Open-source tools for quantitative neuropathology from brain tissue slab photography

Brain banks and neuropathology laboratories routinely photograph tissue slabs during dissection of the brain before downstream processing and histology. These images are principally used for archival purposes and documentation, and not for analysis. Meanwhile, MRI is the gold standard used both in vivo and ex vivo for quantitative morphometric analysis, but requires specialized equipment, expertise, and cost, limiting its accessibility. We present Freesurfer's Photo Tools, a suite of open-source tools for routine brain dissection photographs to perform quantitative analysis without the need for MRI. Our tools use domain-randomized deep learning to enable high-resolution 3D segmentation, surface-based analysis, super-resolution, MRI synthesis, and multimodal registration. By bridging neuropathology and neuroimaging data, our suite opens new possibilities for postmortem studies, including cataloging, guided sectioning, longitudinal analysis, and large-scale analysis on retrospective data. These tools are freely available with the goal of leveraging neuropathology images as a resource for the research community.

Speaker: Jonathan Williams Ramirez (MS. Research Technologist, MGH and Harvard-MIT, HST Martinos Center for Biomedical Imaging)