Bioinformatician with focus on research support within image analysis

Uppsala University, Department of Information Technology

The announced position is placed at the Vi3-Division of the Department of Information Technology, but is also part SciLifeLab BioImage Informatics Facility (BIIF) as described below. The Department of Information Technology  is a broad environment with a leading position within research as well as education at all levels. The Vi3-Division gathers a unique combination of expertise in computerized image processing, human computer interaction, and computing education. SciLifeLab BIIF is administratively placed here, and offers education and research support within digital image processing and analysis for life science applications. Read more at http://www.scilifelab.se/facilities/bioimage-informatics/ .

Science for Life Laboratory, or SciLifeLab , is a Swedish national center for molecular bioscience research with focus on health and environmental research. The center combines front line technical expertise with advanced knowledge in translational medicine and molecular biosciences. SciLifeLab is a national resource coordinated by Karolinska Institutet, the KTH Royal Institute of Technology, Stockholm university and Uppsala university, but the collaboration includes many more universities. SciLifeLab was formed 2010, and approximately 1 500 persons are currently working within the center, where 1/5 work with the facilities offering support for researchers with the life sciences. BIIF is one of the SciLifeLab facilities.

BIIF is additionally part of NMI, the National Microscopy Infrastructure within the life science in Sweden , Euro BioImaging , and NBIS, the National Bioinformatics Infrastructure Sweden , engaging approximately 100 bioinformaticians spread all across Sweden. BIIF is thus well connected with both image acquisition and data analysis infrastructure.

We are looking for a bioinformatician with strong interest in developing, implementing and adjusting image analysis tools for quantitative analysis of microscopy data. Much focus is on large scale analysis based on machine learning and deep learning/AI. You will work with shorter and longer projects and offer research support via the BIIF nodes in Uppsala and Stockholm, and other universities in Sweden. The appointment also includes duties in the form of organizing user meetings/courses and workshops in digital image processing and analysis with life science applications. Supervision of MSc theses in the area is also part of the duties, as well as some involvement in research projects within Carolina Wählby’s research group.

You should have a master degree and/or PhD degree within digital image analysis, image processing or similar, or alternatively in bioinformatics, biomedicine, biology or similar. Documented experience of programming and development of digital image analysis methods is a requirement. Excellent communication in English, both written and spoken, is a requirement.

Experience from developing and working with machine learning and deep learning with applications in microscopy, such as tissue analysis, is meriting. Experience from postdoctoral studies (or corresponding within other settings) focused on large-scale data analysis and visualization is meriting. Especially meriting is proficiency in using and developing algorithms and analysis pipelines intended for identification and segmentation of cells and microorganisms in culture or in tissue sections, and quantification of biological parameters for these. Experience in giving workshops and supervision are also meriting, as well as work on research reproducibility.

The application should include a letter where the applicant describes the motivation for applying for this position, the relevant qualifications, and research interests. The application should also include a CV and links to relevant publications and contact information for at least two reference persons. We would also like to know the earliest possible starting date.

The employment is a permanent position, probationary period of six months will be applied. Scope of employment 100%. Starting date April 1st 2024 or as agreed. Placement: Uppsala

For further information about the position, please contact: 

Carolina Wählby, [email protected] or Anna Klemm, +46727010657, [email protected].

Please submit your application by 29 February 2024, UFV-PA 2024/375.

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