Tensor Image Registration Library: Automated Non-Linear Registration of Sparsely Sampled Histological Specimens to Post-Mortem MRI of the Whole Human Brain

Abstract

Highlights 29 30• TIRL: new framework for prototyping bespoke image registration pipelines 31• Pipeline for automated registration of small-slide histology to whole-brain MRI 32• Slice-to-volume registration accounting for through-plane deformations 33• No need for serial histological sampling 34 35Abstract 36 37 There is a need to understand the histopathological basis of MRI signal characteristics in 38 complex biological matter. Microstructural imaging holds promise for sensitive and specific 39 indicators of the early stages of human neurodegeneration but requires validation against 40 traditional histological markers before it can be reliably applied in the clinical setting. 41Validation relies on a precise and preferably automatic method to align MRI and histological 42 images of the same tissue, which poses unique challenges compared to more conventional 43 MRI-to-MRI registration. 44 45A customisable open-source platform, Tensor Image Registration Library (TIRL) is presented. 46Based on TIRL, a fully automated pipeline was implemented to align small stained histological 47

The Digital Brain Bank, an open access platform for post-mortem datasets

“…Comparisons between ALS and control brains over the corpus callosum (c) reveal changes in fractional anisotropy (FA, normalised to Par/Temp/Occ lobe), with biggest changes associated with motor regions (Hofer & Frahm, 2006) ( * = p < 0.05; * * = p < 0.05 following multiple comparison correction). Accurate MRI-histology coregistrations facilitates cross-modality comparisons, and (d) displays an example MRI-histology coregistration over the visual cortex of a single ALS brain achieved using the Tensor Image Registration Library (TIRL) (Huszar et al, 2019 (Jucker & Walker, 2013).…”

“…MRI and microscopy) datasets on the Digital Brain Bank website is achieved with Tview. An example Tview implementation is available at open.win.ox.ac.uk/DigitalBrainBank/#/tileviewer, where cross-modality coregistrations were performed using the Tensor Image Registration Library (TIRL) (Huszar et al, 2019) and FNIRT (Andersson, Jenkinson, Smith, & others, 2007;Jenkinson, Beckmann, Behrens, Woolrich, & Smith, 2012), both available as part of FSL. Code for Tview is available at https://git.fmrib.ox.ac.uk/thanayik/slideviewer.…”

Methods for quantitative susceptibility and R2* mapping in whole post-mortem brains at 7T applied to amyotrophic lateral sclerosis

“…Second, registration between histology slides and MRI data was not performed, requiring us to correlate at the level of region-of-interest rather than pixel-wise. A pipeline that enables automated registration of histology slides to 3D MRI images using dissection photos as an intermediary is currently under development ( Huszar et al., 2019 ). This registration pipeline aims to enable pixel-wise comparisons between MRI and histology acquired within the same sample.…”

Methods for quantitative susceptibility and R2* mapping in whole post-mortem brains at 7T

“…Second, registration between histology slides and MRI data was not performed, requiring us to correlate at the level of region-of-interest rather than pixel-wise. A pipeline that enables automated registration of histology slides to 3D MRI images using dissection photos as an intermediary is currently under development [56].…”