​​​​​Flow Cytometry

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​​​​​​​​​​​​​​​​Flow Cytometry is a powerful application which, with the unique interplay of 3 main systems: fluidics, optics, and electronics, allows for defining the phenotypic and functional properties of, for example, cells. In tagging the cells of interest with a fluorescent probe and delivering the cells via the fluidics system to the point of laser interrogation, the fluorescent probe is activated and emits a light signal. Conversion of the signal to a readable format, allow users to analyse amongst various other, parameters such a granularity, frequency and function of specific cells within a heterogenous population. Flow Cytometry can also be employed to investigate synthetic entities such as nanoparticles. Contact us​​ as the possibilities are endless.

Specific applications in the field include: Any discipline investigating living or non-living elements (from cells and microorganisms to polymers and particles) that requires analyses on interaction, activation, function, frequency, size, granularity, phenotypic characterisation, etc. Examples include Viability assessment, Ploidy analyses, Apoptosis and Oxidative stress assays, Cell cycle arrest in cancer therapies, Phenotyping, Counting, and detection of various rare abnormal cell populations.

Flow cytometers at CAF:​

The CAF Flow Cytometry unit houses 4 different formats of flow cytometers, which are listed below:

1. Conventional Flow Cytometer

Conventional flow cytometers have been instrumental in various applications such as Immunology, Infectious diseases, Oncology, etc. Over time, the technology developed from the limited 3-4 to the greater 8-13 channels instruments, the latter of which kick-started the multi-parameter era in Flow Cytometry. The availability of more channels has broadened, particularly, the field of Immunology which has progressed immensely in the characterisation of events that, specifically, required more than 4 channels (i.e., memory and regulatory T cells, cellular activation, and functional studies) to conduct detailed analyses.

Location: Tygerberg Medical campus

Model: Beckman Coulter DxFLEX flow cytometer

Signature features: 13-channel, 3-laser instrument approved for clinical applications.

For more information, please visit:

DxFlex Flow Cytometer Performance Characteristics and Configuration​

2. Imaging Flow Cytometer

An Imaging Flow Cytometer is an instrument that operates like a conventional flow cytometer, however, it has the added advantage of providing images of every event acquired. In this state-of-the-art technology, the speed and quantitative properties of flow cytometry is combined with the detailed imagery properties of microscopy and it is all delivered via one unique instrument.

Location: Tygerberg Medical campus 

Model: The AMNIS® ImageStreamX Mk II from Cytek.

Signature features:  9-10 channel, 7-laser instrument, providing microscope images of all events.

​For more information, please visit

AMNIS ImageStreamX MkII​ Flow Cytometer Performance Characteristics and Configuration​


3. Full Spectrum Flow Cytometer

Full Spectrum Flow Cytometry utilizes the principles of Conventional Flow Cytometry but differs in its optical capabilities. The technology has transcended from the conventional one fluorochrome: one detector configuration to a one fluorochrome: multi-detector model. Whereas in Conventional Flow Cytometry only the emission peak of a fluorochrome (i.e., APC: 660 nm) is measured, Full Spectrum Flow Cytometry utilizes the full emitted light signature of a fluorochrome (APC: 600 to 750 nm). The great advantage of the technology is that it 1) permits the use of related fluorochromes i.e., APC and Alexa Fluor 647, in the same panel due to difference in their full spectrum signature - in conventional flow cytometry these fluorochromes are routinely not used in the same panel -  and 2) allows for the design of panels that can now analyse a large number (>30) of parameters, simultaneously.

Another great benefit to full spectrum flow cytometer is the ability to define the autofluorescence profile of cells (e.g., macrophages, stem cells and bronchoalveolar lavage cells are notorious for having a high auto fluorescent signal) which is removed/minimized from the sample data.

Location: Tygerberg Medical campus

Model: Cytek Full Spectrum Flow Cytometer

Signature features48-channel, 4-laser instrument, autofluorescence profiled and removed

For more information, please visit

Cytek Aurora Full Spectrum Flow Cytometer Performance Characteristics and Configuration​

4. Cell Sorter Flow Cytometer

Cell Sorter Flow Cytometers applies the principles of flow cytometry in an innovative technology designed to extract cells of interest from a heterogenous suspension, and retain it separately for further analyses. The application of cell sorting involves high-voltage deflection plates that directs passing charged droplets (which contains the cells/particles of interest) into the appropriate collection tube.

Location: Stellenbosch Main campus (BSL2 Laboratory)

Model: BD FACSMelody™ cell sorter

Signature features: 9 channel, 3-laser instrument, 4-way sorting

For more information, please visit

BD FACSMelody Cell Sorter Performance Characteristics and Configuration


How to make a booking:

To use/book the flow cytometers of CAF at Tygerberg or Stellenbosch, registration is required where you also will receive a CAF ID. Please click on the link to complete the CAF Client Registration Form and to obtain your unique CAF ID.

Once you have your CAF ID, select the booking system you would like to use (the one to choose would be CAF Flow Cytometry unit), go to "Sign In" and click on “Create a New User Account" and complete the booking registration form. Once registered you can book any of the CAF Booking systems, not only the one you used to sign up for.

To make a booking, click on "CAF Flow Cytometry Unit" on the booking system and a webpage will open with a calendar to the right. Click on the day you would like to book, find the instrument of interest, and click on the time you wish to book. Complete the pop-up window and click on create booking. If you have not been signed off as an independent user of the instrument or require CAF to perform your sample analyses, please also book for assistance (Dr Dalene de Swardt- Tygerberg campus; Lize Engelbrecht- Stellenbosch campus).

Please note that a sample submission form needs to be completed when bookings are made for the BD FACSMelody cell sorter.