An automated pipeline for extracting quantitative histological metrics for voxelwise MRI-histology comparisons
Creators
- 1. Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- 2. Department of Radiology, University of Chicago, Chicago, IL, USA.
- 3. Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- 4. Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
Description
We propose an automated pipeline to extract a quantitative measure for histological staining density (stain area fraction) from immunohistochemical (IHC) stains for voxelwise MRI-histological comparisons. This pipeline addresses IHC artefacts and is generalisable to multiple stains. We applied the pipeline to post-mortem human brain data to generate stain area fractions maps for myelin, neurofilaments, and microglia. We use this pipeline to help perform whole-slide voxelwise comparisons between MRI- and IHC-derived parameters. Our results question some previously reported MRI-histology correlations and emphasize the need to consider multiple microstructural sources when explaining MRI signals.
Files
ihcpy-v1.0.zip
Files
(6.0 MB)
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