Research Software Developer

Research Software Developer (SRI) - Physical Sciences - Regular Full-time Join to apply for the Research Software Developer (SRI) - Physical Sciences - Regular Full-time role at Sunnybrook . One of Canada’s Top 10 Research Hospitals, Sunnybrook Research Institute develops innovations in care for the more than 1.3 million patients the hospital cares for annually. The 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. The Artificial Intelligence and Computational Neurosciences (AICONS) Lab is seeking a research software developer for the Physical Sciences Platform & Hurvitz Brain Sciences Program, Sunnybrook Research Institute of the University of Toronto, under the supervision of Dr. Maged Goubran. The successful candidate will assist with the development, optimisation and maintenance of an automated computational pipeline (MIRACL – Multi‑modal Image Registration & Connectivity Analysis) that couples MRI images with cellular information from cleared brain tissue (3‑D histology images with lightsheet microscopy) and 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. The pipeline is used by many collaborating groups within Canada and internationally in the USA, Germany and Switzerland. 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. Opportunities exist for contributing to publications and presenting at international conferences and workshops focused on novel computational tools for neuroscience research and the development of AI and image‑analysis algorithms. Qualifications Post‑secondary degree in computer science, engineering, medical biophysics, biomedical engineering or related field. 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 and Benefits Compensation depends on Education And Experience. This position includes health and dental benefits, vacation days, and membership in our pension plan with HOOPP. Eligibility 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. Accessibility 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. Diversity & Inclusion 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. Job Details Seniority level: Entry level Employment type: Full‑time Job function: Engineering and Information Technology Industries: Hospitals and Health Care Location: Toronto, Ontario, Canada #J-18808-Ljbffr