Advanced FISH Technologies

Infrastructure Unit

Contact +46702089245 Alfa 4, SciLfeLab, Stockholm

Recent user publications

The publications in this database are the result of research conducted at the units of SciLifeLab – both in user projects and technology development.


SciLifeLab Staff

Magda Bienko, Platform Scientific Director
Nicola Crosetto, Facility Scientific Coordinator
Quentin Verron, Head of Unit / Research engineer
Erik Wernersson, Research engineer
Emma Inns, Invoice assistance

Associated unit staff

Katarina Gradin, Technician
Britta Bouwman, Research engineer
Wenjing Kang, Post doctor
Luuk Harbers, PhD student
Roberto Ballarino, PhD student
Wing Hin Yip, PhD student

Guide line: how to prepare your samples for iFISH

Available probe list



Advanced FISH Technologies(AFT)

The AFT Facility enables researchers to access our extensive expertise of DNA and RNA single-molecule fluorescence in situ hybridization (smFISH) assays and our growing repository of oligo-based smFISH probes.

We offer three main services, which can be delivered alone or in combination:

  • Design of DNA/RNA smFISH probes against any organism of interest for which a reference genome/transcriptome is available (service area 1)
  • Enzymatic production of smFISH probes starting from oligopools, either already available at our unit or custom-designed and purchased for the user (service area 2)
  • DNA/RNA smFISH on fixed cells, frozen and FFPE tissue sections (service area 3)

We design and produce probes for DNA and RNA smFISH using our iFISH pipeline and proprietary software specifically designed for highly efficient search and multi-alignment of oligonucleotide sequences. For smFISH experiments, we rely on our custom-built epifluorescence microscope (Nikon Ti-E) equipped with an ultra-sensitive camera (Andor) and add-on tools specifically tailored for smFISH.

At present, we do not offer highly multiplexed smFISH assays such as MERFISH or seqFISH, however we are setting up the technology to do so, so stay tuned!


Below you can find a list of services that we are currently offering and their relative prices. For more details, please schedule a consultation appointment with us and we will discuss your needs and what we can offer. Please note that these prices are an approximate estimate for your information. Actual prices will be provided in a quote following consultation of your specific requirements.

For FISH probe design and production, the expected turnaround time from first-contact to service-delivered is 4 weeks. For full smFISH services (hybridization and imaging), the turnaround time may be longer depending on multiple factors, including probe and sample availability as well as requirement for optimization. Based on your specific project, we will agree on a project roadmap and make a turnaround time estimate.

We prioritize our services according to the following criteria (in decreasing order of importance):

1) Service required for the revision of a manuscript by a user in academia > Service not needed for an imminent publication

2) Probe design and production > Full FISH service

3) Academic users > Private company users

AFT price list 2021-2022

The prices listed in the table above apply to individual researchers at academic institutions in Sweden or the EU. For researchers at academic institutions outside the EU, we apply a 10% increment to all prices. For private companies, we apply a 50% increment to all prices.

Additionally, we charge a 22.5% Karolinska Institute overhead on all services.

The prices above are estimated for 1 or 10 samples. For samples between 1 and 10, please contact us for a more precise estimate. For over 10 samples, please contact us so that we can assess the feasibility and provide a price estimate.

Shipping costs are not included in the price list above. Unless otherwise requested by the customer, we will utilize the official shipping company of Karolinska Institutet (Your Special Delivery System, YSDS) and add shipping costs to your invoice.


Here are some examples of applications of the services that we offer:

  • Validation of gene expression differences detected by single-cell RNA-seq or spatial patterns of gene expression detected by spatial transcriptomics: RNA smFISH can be used to confirm differences in gene expression between cells and/or tissue regions or to study the spatial distribution of cells expressing a particular gene/set of genes of interest in a tissue (max 5 genes per sample) in a small subset of samples (less than 10)
  • Visualization of genomic loci of interest for which commercial DNA FISH probes are not available: DNA FISH can be used to confirm the presence of chromosomal translocations, amplifications, or deletions, or to study the spatial arrangement of one or more chromosomes or sub-chromosomal regions in the cell nucleus, in cultured cells or tissue sections

Last updated: 2023-11-13

Content Responsible: David Gotthold(