Research engineer position in Imaging-based Spatial Omics

Stockholm, Sweden (SE)
Monthly salary
March 24 2021
Position Type
Full Time
Organization Type

Are you technology-driven and expert in microscopy and microfluidic systems?

A Research Engineer position is immediately available in the Bienko Lab ( at Science for Life Laboratory ( and Karolinska Institute in Stockholm, Sweden.

We develop and apply cutting-edge microscopy (PMID: 30967549) and sequencing based (PMID: 32451505) methods to study genome organization in healthy and diseased cells.

We are looking for an expert in microscopy and microfluidics to lead the design and implementation of integrated microscopy and microfluidic systems for high-throughput fluorescence in situ hybridization (FISH) assays such as MERFISH and seqFISH.

You will be part of a dynamic and international research environment where you will work alongside experts in FISH technologies and image analyses and contribute to the development of new high-throughput microscopy methods.

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


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 Facility 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 facility, 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 facility 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.


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