Photobleaching and Bleaching Effects

Bleaching (also photobleaching) is the progressive fading of the emission intensity of the sample under study. This in particular affects images from Widefield 3D, Widefield time series, Spinning Disc time seriese, Confocal time series and STED time series.


The performance of a fluorescence microscope depends on the chemical components that function as emission dyes inside the sample. There are many mechanisms that affect the amount of light emitted from the fluorescent molecule. These mechanisms not only depend on the kind of fluorescent molecules but also on the environment of the sample. This will result in a lifetime for each fluorescent molecule which determines how many absorption-emission cycles can be undergone before the molecule becomes unusable. Here are some of the popular theories regarding the origin of photobleaching.

The main cause of photobleaching seems to be the reaction of excited fluorescent molecules with oxygen molecules dissolved in the sample. It is possible for a dye molecule to cross over to a secondary excited state which lives longer and is more reactive than the conventional excited state. This makes it possible for it to react with oxygen. When the secondary excited state reacts with oxygen the life time increases even further and thus surpressing the emission intensity subtantially.

Organic reaction
A second viable explaination of photobleaching is the reaction of dye molecules with organic molecules from the environment. When the dye molecules cross over to the more reactive and long-lived excited state the molecules can undergo a irreversible chemical reaction with intracellular organic molecules such as proteins and lipids. The result is a new molecule that can not fluoresce.

Multi-photon events
Photobleaching can also be caused by absorption of one or more photons by a fluorescent molecule in an already excited state. If it is hit by another photon it can either cross to a more reactive state or it can ionize. In case of the reactive state it can lead to one of the previous mentioned processes. In case of ionization the molecule will also be unable to fluoresce. However, for these events to occur the excitation intensity needs to be several orders higher than for one-photon events.


A lot of research has been done on this subject. The kind and magnitude of bleaching depends on the composition of the dye molecule and the environment of the sample. Therefore the first step for bleaching reduction is choosing the most photostable fluorescent molecule. Secondly, one can reduce bleaching by deoxygenating the sample. This can be done by passing N2 through the sample or by using oxygen scavengers such as ascorbic acid.

Bleaching Correction

Huygens Professional and Huygens Essential have a tool (Equalize Flux) that corrects for bleaching in some situations. See Bleaching Mode for more details. See also Bleaching Vs Sampling.
Since Huygens 17.04, both Essential and Professional include an advanced Bleaching Corrector tool for more interactive control on bleaching correction in z-stacks and time series.

Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands

Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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