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 establish a workflow integrating agarose-saccharose brain embedding, ultra-high field 7T MRI acquisition, reusable 3D-printed cutting guides, and semi-automated MRI-blockface alignment. Postmortem brains are stabilized in the embedding medium and scanned using optimized MRI protocols. Coronal sectioning is guided by standardized 3D-printed cutting guides, and knife traces are digitally matched to MRI planes. White matter lesions are segmented on MRI and aligned for histopathological sampling. This approach is validated in over 100 postmortem human brains.

Results: The workflow enables reproducible brain sectioning, minimizes imaging artifacts, and achieves precise spatial alignment between MRI and histology. Consistent, high-resolution MRI data facilitated accurate lesion detection and sampling. The use of standardized cutting guides and alignment protocols reduce variability and improve efficiency.

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

Keywords: 3D printing; MRI-guided histology; White matter lesions; neuroimaging workflow; postmortem brain imaging; ultra-high field MRI.

Figure 1

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 2

Workflow of the MRI-guided sampling of white matter lesion.

Figure 3

Example of acquired MR contrasts for the postmortem brain MRI.

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, the knife leaves visible traces on the surface of the agarose. These traces are manually highlighted w th a dashed blue line. A virtual reconstruction plane (pink line) is aligned to match the orientation of 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 highlighted in blue, and the current slice position is marked with a blue dashed line. The pink plane denotes the current reconstruction plane in the MRI, aligning with the cutting orientation. D) The visual match between MRI and blockface images are confirmed for each slab before advancing to the next cutting plane.

Figure 6

Detection of white matter lesion on T2-SPACE and overlay on a grayscale blockface photo.

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 dashed 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.