Analysis, Anla. Chem. 63, pages 1425-1432, 1991
[16] F. H. Kaiser The varimax Criterion for Analytic Rotation in Factor Analysis, Psyhometrika 23, pages 187-200, 1958
[17] M. Forina, C. Armanio, S. Lanteri and R. Leardi Methods of VARIMAX rotations ini factor analysis with applications in clinical and food chemistry, Journal of Chemometrics, Vol. 2, pages 115-125, 1998