Fully automated registration of vibrational microspectroscopic images in histologically stained tissue sections

Abstract

BackgroundIn 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.ResultsWe 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0804-9) contains supplementary material, which is available to authorized users.

Label‐Free Molecular Imaging of Biological Cells and Tissues by Linear and Nonlinear Raman Spectroscopic Approaches

“…Yang et al [55] developed an acquisition process to co-align hyperspectral microscopic data with subsequently measured stained sections.They showed the robustness of their method and applied it to the acquisition of Fourier transform infrared (FTIR) microscopic images to stained section images and CARS images to histopathologic images.K rauss et al [56] acquired Raman images with their fluorescence-stained counterpart using hierarchical clustering to identify the best matching clusters with ac omponent from the fluorescence images.T he advantage of this approach is that the method is at least semi-automatic.…”

“…Yang et al . developed an acquisition process to co‐align hyperspectral microscopic data with subsequently measured stained sections.…”

Deep learning a boon for biophotonics?

“…Additionally, the FTIR imaged cores of tissue microarrays were registered with their histopathologically stained counterparts. This work also presented the registration of CARS images within histopathological staining images . Although this approach is robust and reliable for diverse microscopic technologies, it requires preprocessing of the samples acquired from various modalities.…”

Markerfreie molekulare Bildgebung biologischer Zellen und Gewebe durch lineare und nichtlineare Raman‐spektroskopische Ansätze

“…Yang et al . entwickelten ein Registrierungsverfahren, um hyperspektrale mikroskopische Daten mit nachfolgend gefärbten Dünnschnitten auszurichten.…”