Fusion of rat brain histology and MRI using weighted multi-image mutual information

Abstract

Introduction -Fusion of histology and MRI is frequently demanded in biomedical research to study in vitro tissue properties in an in vivo reference space. Distortions and artifacts caused by cutting and staining of histological slices as well as differences in spatial resolution make even the rigid fusion a difficult task. Stateof-the-art methods start with a mono-modal restacking yielding a histological pseudo-3D volume. The 3D information of the MRI reference is considered subsequently. However, consistency of the histology volume and consistency due to the corresponding MRI seem to be diametral goals. Therefore, we propose a novel fusion framework optimizing histology/histology and histology/MRI consistency at the same time finding a balance between both goals.Method -Direct slice-to-slice correspondence even in irregularly-spaced cutting sequences is achieved by registration-based interpolation of the MRI. Introducing a weighted multi-image mutual information metric (WI), adjacent histology and corresponding MRI are taken into account at the same time. Therefore, the reconstruction of the histological volume as well as the fusion with the MRI is done in a single step.Results -Based on two data sets with more than 110 single registrations in all, the results are evaluated quantitatively based on Tanimoto overlap measures and qualitatively showing the fused volumes. In comparison to other multi-image metrics, the reconstruction based on WI is significantly improved. We evaluated different parameter settings with emphasis on the weighting term steering the balance between intra-and inter-modality consistency.

A Survey of Methods for 3D Histology Reconstruction

“…The main advantages of using them are the shortcuts in the process (e.g., no dehydration is needed), and their better preservation of antigens for immunohistochemistry. They were used in Annese et al (2014); Stille et al (2013); Annese (2012); Choe et al (2011); Palm et al (2010Palm et al ( , 2008; Dauguet et al (2007c). The different stages of frozen sections preparation consist of:…”

Towards ultra-high resolution fibre tract mapping of the human brain - registration of polarised light images and reorientation of fibre vectors

“…Others have used reference data like blockface (Kim et al, 1997; Čapek et al, 2009) or magnetic resonance (MR) images obtained prior to histological processing of mouse (Yushkevich et al, 2006), rat (Palm et al, 2008) or monkey (Rangarajan et al, 1997; Malandain et al, 2004) brains to align section images. Especially for large human brains, reference data are necessary considering the complex shape of the surface.…”

Resolving the Three-Dimensional Histology of the Heart

“…Methods have been proposed to reconstruct 3D volumes from histology sections, particularly for the brain [25,26,27], with leading examples projecting right through to mapping functional observations to structural substrates [28]. Other examples include skeletal muscle [29] and the atrio-ventricular node of rabbit heart [30].…”