Professional Experience

Senior DSP/ML Engineer

Synex Medical, Toronto, Canada

2024 - Present

  • Developed advanced signal processing techniques for solving inverse problems in magnetic resonance data, including denoising, filtering, MRI signal reconstruction, and preprocessing
  • Designed and implemented an end-to-end machine learning pipeline with CI/CD integration for model training, tracking, and selection

Instructor

University of Calgary and SAIT, Canada

2023 - 2024

  • Advanced Topics in Image Analysis and Machine Learning (co-instructor)
  • Operating Systems
  • Software Security

Postdoctoral Fellow

Advanced Imaging and AI Lab, University of Calgary

2023 - 2024

  • Developed innovative deep learning-based MRI reconstruction framework integrating deep registration model and transformer-based enhancement network
  • Incorporated prior subject-specific information using deep learning techniques, enabling 4 times faster MRI acquisitions
  • Developing MRIntelligence, a software application for integrating advanced MRI reconstruction and analysis techniques into clinical workflows

Marie Skłodowska-Curie Fellow

Czech Academy of Sciences, Czech Republic

2019 - 2023

  • Led research and development of innovative techniques for magnetic resonance spectroscopic imaging analysis
  • Designed open-source solutions for magnetic resonance signal processing using Python and Java
  • Participated in jMRUI software package development, utilized by 4,550+ researchers worldwide
  • Published 10 papers in top conferences and journals

Education

Ph.D. in Biomedical Engineering

2019 - 2023

Brno University of Technology

Dissertation: Development of new artificial intelligence functionalities for magnetic resonance spectroscopic signals processing

M.Sc. in Biomedical Engineering

2015 - 2018

Amirkabir University of Technology

Dissertation: Design and fabrication of a Lab-on-chip device for assessment of cancer cells viability during electrical stimulation

B.Sc. in Electrical Engineering

2010 - 2015

Zanjan University

Dissertation: Wireless System Network Simulator Software

Technical Skills

Programming Languages

Java Python C++

Frameworks & Libraries

PyTorch JAX FSL ITK MONAI TorchIO scikit-image SimpleITK pydicom NiBabel

Software & Tools

MatLab jMRUI 3D Slicer LC-MODEL FiTAID Image-J FreeSurfer

Selected Publications

Physics-informed Deep Learning Approach to Quantification of Human Brain Metabolites

IF: 7.7

Computers in Biology and Medicine, 2023

Shamaei, A, Starcukova, J, Starcuk, Z

Model-informed unsupervised deep learning approaches to frequency and phase correction of MRS signals

IF: 3.3

Magnetic Resonance in Medicine, 2023

Shamaei, A, Starcukova, J, Pavlova, I, Starcuk, Z

Water removal in MR spectroscopic imaging with Casorati singular value decomposition

IF: 3.3

Magnetic Resonance in Medicine, 2024

Shamaei, A, Starcukova J, Rizzo R, Starcuk Z

Open Source Projects

Deep-MRS-Quantification

Model-Constrained Deep Learning Approach to the Quantification of MR Spectroscopy Data

View Project

DeepFPC

Model-Informed unsupervised DL Approach to Frequency and Phase Correction of MRS Signals

View Project

BrukerEyes

Cross-platform open-source package for Bruker Datasets management

View Project

NIfTI-MRS

JAVA package providing Reading/Writing interface for NIfTi MRS format

View Project

Awards & Achievements

🥇

First Place, ISMRM MRS Challenge

AI-based Brain Metabolite Fitting, Boston MA - Fall 2024

💰

Lab2Market Validate Program

Offered $15,000 grant (declined) - Fall 2024

☁️

AWS Cloud Credit Award

$10,000 AWS cloud credit for research on decreasing MRI acquisition time using deep learning - Fall 2023

🏆

ISMRM 2023 MR Spectroscopy Study Group Award

Annual business meeting recognition - Spring 2023