An automated pipeline for extracting quantitative histological metrics for voxelwise 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 heavy manual intervention. Here, we introduce an automated pipeline to extract quantitative histology metrics (stained area fraction) from multiple immunohistochemical (IHC) stains. The pipeline is designed to directly address key IHC artefacts related to tissue staining and slide digitisation. This pipeline was applied to post-mortem human brain data from multiple subjects, relating MRI parameters (FA, MD, R2*, R1) to IHC slides stained for myelin, neurofilaments, microglia, and activated microglia. Utilising high-quality MRI-IHC coregistration, we then performed whole-slide voxelwise comparisons (simple correlation, partial correlation, and multiple regression analyses) between multimodal MRI- and IHC-derived parameters. The pipeline was found to be reproducible, robust to some artefacts, and generalisable across multiple IHC stains. Our partial correlation results suggest that some simple MRI-IHC correlations should be interpreted with caution, due to the colocalisation of certain tissue features (e.g. myelin and neurofilaments). Further, we find activated microglia to consistently be the strongest predictor of DTI FA, which may suggest the sensitivity of diffusion MRI to neuroinflammation. Taken together, these results show the utility of this approach in carefully curating IHC data and performing multimodal analyses to better understand microstructural relationships with MRI. ### Competing Interest Statement The authors have declared no competing interest.