Data from: Precise MRI-histology coregistration of paraffin-embedded tissue with blockface imaging

Magnetic resonance imaging (MRI) provides 3D spatial information on
tissue, yet it lacks at the molecular level. In contrast, histology
provides cellular and molecular information, but it lacks the 3D spatial
context and direct in vivo translation. Coregistering the two is key for
the 3D-embedding of histological details, validating pathological MRI
findings, and finding quantitative imaging biomarkers of neurodegenerative
diseases. However, coregistration is challenging due to non-linear
distortions of the tissue from histological processing and sectioning
leading to microscopic and macroscopic nonlinear 3D deformations between
specimen MRI and stained histology sections. To address this, we developed
a novel pipeline integrating robust optical approaches with innovative 2D
and 3D registration algorithms to achieve precise volumetric alignment of
specimen MRI data with histological images. On a variety of brain tissue
specimens from distinct anatomical regions and across multiple species,
our methodology generated blockface volumes with minimal distortion and
artifacts. Using these blockface volumes as an intermediary, we achieve a
precise alignment between MRI and histology slides, yielding registration
results with an overlapping Dice score of ~90% for whole tissue alignment
between MRI and blockface volumes, and >95% for 2D MRI-histology
registration. This correlative MRI-histology pipeline with robust 2D and
3D coregistration methods promises to enhance our understanding of
neurodegenerative diseases and aid the development of MRI-based disease
biomarkers.