Robust and automatic brightness evaluation for fluorescent spots

Posted by Kyle Michael Douglass on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Robust-and-automatic-brightness-evaluation-for-fluorescent-spots-tp7585583.html

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Hello everyone,

Would anyone be able to point me towards some recommended papers or
open-source software for automatic and robust evaluation of the
fluorescence signal strength from fluorescence-labeled nuclear loci such
as one might observe in FISH experiments?

Automatic segmentation and detection of the spots is not a problem;
however, quantifying the fluorescence signal strength in our data is
tricky because

1) different nuclei have different background fluorescence levels,
2) different loci within the same nucleus sometimes lie within a few
pixels of one another, which confounds automated local background estimates,
3) the loci do not necessarily possess circular symmetries, and
4) we have several hundred images to process, so manual methods are not
feasible.

I appreciate the feedback. Cheers, and happy Friday.

Kyle

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Kyle M. Douglass, PhD
Post-doctoral researcher
The Laboratory of Experimental Biophysics
EPFL, Lausanne, Switzerland
http://kmdouglass.github.io
http://leb.epfl.ch