Jiacheng Li

Pulkit Khandelwal, Michael Tran Duong, Shokufeh Sadaghiani et al.

Postmortem MRI allows brain anatomy to be examined at high resolution and to link pathology measures with morphometric measurements. However, automated segmentation methods for brain mapping in postmortem MRI are not well developed, primarily due to limited availability of labeled datasets, and heterogeneity in scanner hardware and acquisition protocols. In this work, we present a high resolution of 135 postmortem human brain tissue specimens imaged at 0.3 mm$^{3}$ isotropic using a T2w sequence on a 7T whole-body MRI scanner. We developed a deep learning pipeline to segment the cortical mantle by benchmarking the performance of nine deep neural architectures, followed by post-hoc topological correction. We then segment four subcortical structures (caudate, putamen, globus pallidus, and thalamus), white matter hyperintensities, and the normal appearing white matter. We show generalizing capabilities across whole brain hemispheres in different specimens, and also on unseen images acquired at 0.28 mm^3 and 0.16 mm^3 isotropic T2*w FLASH sequence at 7T. We then compute localized cortical thickness and volumetric measurements across key regions, and link them with semi-quantitative neuropathological ratings. Our code, Jupyter notebooks, and the containerized executables are publicly available at: https://pulkit-khandelwal.github.io/exvivo-brain-upenn

Ruirui Li, Mingming Li, Jiacheng Li et al.

We develop a connection sensitive attention U-Net(CSAU) for accurate retinal vessel segmentation. This method improves the recent attention U-Net for semantic segmentation with four key improvements: (1) connection sensitive loss that models the structure properties to improve the accuracy of pixel-wise segmentation; (2) attention gate with novel neural network structure and concatenating DOWN-Link to effectively learn better attention weights on fine vessels; (3) integration of connection sensitive loss and attention gate to further improve the accuracy on detailed vessels by additionally concatenating attention weights to features before output; (4) metrics of connection sensitive accuracy to reflect the segmentation performance on boundaries and thin vessels. Our method can effectively improve state-of-the-art vessel segmentation methods that suffer from difficulties in presence of abnormalities, bifurcation and microvascular. This connection sensitive loss tightly integrates with the proposed attention U-Net to accurately (i) segment retinal vessels, and (ii) reserve the connectivity of thin vessels by modeling the structural properties. Our method achieves the leading position on DRIVE, STARE and HRF datasets among the state-of-the-art methods.