Hi Patricia,
I think that the part of the problem is that the two images appear to be
quit different in the intensity of the spheroids with respect to the
background (dark in Cell1, fainter in Cell2 images). Also Cell1 seems to
have lots of cells migrating out, compare to Cell2 which is more compact?
The following script segments reasonably well Cell2, but overestimates
the are in Cell1 because of the number of detached cells from the main
cluster. Hope it gives you some ideas on alternative ways of
segmentation and perhaps you can adjust the phase microscope to get the
more uniform images?
The BinaryFilterReconstruct is from the Morphology collection and
reduces the potential artefacts which are not spheroids, you might have
to increase the number of erosions for other images).
a=getTitle();
run("Select None");
run("Duplicate...", "title=proc");
selectImage("proc");
run("32-bit");
run("Top Hat...", "radius=2");
run("Top Hat...", "radius=5 light don't");
setAutoThreshold("Default dark");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Fill Holes");
run("BinaryFilterReconstruct ", "erosions=3 white");
run("Create Selection");
selectImage(a);
run("Restore Selection");
Hope it is useful
Gabriel
On 04/03/2024 08:35, OBEID Patricia wrote:
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Hello,
I would like to segment spheroids that are in microcavities.
For the first cell, all is ok.
Here are a few lines from my macro:
run("Duplicate...", " ");
run("Invert LUT");
setAutoThreshold("Moments dark");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Invert LUT");
run("Analyze Particles...", "size=6000-80000 display summarize add");
For the second cell, my problem is that I'm working in white light and the
edges of the wells are also detected ....
One solution might be to do a threshold on the edges of the wells and the
outside and remove these areas, then do a new threshold to detect spheroids,
but I don't know how to write these lines of code ... :-(
Thanks for any help and/or suggestions you can give me.
Good day to all
Patricia
The images are here :
https://filesender.renater.fr/?s=download&token=f580e06e-6f9a-4e4b-8696-b99037472bdc
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