title: Fully automated registration of vibrational microspectroscopic images in histologically stained tissue sections.
abstract: BACKGROUND
  In recent years, hyperspectral microscopy techniques such as infrared or Raman microscopy have been applied successfully for diagnostic purposes. In many of the corresponding studies, it is common practice to measure one and the same sample under different types of microscopes. Any joint analysis of the two image modalities requires to overlay the images, so that identical positions in the sample are located at the same coordinate in both images. This step, commonly referred to as image registration, has typically been performed manually in the lack of established automated computational registration tools.
  
  
  RESULTS
  We propose a corresponding registration algorithm that addresses this registration problem, and demonstrate the robustness of our approach in different constellations of microscopes. First, we deal with subregion registration of Fourier Transform Infrared (FTIR) microscopic images in whole-slide histopathological staining images. Second, we register FTIR imaged cores of tissue microarrays in their histopathologically stained counterparts, and finally perform registration of Coherent anti-Stokes Raman spectroscopic (CARS) images within histopathological staining images.
  
  
  CONCLUSIONS
  Our validation involves a large variety of samples obtained from colon, bladder, and lung tissue on three different types of microscopes, and demonstrates that our proposed method works fully automated and highly robust in different constellations of microscopes involving diverse types of tissue samples.
authors.affiliation: Department of Biophysics, CAS-MPG Partner Institute and Key Laboratory for Computational Biology, 320 Yueyang Road, Shanghai, 200031, China. yangchen@picb.ac.cn.
authors.forename: Chen
authors.initials: C
authors.lastname: Yang
authors.affiliation: Department of Biophysics, Ruhr-University Bochum, Universitätsstraße 150, Bochum, 44780, Germany. daniel.niedieker@bph.rub.de.
authors.forename: Daniel
authors.initials: D
authors.lastname: Niedieker
authors.affiliation: Department of Biophysics, Ruhr-University Bochum, Universitätsstraße 150, Bochum, 44780, Germany. fred@bph.rub.de.
authors.forename: Frederik
authors.initials: F
authors.lastname: Grosserüschkamp
authors.affiliation: Department of Biophysics, Ruhr-University Bochum, Universitätsstraße 150, Bochum, 44780, Germany. melanie.horn@bph.rub.de.
authors.forename: Melanie
authors.initials: M
authors.lastname: Horn
authors.affiliation: Institute of Pathology, Ruhr-University Bochum, Bochum, Germany, Bürkle-de-la-Camp-Platz 1, Bochum, 44789, Germany. andrea.tannapfel@rub.de.
authors.forename: Andrea
authors.initials: A
authors.lastname: Tannapfel
authors.affiliation: Department of Biophysics, Ruhr-University Bochum, Universitätsstraße 150, Bochum, 44780, Germany. angela@bph.rub.de.
authors.forename: Angela
authors.initials: A
authors.lastname: Kallenbach-Thieltges
authors.affiliation: Department of Biophysics, CAS-MPG Partner Institute and Key Laboratory for Computational Biology, 320 Yueyang Road, Shanghai, 200031, China. gerwert@bph.rub.de.|Department of Biophysics, Ruhr-University Bochum, Universitätsstraße 150, Bochum, 44780, Germany. gerwert@bph.rub.de.
authors.forename: Klaus
authors.initials: K
authors.lastname: Gerwert
authors.affiliation: Department of Biophysics, Ruhr-University Bochum, Universitätsstraße 150, Bochum, 44780, Germany. axel.mosig@bph.rub.de.
authors.forename: Axel
authors.initials: A
authors.lastname: Mosig
mesh_terms: D000465:Algorithms; D003106:Colon / Q000166:cytology*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008168:Lung / Q000166:cytology*; D008853:Microscopy / Q000379:methods*; D010363:Pattern Recognition, Automated; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods; D013059:Spectrum Analysis, Raman / Q000379:methods; D046888:Tissue Array Analysis; D001743:Urinary Bladder / Q000166:cytology*