Bridging Neuroimaging and Neuropathology: A Comprehensive Workflow for Targeted Sampling of White Matter Lesions

Abstract

Background and purpose: White matter lesions are common imaging biomarkers associated with aging and neurodegenerative diseases, yet their underlying pathology remains unclear due to limitations in imaging-based characterization. We aim to develop and validate a comprehensive workflow enabling precise MRI-guided histological sampling of white matter lesions to bridge neuroimaging and neuropathology.

Methods: We established a workflow integrating agar-sucrose brain embedding, ultrahigh field 7 Tesla (7T) MRI acquisition, reusable three-dimensional (3D) printed cutting guides, and semiautomated MRI-blockface alignment. Left hemispheric postmortem brains were stabilized in the embedding medium and scanned using optimized MRI protocols. Coronal sectioning was guided by standardized 3D-printed cutting guides, and knife traces were digitally matched to MRI planes. White matter lesions were segmented on MRI and aligned for histopathological sampling.

Results: The workflow enabled reproducible brain sectioning, minimized imaging artifacts, and achieved precise spatial alignment between MRI and histology. For demonstration, detailed results from two representative brains were presented in this article. Consistent, high-resolution MRI data facilitated accurate lesion detection and sampling. The use of standardized cutting guides and alignment protocols reduced variability and improved efficiency.

Conclusions: Our cost-effective, scalable workflow reliably linked neuroimaging findings with histological analysis, enhancing the understanding of white matter lesion pathology. This framework held significant potential for advancing translational research in aging and neurodegenerative diseases.

Keywords: MRI‐guided histology; neuroimaging workflow; postmortem brain imaging; three‐dimensional (3D) printing; ultrahigh field MRI; white matter lesions.

FIGURE 1

Workflow of MRI‐guided sampling of white matter lesion. The left hemisphere is first embedded in agar/sucrose solution and imaged using ultrahigh field 7 T MRI. The brain is then sectioned using a custom three‐dimensional‐printed cutting guide to ensure precise alignment with MRI slices. White matter lesions are identified on MR images, and corresponding tissue samples are extracted from the matched histological sections for further analysis.

FIGURE 2

Three‐dimensional (3D) rendering of the 3D printed container with cutting guides. (A) The 3D model of the cutting guides (grey), the container enclosure (red), and the sealing lid (yellow). (B) 3D rendering shows the fit of the container to the RF coil's inner dimensions.

FIGURE 3

Example of acquired MR contrasts for postmortem brain MRI. T2 SPACE, T2 sampling perfection with application‐optimized contrast using different flip angle evolution; T1w, T1‐weighted image from magnetization‐prepared two rapid gradient echo (MP2RAGE) sequence; T1 map, quantitative T1 relaxation time map from MP2RAGE acquisition.

FIGURE 4

Brain cutting process. (A) The sealed container with the lid in place. (B) After removing the lid, the brain and cutting guide are visible, embedded in agarose. (C) The container is removed, and the brain is sectioned using a knife guided by the cutting columns. (D) The brain is fully sectioned; both the agarose and brain maintain their structural integrity. (E) The cutting guides are removed, leaving the slabs embedded in agarose. (F) The slabs are arranged and photographed.

FIGURE 5

Alignment of MRI virtual cutting planes with knife traces on blockface photographs. (A) After sectioning the brain using the cutting guides, knife traces become visible on the agarose surface and are manually highlighted with a dashed blue line. The pink line represents the coronal virtual plane used for alignment, whereas the yellow line represents the axial virtual plane (shown for reference but not used during the alignment process). During alignment, the coronal virtual plane is oriented to match the knife trace and positioned to pass through the corresponding column pair. (B) During alignment, each MRI coronal slice is visually matched to the corresponding blockface photograph before proceeding to the next slice. (C) As alignment progresses, previously matched knife traces are marked with thin blue dashed lines, whereas the current slice position is indicated by a thicker blue dashed line. The pink coronal plane shows the current MRI reconstruction plane, aligned with the cutting orientation. The yellow line indicating the axial plane is shown for reference but not used during the alignment process. (D) The visual match between MRI and blockface images is confirmed for each slab before advancing to the next cutting plane.

FIGURE 6

Detection of white matter lesion (arrow) on T1‐weighted MRI with corresponding blockface photograph. (A) T1‐weighted MR image serving as input for our in‐house deep learning model. (B) Automated lesion segmentation mask overlaid on the MR image. (C) Corresponding blockface photograph after image registration and alignment. (D) Lesion mask transferred from MRI to the aligned blockface photograph for histological sampling guidance. The white matter lesion was automatically segmented from the T1‐weighted MRI using our deep learning model, and the resulting mask was subsequently registered to the blockface photograph to guide precise histological sampling.

FIGURE 7

Alignment of T2‐SPACE with blockface photos of the brain sample 1. The yellow dashed lines indicate that the first two and last two slices are cut freehand without the cutting guides, and the blue dotted lines indicate that the slices were cut with the cutting guide. The white solid arrows point to the locations of periventricular lesions, and the white dashe arrows point to the location of the deep white matter lesion.

FIGURE 8

Alignment of T2‐SPACE with blockface photos of the brain sample 2. The dashed yellow lines indicate that the first two and last two slices are cut freehand without the cutting guides, and the blue dotted lines indicate that the slices are cut with the cutting guide. The white solid arrows point to the locations of periventricular lesions.