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What is a “mask” and how do you use it?

A mask or single mask is when one channel of a multichannel scan is used to identify objects of interest. The area of this object is analyzed for pixel intensity in the other image channels where they may or may not have a fluorescent signal. For example, Hoechst stained cells are identified as the mask, and the second channel is green looking for GFP expression within that cell. This provides a total count and GFP count, therefore % GFP expression can be calculated.

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