http://imagej.273.s1.nabble.com/quantifying-focal-adhesions-tp3690483p3690485.html
the FFT bandpass filter. You may be able to filter out the
> Hello,
> I have a similar probem.There are several ways to deal with it.
> You
> can try the "Process=>Binary=>Find Maxima" command which finds the
> local maxima in brightness within certain noise tollerance limits
> (say
> for example 40 brightness
> levels)(
http://rsb.info.nih.gov/ij/docs/menus/process.html#binary)
> .
> You can try also try either the build in "Subtract background"
> command
> or the "Background subtractor" plugin (
>
http://www.mosaic.ethz.ch/Downloads/bgs ). The two latter produce
> not
> a thresholded binary image but keep the format of the images
> instead,
> however the filtered images are very easily thresholded.
> If this still doesn't work either you may want to try some more
> advanced form of morphological filtering (for example the
> "GreyScaleTopHat"or "Find regional Maxima" macros from Landini's
> Morphology collection of plugins is very useful"
> Good luck!
> --
> Stoyan P. Pavlov, MD
> Departament of Anatomy, Histology and Embryology
> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> Prof. Marin Drinov Str.55
> 9002 Varna
> Bulgaria
> Tel: +359 (0) 52 - 677 - 050 #2638
> e-mail:
[hidden email]
>
> On Thu, Nov 12, 2009 at 4:52 AM, David Knecht ATT
> <
[hidden email]> wrote:
> > We are trying to come up with a way to quantify the difference in
> the
> > number/size of focal adhesions in cells under different
> conditions. The
> > images were taken on a widefield scope and so there is significant
> and
> > variable cellular background fluorescence. The focal adhesions
> themselves
> > have pixel values above the local background that surrounds them,
> so they
> > are easy to pick out by eye, but you can't threshold easily
> because there
> > vary in intensity and there are other areas of the cell which have
> the same
> > or higher and lower pixel values than the focal adhesions we want
> to target.
> > Is there a way of classifying/thresholding that will compare
> structures to
> > the local background surrounding it so as to allow it to be
> identified and
> > quantified? Thanks- Dave
> >
> > Dr. David Knecht
> > Department of Molecular and Cell Biology
> > Co-head Flow Cytometry and Confocal Microscopy Facility
> > U-3125
> > 91 N. Eagleville Rd.
> > University of Connecticut
> > Storrs, CT 06269
> > 860-486-2200
> > 860-486-4331 (fax)
> >
>
>
>
> --
> Dr. Stoyan P. Pavlov, MD
> Departament of Anatomy, Histology and Embryology
> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> Prof. Marin Drinov Str.55
> 9002 Varna
> Bulgaria
> Tel: +359 (0) 52 - 677 - 050 #2638
> e-mail:
[hidden email]
Joel B. Sheffield, Ph.D.