Research assistant for digital pathology

Do you want to contribute to top quality medical research?

The Department of Medical Epidemiology and Biostatistics conducts research in epidemiology and biostatistics across a broad range of areas within biomedical science. The department is among the largest of its type in Europe and has especially strong research profiles in psychiatric, cancer, reproductive, pediatric, pharmaco, genetic, and geriatric epidemiology, eating disorders, precision medicine, and biostatistics.

Part of the success of our department is due to our collaborative spirit where one factor is that researchers at the Department share and co-finance common resources (e.g., IT and an applied biostatistics group). The department is situated at campus Solna. Further information can be found at http://ki.se/en/meb

The research group is affiliated with the national Data Driven Life Sciences (DDLS) program and SciLifeLab (https://www.scilifelab.se/researchers/kimmo-kartasalo/). We conduct international cutting-edge research in computational pathology and artificial intelligence (AI). Specifically, the group has for several years worked with AI-based models to assist pathologists in their assessment of prostate biopsies.

The core competences of the group include large-scale image processing and analysis, development of deep learning based AI algorithms, and efficient utilization of supercomputing systems. Our backgrounds range from computer science and mathematics to biotechnology and medicine, and we embrace a highly collegial and flexible working culture.

Your mission

The aim of this project is to evaluate the feasibility of using generative artificial intelligence (Gen-AI) in a novel manner to streamline histopathological diagnostics by eliminating one of the key processes in histology: staining of tissue samples. You will develop AI models based on e.g. generative adversarial networks (GAN) to virtually stain and unstain digitised tissue samples to enable development of AI algorithms capable of diagnosing prostate cancer from unstained tissue specimens. Depending on the progress of the project, downstream AI models for predicting molecular biomarkers from the digitized unstained specimens may also be developed. The project initially involves hands-on data collection in the form of scanning digital specimens to be used as training and evaluation data.

Your responsibilities include: 1) digitizing glass slides of both stained and unstained prostate biopsies into high-resolution images with digital pathology scanners; 2) developing Gen-AI models to virtually stain and unstain samples; 3) training and evaluating diagnostic and molecular-predictiveAI models capable of processing unstained specimens.

The position is a full time employment of 3 months (June 1 – August 31, 2025). The work can only be conducted on site in Solna.

Your profile

The applicant is expected to possess the following skills and experience:

- Experience of whole slide scanning, preferably on Hamamatsu and Grundium instruments.
- Experience of processing whole slide image data from Leica, Hamamatsu, Philips and/or Grundium scanners using libraries such as OpenSlide or OpenPhi.
- Experience of developing GANs or comparable AI models for whole slide data in PyTorch.
- Experience of high-performance computing on Linux servers and GPU compute clusters.
- Familiarity with Python.
- Familiarity with version control tools e.g. Git.
- Ability to work well independently and together with others.
- Ability to communicate with colleagues in English.
- A thorough, meticulous approach to research.

The following skills and experience are considered meriting:

- Hands-on experience of performing histological sample preparation.
- Experience of whole slide scanning and processing of unstained histology slides and understanding of the technical challenges associated with these types of samples.
- Knowledge of and interest in pathology, oncology or other relevant medical fields.
- International and interdisciplinary research experience.

Other knowledge in biomedicine, digital pathology or computer science is an advantage. Great emphasis is placed on personal suitability.

What do we offer?

International staff
Choose to work at KI – Ten reasons why

A creative and inspiring environment with wide-ranging expertise and interests. Karolinska Institutet is one of the world's leading medical universities. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. Karolinska Institutet is also a state university, which entitles you to several good benefits through our collective agreement. And you get to practice freely in our modern wellness facilities, where trained staff are on site.

Location: Solna

Application

Welcome to apply!

The application is to be submitted through the Varbi recruitment system.In this recruitment, you will apply with your CV without a personal letter. Instead, you will answer some questions about why you are applying for the job in the application form. 

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