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

## TL;DR

This paper introduces a fully automated method to align images from different microscopes used in tissue analysis, improving accuracy and efficiency in diagnostic studies.

## Contribution

The novel contribution is a robust, fully automated image registration algorithm for vibrational microspectroscopic and histopathological images.

## Key findings

- The algorithm successfully registers FTIR images with histopathological staining images.
- It also registers CARS images within histopathological staining images.
- The method works across diverse tissue types and microscope types.

## Abstract

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.

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.

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.

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