Job Description

One of Canada's Top 10 Research Hospitals, Sunnybrook Research Institute is developing innovations in care for the more than 1.3 million patients the hospital cares for annually.
Sunnybrook Research Institute is the research enterprise of Sunnybrook Health Sciences Centre, a teaching hospital fully affiliated with the University of Toronto. Research spans three Toronto-based campuses, eight programs and three scientific platforms. Our main aims are to understand and prevent disease, and to develop treatments that enhance and extend life. Our vision is to invent the future of health care. Each year, we conduct about $100 million in research across 500,000 square feet, including in the world's first Centre for Research in Image-Guided Therapeutics.
Our is seeking a research software developer, at the Physical Sciences Platform & Hurvitz Brain Sciences Program, Sunnybrook Research Institute of the University of Toronto, under the supervision of .
The successful candidate will be responsible for assisting with the development, optimization and maintenance of an automated computational pipeline ( : Multi-modal Image Registration And Connectivity anaLysis), that couples MRI images with cellular information from cleared brain tissue (3D histology image with lightsheet microscopy) and the reference atlases to probe brain-wide circuit alterations across spatial scales. MIRACL enables the segmentation, registration, and analysis of histological features across the whole brain or multiple neuronal circuits, as well as along the length of specific fibre tracts. This pipeline is being used by many collaborating groups within Canada, and internationally in countries including USA, Germany, and Switzerland. Dr. Goubran's lab develops novel computational & AI tools to probe, predict and understand neuronal and vascular circuit alterations in neurological disorders, including Alzheimer's disease, stroke, and traumatic brain injury. The lab consists of a diverse, multidisciplinary team of engineers, neuroscientists, and software developers. This dynamic and collegial research environment provides opportunities to participate in pioneering AI and computational tool development that will be used to understand and treat neurological diseases. In addition to working on MIRACL, the successful candidate will assist on several ongoing projects in the lab, including the investigation of structural and functional brain connectivity and their associations with the spread of pathological proteins and cognition in Alzheimer's disease. The candidate will be expected to work independently and as a team member with investigators, staff, graduate/undergraduate students, and clinicians. There will be opportunities for contributing to publications, and presenting at/attending international conferences and workshops, focused on novel computational tools for neuroscience research and developing AI and image analysis algorithms.
Qualifications:

• Post-secondary degree in computer science, engineering, medical biophysics, biomedical engineering, or related field
• A passion for computer programming, with strong skills in Python
• Experience with machine and deep learning (sklearn, Pytorch, Tensorflow, Keras, etc.) and/or AI based neuroimaging analysis
• Sound knowledge of object-oriented design and programming
• Intermediate knowledge of Linux and scripting
• Demonstrated ability to learn quickly
• Experience with version control systems (Git) and the software development/testing life cycle
• Ability to quickly get up to speed with unfamiliar code bases and identify areas of improvement

Assets

• Python software packaging (Docker/Singularity), virtual environments, Anaconda/Conda, Jupyter/IPython
• Advanced knowledge of Linux, including scripting and system administration
• Experience with HPC computing (e.g. Compute Canada)
• Working knowledge of FSL, ITK or neuroimaging software
• Working knowledge of R or MATLAB
• Experience with continuous integration (e.g. CircleCI) and test-driven development

Compensation depending on education and experience.
This position includes health and dental benefits, vacation days, and membership in our pension plan with HOOPP.
In accordance with Canadian Employment and Immigration guidelines, applicants must be eligible to work in Canada. In accordance with Canadian immigration requirements, this advertisement is directed initially to Canadian citizens and permanent residents.
Sunnybrook Research Institute is committed to providing accessible employment practices that are in compliance with the Accessibility for Ontarians with Disabilities Act (AODA). If you require accommodation for disability during any stage of the recruitment process, please indicate this in your cover letter.
Sunnybrook Research Institute is strongly committed to inclusion and diversity within its community and welcomes all applicants including but not limited to: visible minorities, all religions and ethnicities, persons with disabilities, LGBTQ2S+ persons, and all others who may contribute to the further diversification of ideas.
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If you are looking for an exciting opportunity and to build a career in an innovative and dynamic organization, submit your resume by clicking on Apply Now below.
Sunnybrook Health Sciences Centre is committed to providing accessible employment practices that are in compliance with the Accessibility for Ontarians with Disabilities Act (AODA). If you require accommodation for disability during any stage of the recruitment process, please indicate this in your cover letter.
Sunnybrook Health Sciences Centre is strongly committed to inclusion and diversity within its community and welcomes all applicants including but not limited to: visible minorities, all religions and ethnicities, persons with disabilities, LGBTQ persons, and all others who may contribute to the further diversification of ideas.

Skills Required