Appendix 4: Safety

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Bench top flow cytometers

Bench top cytometers are fully enclosed. The biological hazards associated with them relate to sample preparation rather than the instrument itself. Normal laboratory safety procedures should be followed when preparing and handling biological samples. 
It is best, whenever the experiment permits, to fix samples before analysis. After running unfixed samples, the sample lines should be decontaminated by running a disinfectant, such as dilute bleach. The contents of the waste container should be sterilised by the addition of disinfectant before disposal in compliance with your institution's guidelines.

Cell sorters

The comments above on biologically hazardous materials apply. In addition, there are three hazards associated with instruments that sort cells by drop deflection (see Chapter 2, Section 2.7) - the laser beam, the creation of aerosols during the sorting process and the high voltage applied to the deflection plates.


The laser beams will burn the retina of the eye and cause permanent damage. They should normally be fully enclosed. However, when they are being aligned, the beam may be exposed. 
During alignment, any uninvolved personnel should be excluded from the room. No shiny metal object (which can reflect a laser beam into someone's eye) should be brought near to a laser beam; rings and bracelets should be removed or securely covered.
Safety goggles are available and should be worn whenever practicable when working with exposed beams. Local rules for the operation of lasers should be discussed and agreed with your laser safety officer.

Aerosol formation

There is a risk of aerosols containing biological particles being created from the stream emerging from the flow cell of a cell sorter. An aerosol may be created whether the instrument is actually sorting or not. There is an increased probability of aerosol formation during sorting, particularly if something goes wrong, for example, dirt in the flow chamber orifice.
While samples are being analysed or sorted, the door to the sorting chamber should be closed. Some instruments permit the application of a slight negative pressure to prevent droplets escaping into the laboratory. This should always be switched on.
The necessity for further precautions depends on the sample being analysed. These precautions should be determined in consultation with the authorised Laboratory Safety Officer.
If a sample is brought from another laboratory, any hazard likely to arise from the sample must be clearly established before commencing analysis. It is particularly important that anyone bringing transfected cells for sorting should tell the operator what genes have been introduced to the cells and the hazards associated with these genes.

High voltage

Before cleaning the area around the sorting nozzle, it is essential that the high voltage on the deflection plates is turned off. If sorting has been stopped because of a blockage, sheath fluid can be sprayed onto the plates themselves, necessitating their cleaning.


Schmid, I., Lambert, C., Ambrozak, D., Marti, G.E., Moss, D.M., Perfetto, S.P. (2007) International Society for Analytical Cytology Biosafety Standard for Sorting of Unfixed Cells.Cytometry 71: 414-437.