Flow Cytometry Core Facility

The Flow Cytometry Core Facility offers a range of flow cytometric techniques.

The Flow Cytometry Core Facility offers access to high-end FACS analysis and state-of-the-art cell sorting capabilities, actively providing scientists with adaptive setups and dedicated support.



We offer a wide range of flow cytometric techniques, hands-on service, data analysis, and tailored training sessions for users inside and outside EMBL. Our facility strives to meet researchers’ specific needs by providing dedicated help with experimental design, enabling the highest possible resolution in terms of analysis and product. We have recently upgraded the facility to provide access to S2 cell sorting services and improved our general sorting set up to meet the growing need for high-parametric and aseptic sorting.

We work with equipment from Beckman Coulter, Becton Dickinson, Cytek Biosciences, and Coherent Inc. The EMBL Flow Cytometry platform is open to test new technological developments to serve the needs of the scientific community.

Figure 1: Flow cytomery applications used by EMBL researchers: Cell cycle analysis and Phenotyping of immune cells.

Major projects and accomplishments

  • Full spectral cytometry for multi-parametric analysis of cell populations with high autofluorescence and/or low levels of expression of key biomarkers.
  • Single-cell sorting for single cell quantitative genome, transcriptome, CRISPR/Cas9 genome editing and in vitro studies.
  • Establishment of clonal cell lines carrying fluorescent protein-tagged genome-edited genes for 4D life cell imaging, and assessment of protein interactions and concentrations during mitosis.
  • High-parametric S2 cell sorting service with dedicated equipment.
  • High-throughput sorting of tissue-specific nuclei from Drosophila melanogaster embryo as a preparative step in the analysis of genome regulatory activity during tissue development.
  • In-house Flow Cytometry course in cooperation with the German Cancer Research Center (DKFZ).
  • Flow Cytometry data analysis workshops at EMBL-Heidelberg and EMBL-Rome.
  • Five-day EMBL Course for Hands-on Flow Cytometry held once a year. 
  • Five-day EMBO Practical Course on cell sorting held once every two years. 

Services provided

  • Complex multi-color analysis of cell populations based on light scatter and fluorescent probes content by conventional and spectral cytometry.
  • Extensive support for basic and complex cell cycle analysis and apoptosis assays.
  • Full-service sorting of rare populations out of a heterogeneous sample. Cell cloning, particle enrichment, and high purity bulk sorts.
  • High-recovery and indexed single-cell sorting for sequencing.
  • We offer to our researchers’ advice in experimenrtal design and dedicated training sessions in the use of our flow cytometers, cell sorters and data analysis software
  • We offer to our researchers’ advice and dedicated training sessions in the use of flow cytometry, instrument operation, and post-acquisition data analysis.
  • Developing of novel flow cytometric techniques to meet EMBL’s diverse scientific needs.


Flow Cytometry Core Facility
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Tel: +49 6221 387-8341
E-mail: diana.ordonez@embl.de

Reservations, trainings and consultations:
E-mail: fccf-team@embl.de