Flow Cytometry Unit

  • State of the art equipment and expertise
  • Validated flow cytometry panels for human and mouse cells
  • Panel design and panel optimization
Flow Cytometry Unit Flow Cytometry Unit


At the Flow Cytometry Unit (FCU) of Hasselt University, we can provide a tailor-made approach for (single) cell analyses. This can go from broad immunophenotyping of human samples, to sorting of transgenic/transfected mouse cells, to preparation of single cell libraries for downstream RNA-sequencing. The FCU team assists you at every step, from experimental design to sample preparation, acquisition and even data analysis.


Flow Cytometry Unit

BD LSRFortessa

The BD LSRFortessa is equipped with four lasers and can detect forward scatter (FSC), side scatter (SSC) and up to 16 colours simultaneously. It is coupled with a high throughput sampler (HTS), allowing the acquisition of samples in 96-wells plates.

Flow Cytometry Unit

BD FACSCalibur

The BD FACSCalibur is equipped with one laser (blue; 488 nm) and can detect FSC, SSC, and three colours simultaneously.


Flow Cytometry Unit


The BD FACSAria II is equipped with two lasers and can detect FSC, SSC and up to 7 colours simultaneously. It can sort up to 10 000 events per second with high accuracy. Cells can either be sorted into 5 ml tubes, allowing for sorting of four populations at the same time, or directly onto glass slides or in 96/384 well plates (one population at the time). This platform allows for single cell sorting for further downstream processing, for instance for single cell RNA sequencing.

Flow Cytometry Unit

BD FACSAria Fusion

The BD FACSAria Fusion is equipped with four lasers and can detect FSC, SSC and up to 16 colours simultaneously. Its setup is equivalent to that of the BD LSRFortessa, which makes it possible to use the same panel for acquisition and for sorting of cells. It is integrated in a BSL2 cabinet, which allows for sterile sorting for downstream cell culture. Similar to the BD FACSAria II, cells can be sorted into 5 ml tubes, allowing for sorting of four populations at the same time, or directly onto glass slides or in 96/384 well plates (one population at the time).


Flow Cytometry Unit

BD RhapsodyTM Express

The BD Rhapsody Express is a bench-side system for high throughput targeted single-cell RNA-Seq analysis, starting from single-cell suspensions. The workflow is designed and optimized to remove cell imaging during the process.
We have experience with the single cell sort and preparation of the different libraries. Sequencing is outsourced to any desired external partner.


Software packages: FACSDiva 9.0; FlowJo 10.7 with additional plug-ins; OMIQ

  • Manual gating for analysis of complex datasets (up to 18 parameters)
  • Manual gating for analysis of rare immune cell subsets
  • Cell proliferation and suppression analysis
  • Cytometric bead array data analysis
  • Clustering algorithms (e.g. FlowSOM, t-SNE, UMAP, …)

Analysis Flow Cytometry Unit


We offer the use of validated panels for broad immunophenotyping of human or mouse samples, or for specialized characterization of T and B cells. They can be discussed upon request. In addition, we have years of experience with building multicolour panels, and can provide help with the design and optimization of custom panels.


  • Human general immune cell panel (T cells, B cells, monocytes, NK cells)
  • Human T cell subset panel (naive, memory Th cells, Tregs)
  • Human B cell subset panel (all developmental B cell stages)
  • Mouse inflammation panel (T cell subsets, B cells, monocytes/macrophages)


  • Dedicated cell culture labs for primary human andmouse cells & cell lines
  • Incucyte® live cell analysis system
  • Facilities for downstream analysis: qPCR, westernblot, immunocytofluorescence, …
  • Advanced microscopy centre (https://www.uhasselt.be/aomc) for state of the art imaging
  • Immune status monitoring can also be established viaseveral validated qPCR panels present at BIOMED tostudy immune cell subsets and related cytokines andneurotrophic factors.


  • Hoeks C. et al., Int J Mol Sci. May 2021, doi:10.3390/ijms22115660
  • Bogie J. et al., Therapeutic Advances in Chronic Disease. January 2020,doi:10.1177/2040622320947378
  • Fraussen J. et al., Journal of Immunology, September 2019, DOI: https://doi.org/10.4049/jimmunol.1801236
  • Montes Diaz G. et al., Scientific Reports 2018,https://doi.org/10.1038/s41598-018-26519-w
  • Dhaeze T. et al., Journal of Immunology. August2015, DOI: https://doi.org/10.4049/jimmunol.1500759
  • Claes N. et al., PlosOne. October 2014, https://doi.org/10.1371/journal.pone.0111115

For an up-to-date list visit:


  • Fee-for-Service: performing the relevant experiments for you.
  • Consultancy and training: guiding your experimental set-up and training researchers at your location or at our facilities.
  • Research collaboration: open for joint grant applications when the project is complementary with our own research lines and goals.


dr. Leen Willems

Leen Willems 3

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