Research engineer position in Imaging-based Spatial Omics

Karolinska Institutet

Application deadline

April 30, 2021

Research engineer position in Imaging-based Spatial Omics

Karolinska Institutet

research engineer position in Imaging-based Spatial Omics is immediately available in the Bienko Lab ( at Karolinska Institute in Stockholm.

You will lead the design and implementation of integrated microscopy and microfluidic systems suitable for high-throughput fluorescence in situ hybridization (FISH) assays, such as MERFISH (PMID: 25858977) and seqFISH (PMID: 30911168), as well as for new methods that will be developed in house.

These methods enable the visualization of hundreds of DNA loci or RNA transcripts directly in cells or tissue sections, preserving spatial information about the biological context in which they are detected.

The research group

The Bienko lab has a long-standing track record in DNA/RNA FISH methods ( and has recently obtained funding to establish a pilot Unit for Advanced FISH Technologies (AFT) within the Single Cell and Spatial Biology National Platform at the Science for Life Laboratory ((

In our lab, we develop and apply high-resolution FISH methods to understand how chromatin is spatially organized in the nucleus of mammalian cells, how dynamic is this organization during the cell division cycle and cell differentiation, and how genomic structural variants associated with various diseases exert their pathogenic effects by disrupting the 3D chromatin architecture.

As a technology developer, you will work both in the Bienko lab and within the AFT unit, being part of a dynamic and international research environment where you will have the opportunity to network with scientists from very diverse fields and backgrounds, fostering your creativity and shaping your project in non-conventional ways.

Your mission

You will leverage on the existing state-of-the-art microscopy infrastructure in the Bienko lab (two custom-made Nikon Ti-E microscopes specifically tailored for single-molecule DNA and RNA FISH) and integrate it with a suitable microfluidic system, aiming at performing MERFISH, seqFISH and alike.

Once the system is up-and-running and MERFISH/seqFISH is working in our lab, you will be in charge of securing smooth operations within the AFT unit and in parallel work to develop new assays for spatially resolved genomics and transcriptomics.  

In all these efforts, you will work in synergy with experts in FISH technologies and image analyses, contributing, among other things, to develop and validate open-source software specifically tailored around FISH data.

Our ultimate mission is to develop spatially resolved omic technologies that can help us understand how complex tissues function and how they get disrupted by disease.

Your profile

  • You hold a MSc in engineering or equivalent and have a strong expertise in microscopy and microfluidics.
  • You are technology driven and like to set up new devices/instruments using your skills and knowledge.
  • You are fluent in programming languages such as Matlab or Python and know how to make different types of hardware (a microscope and a fluidic device) and software communicate.
  • You have a problem-solving attitude and like troubleshooting.
  • You like to work in a team and are able to make the best out of interactions with people from very different backgrounds.

What do we offer?

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 better health for all. At Karolinska Institutet, we conduct innovative medical research and provide the largest range of biomedical education in Sweden. Karolinska Institutet is a state university, which entitles employees to several benefits such as extended holiday and a generous occupational pension. Employees also have free access to our modern gym and receive reimbursements for medical care.

Location: Solna, SciLifeLab


Want to make a difference? Join us and contribute to better health for all

Type of employmentTemporary position longer than 6 months
Contract typeFull time
First day of employmentImmediately/upon agreement
SalaryMonthly salary
Number of positions1
Working hours100 %
CountyStockholms län
Reference numberSTÖD 2-1433/2021
ContactMagda Bienko,
Last application date30.Apr.2021 11:59 PM CET

Last updated: 2021-03-24

Content Responsible: David Gotthold(