Posted by
Michael Schmid on
Nov 18, 2016; 5:52pm
URL: http://imagej.273.s1.nabble.com/Create-Mask-from-blurred-ROI-tp5017598p5017602.html
Hi Matt,
you could try 'Find Maxima', which can be limited to values above the
lower threshold and can do a basic watershed segmentation.
(it is a 'seeded' watershed, starting at the maxima found)
For your thumbnail image, the following seems to work:
setThreshold(67, 255);
run("Find Maxima...", "noise=15 output=[Segmented Particles] exclude
above");
For other images, you might need to adjust the noise threshold of 'Find
Maxima' - use the preview function to see how many particles it finds.
HTH,
Michael
________________________________________________________________
On 2016-11-18 17:02, MattLee wrote:
> Hello,
>
> I'm looking to create distinct ROI's from the attached image using
> intensity. From the image it is clear there are 3 cells in the centre
> however when I create a Mask it combines these into a single ROI. Altering
> the threshold doesn't really help either.
>
> Is there a way to outline each cell using the intensity drop of the pixels
> as a sort of Watershed? The Watershed process requires a binary image, but
> converting this image to binary combines them, so is not very helpful.
>
> Thanks.
>
> ROI
> <
http://imagej.1557.x6.nabble.com/file/n5017598/ROI.jpg>
>
> Mask
> <
http://imagej.1557.x6.nabble.com/file/n5017598/Mask.jpg>
>
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