Posted by
Stoyan Pavlov on
Nov 12, 2009; 10:05am
URL: http://imagej.273.s1.nabble.com/quantifying-focal-adhesions-tp3690483p3690486.html
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]
> 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)
>