Re: background removal in fluorescence
Posted by W. Bryan Smith on Sep 20, 2005; 12:27am
URL: http://imagej.273.s1.nabble.com/background-removal-in-fluorescence-tp3704817p3704825.html
yes, here is what i was going to suggest:
While this is not the best method, a
low-tech solution is to acquire 'blank'
images of your sample and use this for
straight subtraction of the background.
If you are doing confocal or multiphoton
imaging, your 'blank' can simply be an
image z-slice in which there is no
relevant pixel data (only noise). If you
have several such images, you can get an
average and subtract the average from each
frame in the z-series. If you are using
epifluorescence it may be a bit tricky,
but you should be able to get a decent
'blank' image by acquiring an image
through the same coverslip/dish (whatever
you are using) without any specimen
present. Again, take a few, get a mean,
and subtract the mean from your real data.
This low-tech solution can work
surprisingly well depending on the
statistics of the background you are
trying to subtract.
bryan
On Tue, 20 Sep 2005, Pedro J Camello wrote:
.' In my opinion (my main experience is ca2+ signals in living cells) the
.' best method is to acquire a background image in an area of the coverslip
.' where there are no cells, using it to substract to the series of images.
.' Sometimes this is difficult if the preparation is too "dense", and if
.' you have to move too far from the area of interest the plane of focus
.' could be different. Now I´m removing to the entire image the average
.' fluorescence from an irregular ROI drawn in the "empty" area surrounding
.' the cells.
.'
.' Martin Wessendorf wrote:
.'
.' > Dear ImageJ folks--
.' >
.' > Has anyone come up with a good method for background subtraction in
.' > images obtained using fluorescence microscopy? In my hands, the
.' > methods that work for brightfield don't work for fluorescence.
.' >
.' > Thanks!
.' >
.' > Martin
.'
.'
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