A pipeline to characterize spinal cord pathology in neurological disorders combining magnetic resonance microscopy and histopathology

BACKGROUND: The length, shape, and size of the spinal cord (SC) present unique challenges for MRI, including the need for high resolution to distinguish anatomical and pathological features along its span. Postmortem MRI offers an opportunity to map SC tissue abnormalities and investigate their histological correlates. METHODS: We developed a pipeline combining postmortem microscopic resolution MRI (MR microscopy; MRM) of whole formalin-fixed SC specimens with targeted histopathological analysis. A gadolinium-based tissue preparation protocol was optimized using SC tissue from common marmosets with experimental autoimmune encephalomyelitis. A custom tissue holder and container were designed to enable postmortem MRI of the entire human SC. Human SC samples from individuals with multiple sclerosis, amyotrophic lateral sclerosis, and intracranial hemorrhage were scanned at 75 μm isotropic resolution on a 9.4 T Bruker system after gadolinium preparation. RESULTS: MRM after gadolinium-based tissue preparation yields images with high signal- and contrast-to-noise ratio while minimizing acquisition times. MRI demonstrates fine anatomical detail and pathological features, including demyelination and neurodegeneration throughout the SC. A complementary custom-made cutting rack enables targeted histological sectioning of MRI-identified regions. This approach provides precise spatial correspondence between imaging and histological findings, demonstrating strong agreement across modalities. CONCLUSIONS: In summary, this pipeline facilitates comprehensive SC assessment by integrating MRM with histology. It enables accurate localization of both subtle and widespread SC pathology and enhances interpretation of MRI signals in the context of neurodegenerative and inflammatory diseases.