Posted by
Michael P Ellis on
Mar 22, 2011; 8:21am
URL: http://imagej.273.s1.nabble.com/declump-those-buggers-tp3685220p3685231.html
Dear Matthias,
Effective and reliable segmentation of the Dapi nuclei is not a trivial task when they are so clumped together.
Below is script I tried for your image that identifies the easy to identify nuclei!. Basic strategy
1. background remove
2. Find maxima as first attempt to locate probable nuclei centres, then applies the result to the original image to cut apart some of the clusters
3.Auto threshold the result and perform Analyse Particles filtering out those particles that are too big (size=250-500), too small or not round enough (circularity=0.50-1.00)
Matched particles are added to the ROI manager for easy access.
//===================================
run("Subtract Background...", "rolling=30");
run("Find Maxima...", "noise=20 output=[Segmented Particles] exclude");
imageCalculator("Multiply create 32-bit", "RGB_(blue).jpg","RGB_(blue).jpg Segmented");
selectWindow("Result of RGB_(blue).jpg");
setAutoThreshold("Default dark");
run("Clear Results");
run("Measure");
run("Analyze Particles...", "size=250-500 circularity=0.50-1.00 show=Outlines display exclude clear add");
selectWindow("Drawing of Result of RGB_(blue).jpg");
selectWindow("Result of RGB_(blue).jpg");
//===================================
If the script is of any use, you will obviously need to modify to work with any image and not just "RGB_(blue).jpg". Hope this is of some help.
-- Michael Ellis
SmartCaptureLite ImageJ plugin available free now at
http://www.dsuk.biz/DSUK/SmartCaptureLite.htmlOn 21 Mar 2011, at 20:19, Matthias Kirsch wrote:
> dear all,
>
> I am struggling with automatic image analysis. One of the first stumbling
> point seems to be segmenting DAPI-stained nuclei in fluorescence images. If
> this is not working reliably, the whole point of processing large numbers of
> images is obsolete. Attached are examples of such clumps (there are many
> more). If segmentation cannot separate them, it would be helpful to have at
> least some way of eliminating false results by just clicking on them, or
> even better, have all identified particles presented in a graph with freely
> chosen measurement as parameters as axes. Then one could click on the
> individual points in the graph and see the corresponding cell in the image
> and then decide whether to keep or discaed it. This should also work the
> other way round, i.e. click on a cell in the image and see the corresponding
> point in the graph. Similarily, it would be most helpful to be able do
> somethig like gating in FACS, i.e. set limits to certain parameters and see,
> which cells fulill them.
>
> I know that this is asking a lot, but I think providing this kind of
> routines in an easy to use plugin would make ImageJ even more attractive and
> competitive than it already is. Of course this applies only for
> 'Non-Cracks'.
>
> Any help would be welcome. Further questions alnosr guaranteed.
>
> Cheers
>
> P.S.: Can only insert jpeg images
> Matthias
http://imagej.588099.n2.nabble.com/file/n6193826/RGB_%28blue%29.jpg
>
> --
> View this message in context:
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