Amir Shamaei at Lake Louise

Biomedical research · Machine learning

Amir Shamaei

I build methods and scientific software at the intersection of medical imaging, signal processing, and machine learning.

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Experience & education

A research path in branches.

career.git symbolic history

career.git — zsh step 01/18

A symbolic Git history: initialize the education branch; commit the bachelor’s and master’s degrees; branch into work; commit the Ph.D. and Marie Curie fellowship in parallel; merge into postdoctoral work; branch and merge the instructor role; then commit the two senior engineering roles.

Work Education
  1. Senior DSP / ML Engineer IISynex Medical · Toronto
  2. Senior DSP / ML EngineerSynex Medical · Toronto
  3. Postdoctoral FellowAdvanced Imaging & AI Lab
    InstructorUniversity of Calgary & SAIT
  4. Marie Skłodowska-Curie FellowCzech Academy of Sciences
    Ph.D. Biomedical EngineeringBrno University of Technology
  5. M.Sc. Biomedical EngineeringAmirkabir University of Technology
  6. B.Sc. Electrical EngineeringZanjan University

Selected work

Research made useful.

Open standards, reproducible tools, and learning-based methods for biomedical signals.

Illustrated overview of the NIfTI-MRS data standard

Open standard · 2022

NIfTI-MRS

A standard data format for magnetic resonance spectroscopy.
Illustrated overview of physics-informed deep learning for MRS quantification

Deep learning · 2023

Physics-informed MRS

Fast, self-supervised quantification of human brain metabolites.
Illustrated overview of deep learning MR spectra quantification in an idealized setting

Deep learning · 2023

Deep MRS quantification

A study of architectures, inputs, ensembles, and training bias.
Illustrated overview of model-informed unsupervised frequency and phase correction of MRS signals

Signal correction · 2023

DeepFPC

Model-informed unsupervised frequency and phase correction for MRS signals.
Illustrated overview of unsupervised domain adaptation for newborn brain MRI skull stripping

Domain adaptation · 2024

Newborn skull stripping

Adapting adult MRI models to newborn data without labels.
Illustrated overview of Spectro-ViT for GABA-edited MEGA-PRESS reconstruction

Vision transformer · 2024

Spectro-ViT

High-quality GABA-edited spectra from one-quarter of the usual transients.
Illustrated overview of CSVD water removal for MR spectroscopic imaging

Signal processing · 2024

CSVD water removal

Fast, scalable water removal for large MR spectroscopic datasets.
Illustrated overview of PHIVE for rapid brain metabolite mapping at 7T

Physics-informed AI · 2026

PHIVE

Rapid spectral fitting and uncertainty-aware brain metabolite mapping at 7T.