Ali Abdollahzadeh

Ali Abdollahzadeh
University of Eastern Finland | UEF · A.I. Virtanen Institute for Molecular Sciences

Doctor of Philosophy

About

21
Publications
2,665
Reads
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110
Citations
Introduction
Ali Abdollahzadeh is currently pursuing the Ph.D. degree with the A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland. His research interests include shape analysis, image processing, machine learning, and their applications in large electron- and light-microscopy image volumes of the brain.
Additional affiliations
November 2017 - November 2021
University of Eastern Finland
Position
  • PhD Student

Publications

Publications (21)
Article
Full-text available
Axonal structure underlies white matter functionality and plays a major role in brain connectivity. The current literature on the axonal structure is based on the analysis of two-dimensional (2D) cross-sections, which, as we demonstrate, is precarious. To be able to quantify three-dimensional (3D) axonal morphology, we developed a novel pipeline, c...
Article
Full-text available
Non-invasive imaging methods have become essential tools for understanding the central nervous system (CNS) in health and disease. In particular, magnetic resonance imaging (MRI) techniques provide information about the anatomy, microstructure, and function of the brain and spinal cord in vivo non-invasively. However, MRI is limited by its spatial...
Article
Full-text available
Mild traumatic brain injury (mTBI) is the most common form of TBI with 10-25% of the patients experiencing long-lasting symptoms. The potential of diffusion tensor imaging (DTI) for evaluating microstructural damage after TBI is widely recognized, but the interpretation of DTI changes and their relationship with the underlying tissue damage is uncl...
Article
Full-text available
We develop a cylindrical shape decomposition (CSD) algorithm to decompose an object, a union of several tubular structures, into its semantic components. We decompose the object using its curve skeleton and restricted translational sweeps. For that, CSD partitions the curve skeleton into maximal-length sub-skeletons over an orientation cost, each s...
Article
Full-text available
Tracing the entirety of ultrastructures in large three-dimensional electron microscopy (3D-EM) images of the brain tissue requires automated segmentation techniques. Current segmentation techniques use deep convolutional neural networks (DCNNs) and rely on high-contrast cellular membranes and high-resolution EM volumes. On the other hand, segmentin...
Article
Full-text available
A system of lymphatic vessels has been recently characterized in the meninges, with a postulated role in ‘cleaning’ the brain via cerebral fluid drainage. As meninges are the origin site of migraine pain, we hypothesized that malfunctioning of the lymphatic system should affect the local trigeminal nociception. To test this hypothesis, we studied n...
Preprint
Differential expression of myelin-related genes and changes in myelin thickness have been demonstrated in mice after chronic psychosocial stress, a risk factor for anxiety disorders. To determine whether and how stress affects structural remodeling of nodes of Ranvier, another form of myelin plasticity, we developed a 3D reconstruction analysis of...
Preprint
Differential expression of myelin-related genes and changes in myelin thickness have been demonstrated in mice after chronic psychosocial stress, a risk factor for anxiety disorders. To determine whether and how stress affects structural remodeling of nodes of Ranvier, another form of myelin plasticity, we developed a 3D reconstruction analysis of...
Article
Background and Objective Advances in electron microscopy (EM) now allow three-dimensional (3D) imaging of hundreds of micrometers of tissue with nanometer-scale resolution, providing new opportunities to study the ultrastructure of the brain. In this work, we introduce a freely available Matlab-based gACSON software for visualization, segmentation,...
Preprint
Full-text available
Background and Objective: Advances in electron microscopy (EM) now allow three-dimensional (3D) imaging of hundreds of micrometers of tissue with nanometer-scale resolution, providing new opportunities to study the ultrastructure of the brain. In this work, we introduce a freely available gACSON software for visualization, segmentation, assessment,...
Article
Full-text available
(1) Background: Transfer learning refers to machine learning techniques that focus on acquiring knowledge from related tasks to improve generalization in the tasks of interest. In magnetic resonance imaging (MRI), transfer learning is important for developing strategies that address the variation in MR images from different imaging protocols or sca...
Data
We prepared ten samples from rats' white matter for serial block-face scanning electron microscopy (SBEM) imaging. We simultaneously acquired SBEM images of the white matter at low- and high-resolutions. The low-resolution datasets were acquired from big tissue volumes of 200 um x 100 um x 65 um with a voxel size of 50 nm x 50 nm x 50 nm. Two-third...
Preprint
Full-text available
Transfer learning refers to machine learning techniques that focus on acquiring knowledge from related tasks to improve generalization in the tasks of interest. In MRI, transfer learning is important for developing strategies that address the variation in MR images. Additionally, transfer learning is beneficial to re-utilize machine learning models...
Article
Purpose Image processing plays a fundamental role in the study of central nervous system, for example in the analysis of the vascular network in neurodegenerative diseases. Synchrotron X-ray Phase-contrast micro-Tomography (SXPCT) is a very attractive method to study weakly absorbing samples and features, such as the vascular network in the spinal...
Article
Full-text available
Hexanucleotide repeat expansion (HRE) in the chromosome 9 open-reading frame 72 (C9orf72) gene is the most common genetic cause underpinning frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). It leads to the accumulation of toxic RNA foci and various dipeptide repeat (DPR) proteins into cells. These C9orf72 HRE-specif...
Preprint
Full-text available
Background A system of lymphatic vessels has been recently characterized in the meninges, with a postulated role in ‘cleaning’ the brain via cerebral fluid drainage. As meninges are the origin site of migraine pain, we hypothesized that malfunctioning of the lymphatic system should affect the local trigeminal nociception. To test this hypothesis, w...
Preprint
Full-text available
Automated segmentation techniques are essential to tracing the entirety of ultrastructures in large three-dimensional electron microscopy (3D-EM) images of the brain tissue. Current automated techniques use deep convolutional neural networks (DCNNs) and rely on high-contrast cellular membranes to trace a small number of neuronal processes in very h...
Preprint
We develop a cylindrical shape decomposition (CSD) algorithm to decompose an object, which is a union of several tubular structures, into its semantic components. We decompose the object using its curve skeleton and translational sweeps. For that, CSD partitions the curve skeleton into maximal-length sub-skeletons over an orientation function, each...
Article
Full-text available
Axonal structure underlies white matter functionality and plays a major role in brain connectivity. The current literature on the axonal structure is based on the analysis of two-dimensional (2D) cross-sections, which, as we demonstrate, is precarious. To be able to quantify three-dimensional (3D) axonal morphology, we developed a novel pipeline, c...
Conference Paper
In cryo-electron microscopy (cryo-EM), the Wiener filter is the optimal operation – in the least-squares sense – of merging a set of aligned low signal-to-noise ratio (SNR) micrographs to obtain a class average image with higher SNR. However, the condition for the optimal behavior of the Wiener filter is that the signal of interest shows stationary...

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Project (1)
Project
3D electron microscopy image segmentation Electron tomography Single particle analysis