Researcher and software developer. Background in applied mathematics and computer science. More than 20 years of experience, including 18 years focused in medical image processing and analysis.

Expert knowledge in image analysis methods for MRI and computer vision. Developed methods for diagnostics of neurological diseases and tracking normal development of the human brain. Co-authored more than 150 academic papers h=45. Consulted for image processing methods and statistical analysis in clinical trials for drug development.

Technical skills

data analysis using R, Python, Julia; machine learning with scikit-learn; deep learning with pytorch; software development with C, C++, Python, Julia

Work experience

• 2020 - present: Academic associate, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal Canada
  • wrote academic papers on image processing methods
  • participated in open competitions on semantic segmentation of medical images
  • supervised research work of MSc and PhD students in biomedical engineering
• 2009 - present: System Administrator, University Lab Douglas Hospital, McGill University, Montreal Canada
  • Managed and maintained a diverse range of workstations and a high-performance computing (HPC) cluster, all running Ubuntu Linux, to support research and academic activities.
• 2019 - 2020: Research scientist, advanced software developer, Rogue Research, Montreal Canada
  • research and development of methods and software for medical image analysis
• 2005 - 2019: Research associate, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal Canada
  • developed methods and software for medical imaging analysis of large population studies, including methods based on deep learning
  • participated in open competitions for methods of neurological disease diagnosis and MRI segmentation
  • maintained open source image processing toolkit for MRI image analysis
  • supervised research work of MSc and PhD students in biomedical engineering
  • co-authored more than 100 academic papers, Scopus citation index h=45
• 2009 - 2019: MRI Acquisition & Analysis Consultant, NeuroRx Research, Montreal Canada
  • Maintained existing analysis software, including image-processing tools and analysis pipelines
  • Optimized code developed in a research environment, and translate it for use in a production environment
  • Defined, designed and implemented novel image-processing tools
  • Documented and tested software
  • Performed statistical data analysis
• 2003 - 2005: Research Scientist, Innovative Scientific Solutions Inc, Dayton OH USA
  • developed image processing methods and software tools for optical measurements in aerodynamic experiments
  • developed data acquisition systems (both software and hardware)

Education

• 1999-2003: Heriot-Watt University (UK) Ph.D. in Digital Image Processing
• 1994-1999: Moscow Institute of Physics and Technology (Russia) M.Sc. in Applied Physics & Mathematics
• Academic CV: http://www.ilmarin.info/cv/

Publications

• orcid.org/0000-0003-3402-7749
• Google Scholar: http://scholar.google.ca/citations?user=4YCK0vQAAAAJ
• Scopus Author ID: 57188953412
• Web of Science ResearcherID: AAG-9572-2019

Languages

• Russian (native), English (fluent), French (basic speaking, reading)

Open source software contributions

• Github profile: vfonov
• Medical image processing toolkit: https://github.com/BIC-MNI/
• Contributed to the following open source software projects:
  • libigl: https://libigl.github.io/
  • Insight Toolkit: http://www.itk.org/
  • ANTs: http://stnava.github.io/ANTs/
  • Pytorch: https://github.com/pytorch/pytorch
• Embedded software development:
  • uIP-based web server on 8bit AVR cpu: https://github.com/vfonov/uhttpd-avr
  • lwiIP-based web server on 8bit AVR cpu: https://github.com/vfonov/lwip-avr
  • low-cost USB JTAG dongle based on 8 bit AVR cpu: https://github.com/vfonov/opendous-jtag
  • enhancements in linux kernel module for camera module in mini2440 board: https://github.com/vfonov/s3c2440camera
  • port of mjpg-streamer optimized for mini2440 board: https://github.com/vfonov/mjpg-streamer-mini2440

Non-academic data analysis articles

• Blog posts on various data science topics: https://habr.com/en/users/ilmarin77/posts/