Junior Research Software Developer- Artificial Intelligence And Computational Neurosciences (Aicons) Lab (2023-4758)

Our Artificial Intelligence and Computational Neurosciences (AICONS) Lab is seeking a Junior research software developer, at 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 be responsible for assisting with the development, optimization and maintenance of an automated computational pipeline (MIRACL: 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.

The ideal candidate will have a B.Sc or M.Sc in computer science, neuroscience, or a related discipline, and will have prior research experience in neuroimaging or AI. Preference will be given to candidates with experience working with advanced neuroimaging analyses or machine learning frameworks.

Requirements

• Post-secondary degree in computer science, engineering, medical biophysics, biomedical engineering, or related field
• 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
• Experience with version control systems (Git) and the software development/testing life cycle
• Intermediate knowledge of Linux and scripting
• Demonstrated ability to learn quickly
• A passion for computer programming, with strong skills in Python
• Ability to quickly get up to speed with unfamiliar code bases and identify areas of improvement

Assets

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

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.

Links

• Temerty Centre for Artificial Intelligence Research and Education in Medicine
• University of Toronto
• Medical Biophysics Goubran profile
• Sunnybrook Research Institute
• Harquail Centre for Neuromodulation
• LC Campbell Cognitive Neurology Research Unit

To Apply For This Position, Please

Send a cover letter and Curriculum Vitae and the names of three potential references to:

Dr. Jonas Osmann

[email protected]

Please put “Junior research software developer” in the subject line.

Deadline for application: Until the position is filled.

We thank you in advance for your interest. Only those candidates selected for an interview will be contacted. No phone calls please. Application screening will continue until a suitable candidate is identified.