Tensor image registration library: Deformable registration of stand-alone histology images to whole-brain post-mortem MRI data.

Background: Accurate registration between microscopy and MRI data is necessary for validating imaging biomarkers against neuropathology, and to disentangle complex signal dependencies in microstructural MRI. Existing registration methods often rely on serial histological sampling or significant manual input, providing limited scope to work with a large number of stand-alone histology sections. Here we present a customisable pipeline to assist the registration of stand-alone histology sections to whole-brain MRI data.

An automated pipeline for extracting histological stain area fraction for voxelwise quantitative MRI-histology comparisons.

The acquisition of MRI and histology in the same post-mortem tissue sample enables direct correlation between MRI and histologically-derived parameters. However, there still lacks a standardised automated pipeline to process histology data, with most studies relying on manual intervention. Here, we introduce an automated pipeline to extract a quantitative histological measure for staining density (stain area fraction, SAF) from multiple immunohistochemical (IHC) stains.

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

Post-mortem magnetic resonance imaging (MRI) provides the opportunity to acquire high-resolution datasets to investigate neuroanatomy and validate the origins of image contrast through microscopy comparisons. We introduce the (open.win.

A method to remove the influence of fixative concentration on postmortem T maps using a kinetic tensor model.

Formalin fixation has been shown to substantially reduce T estimates, primarily driven by the presence of fixative in tissue. Prior to scanning, post-mortem samples are often placed into a fluid that has more favourable imaging properties. This study investigates whether there is evidence for a change in T in regions close to the tissue surface due to fixative outflux into this surrounding fluid.

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

Susceptibility weighted magnetic resonance imaging (MRI) is sensitive to the local concentration of iron and myelin. Here, we describe a robust image processing pipeline for quantitative susceptibility mapping (QSM) and R2* mapping of fixed post-mortem, whole-brain data. Using this pipeline, we compare the resulting quantitative maps in brains from patients with amyotrophic lateral sclerosis (ALS) and controls, with validation against iron and myelin histology.