Abstract #3550

Comparing Fiber Orientation Estimates from CLARITY and Diffusion MRI in Macaque Visual Cortex

Muhamed Barakovic^1,2, Christoph Leuze², Ailey K. Crow³, Qiyuan Tian^2,4, Alessandro Daducci⁵, Jean-Philippe Thiran^1,6, Karl Deisseroth^3,7,8,9, and Jennifer A. McNab²

¹Signal Processing Lab (LTS5), Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland, ²Department of Radiology, Stanford University, Stanford, CA, United States, ³CNC Program, Stanford University, Stanford, CA, United States, ⁴Department of Electrical Engineering, Stanford University, Stanford, CA, United States, ⁵Department of Computer Science, University of Verona, Verona, Italy, ⁶Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland, ⁷Department of Bioengineering, Stanford University, Stanford, CA, United States, ⁸Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, United States, ⁹Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States

Tissue clearing techniques offer new possibilities for reconstructing precise 3D axons trajectories. Here, we cleared a 1.5cmx1.3cmx0.3cm cuboid of rhesus macaque visual cortex using CLARITY 3D histology with a neurofilament stain to highlight axonal projections and compared the CLARITY-based fiber orientation estimate to a diffusion tensor MRI atlas. We found better agreement in grey matter than in white matter, potentially reflecting difficulties estimating the structure tensor in highly saturated regions of the CLARITY sample. This work demonstrates one of the largest and highest quality CLARITY cuboids from a macaque brain and explores key steps in the co-registration and analysis required to make a robust comparison against DTI data.

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