Varadarajan, D. | Search bioRxiv

bioRxiv2020

A novel algorithm to optimize generalized gamma distributed multiplicative noise with implications on speckle removal from OCT images

Optical coherence tomography (OCT) images are corrupted by multiplicative generalized gamma distributed speckle noise that significantly degrades the contrast to noise ratio (CNR) of microstructural compartments in biological applications. This work proposes a novel algorithm to optimize the negative log likelihood of the spatial distribution of speckle. Specifically, the proposed method formulates a penalized negative log likelihood (P-NLL) cost function and proposes a majorize-minimize-based optimization method that removes speckle from OCT images. The optimization reduces to solving an iterative gradient descent problem. We demonstrate the usefulness of the proposed method by removing speckle in OCT images of uniform phantoms with varying scattering coefficients and human brain tissue.

neuroscience↗

bioRxiv2020

Conductance-Based Structural Brain Connectivity in Aging and Dementia

BackgroundStructural brain connectivity has been shown to be sensitive to the changes that the brain undergoes during Alzheimers disease (AD) progression. MethodsIn this work, we used our recently proposed structural connectivity quantification measure derived from diffusion MRI, which accounts for both direct and indirect pathways, to quantify brain connectivity in dementia. We analyzed data from the ADNI-2 and OASIS-3 datasets to derive relevant information for the study of the changes that the brain undergoes in AD. We also compared these datasets to the HCP dataset, as a reference, and eventually validated externally on two cohorts of the EDSD database. ResultsOur analysis shows expected trends of mean conductance with respect to age and cognitive scores, significant age prediction values in aging data, and regional effects centered among sub-cortical regions, and cingulate and temporal cortices. DiscussionResults indicate that the conductance measure has prediction potential, especially for age, that age and cognitive scores largely overlap, and that this measure could be used to study effects such as anti-correlation in structural connections. Impact statementThis work presents a methodology and a set of analyses that open new possibilities in the study of healthy and pathological aging. The methodology used here is sensitive to direct and indirect pathways in deriving brain connectivity measures from dMRI, and therefore provides information that many state-of-the-art methods do not account for. As a result, this technique may provide the research community with ways to detect subtle effects of healthy aging and AD.

neuroscience↗