Undergraduate and graduate level education in bioinformatics (scholarship) - Hiring in process/Finished, not possible to apply

Do you want to contribute to top quality medical research?

We are seeking for a M.Sc level student to help develop computer vision methods for recognizing and tracking cultured cells imaged with live cell microscopy methods. You will work within a multidisciplinary team of experimental and computational scientists to develop machine learning approaches for solving this problem.

Division

The department of Medicine (Solna) is one of the largest at Karolinska Institutet, combining clinical and experimental sciences. Our cardiovascular medicine division features a rich variety of metabolism-oriented research, including immunometabolism and cancer metabolism. We are located in the brand new Bioclinicum research building at the heart of the Solna campus, in close proximity to both Karolinska Hospital and the main research facilities of Karolinska Institutet.

Duties

Your task will be to build a machine learning system that can automatically recognize and track individual cells and identify events such as cell proliferation, death and migration. This will consist of (1) building and training neural network for cell recognition (2) combining the cell recognition network with existing cell tracking methods, and (3) evaluating classification performance to understand how well the system can identify individual cells and their behavior.

Entry requirements

We seek a student with a background in computer science and engineering at the M.Sc level. You should have good knowledge of machine learning methods, especially convolutional networks for image recognition, and in particular U-Net topology networks. Experience with image classification and with time-lapse microscopy images in particular is an advantage. A strong background in programming in general, and programming in Python in particular, is required. Familiarity with the Keras deep learning framework and with cluster computing in Linux environments is an advantage. Good communication skills is an advantage.

Location

The position is located within the Department of Medicine, Solna. The department consists of twelve divisions and each division consists of several research groups. The position is located within the research group of Roland Nilsson. Our lab performs basic research in cellular metabolism, with the ultimate goal is to exploit quantitative knowledge of human metabolism to design more effective treatments of human disease.

Type of scholarship

The scholarships may be granted only to:

• Persons who have been admitted (and registered in Ladok) to KI to study at the undergraduate or graduate level,
• Persons who are admitted (and registered) to undergraduate or graduate level programs at a university with which KI collaborates.

The scholarships can be granted either for studies in an existing course or for a shorter period of practical research experience (documented in an individual study plan/research plan) for admitted students at the undergraduate or graduate level. The scholarships may be awarded for up to 12 months (divided into a maximum of four courses/periods) during the study period. Decisions on scholarships may be made for a maximum of six months at a time.

The scholarships may not be disbursed to any person who received a salary or remuneration from KI during the two-year period immediately preceding the potential disbursement. This provision may be waived if the income received during the preceding two-year period relates to:

• Income of less than 1,000 SEK per year
• Compensation paid to research subjects
• Compensation paid to student representatives on KI boards/committees
• Compensation for work performed that was of an entirely different nature than education and research

Application process

An application must contain the following documents in English or Swedish:

• A complete curriculum vitae
• A complete list of publications
• A summary of current work (no more than one page)

The application is to be submitted on the Varbi recruitment system.

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