Posted by
Straub, Volko A. (Dr.) on
Jul 24, 2018; 6:25am
URL: http://imagej.273.s1.nabble.com/Problem-with-creating-ring-like-ROIs-with-particle-analyzer-tp5020989p5020992.html
Thanks Herbie & Gabriel for your suggestions.
The suggestion to use the 'Enlarge' function with the ROI managers 'XOR feature' to create the rings resulted in significant speed improvements compared to using the 'Make Band' function. The relative speed improvements are dependent on number of particles and image size, and are particularly striking for larger images with many particles. For example, for an image with 120 particles (image size 664x650 pixels), using the XOR approach is about 2x faster than the 'Make Band' approach. For an image with 1300 particles (image size 2504x2320 pixels), the speed improvement is about 5x. I was surprised by this as using the 'XOR feature' requires the temporary creation of 3x as many ROIs (original ROI, enlarge ROI and combination of the two).
Gabriel's suggestion to use binary masks and redirect the measurements to the original image seems even faster, but can cause problems when the creation of the ring masks by dilation and subsequent subtraction of the original image leads to contact between neighbouring particles. This can be avoided by using some non-merging dilation, but I found that the order in which the measurements of the ring masks and the cores (original particles) are shown in the results table are not necessarily the same (probably because some of the rings are incomplete due to the way they where created). This is a problem as I try to compare measurements of the core and the surrounding area, and at the moment I can't figure out a simple way to check that core and surrounding area measurements correspond.
Thanks again,
Volko
________________________________
From: Gabriel Landini <
[hidden email]>
Sent: 23 July 2018 11:22:22
To:
[hidden email]
Subject: Re: Problem with creating ring like ROIs with particle analyzer
On Monday, 23 July 2018 08:00:14 BST Straub, Volko A. (Dr.) wrote:
> However, when
> these regions are added to the ROI manager, the ROIs now include the
> central hole rather than just the ring. So, any subsequent measurements
> using these ROIs measure not just the ring but the ring plus the hole.
This will not strictly answer your question on ROIs but might be a useful
alternative if you do not find a solution.
Rather than using ROIs I prefer using a binary mask of the objects to analyse
and get the pixel data via Redirection. I use Particles 8 for this, it
restricts the data collection to the pixels set in white in the mask. It you
chose redirection it automatically gets the pixel stats (gresycale or RGB).
Cheers
Gabriel
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