Sep 21 – 23, 2021
Europe/Berlin timezone

MRI guided hierarchical sectioning and stitching of brain blocks for alignment of digitized histology to corresponding MR images

Sep 22, 2021, 6:15 PM


Talk Reconstruction Contributed Talks: Reconstruction


Prof. Amir Shmuel (McGill University)Mr Sethu Boopathy Jegathambal (McGill University)


Ex-vivo high-resolution MRI of brain tissue can provide morphological and microstructural information. MR images can also serve as undistorted references for the reconstruction of digitized histology, immunohistochemistry, or clearing techniques. Small-bore scanners, equipped with powerful gradients systems and operating at ultra-high magnetic fields present the optimal conditions for ex-vivo MRI. However, space constraints make it impossible to scan a whole human brain in such small-bore scanners. Imaging a human brain requires a large bore scanner, typically showing limited gradient system performance, constraining the achievable spatial resolution. Importantly, large histology sections cut from large brains are prone to distortions, tears, and folding.
Here we present a method for MRI-guided hierarchical sectioning and stitching of brain blocks for precise alignment of processed tissue images to corresponding MRI volumes. Our method allows the use of small-bore MRI scanners, achieving high-resolution-MRI volumes. The use of small tissue blocks reduces tissue distortions, tears, and foldings. The results show significant improvements relative to current methods for 3D reconstruction of 2D processed tissue images and for aligning processed tissue data to the corresponding MRI volumes.

Primary authors

Prof. Amir Shmuel (McGill University) Mr Sethu Boopathy Jegathambal (McGill University)

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