http://imagej.273.s1.nabble.com/Problem-with-creating-ring-like-ROIs-with-particle-analyzer-tp5020989p5024355.html
(several particles per one Image).
as the dilated ROI (in this case, the ROI 2).
> Good day Volko,
>
> did you try making ring-ROIs from two circular selections using the
> XOR-feature of the ROI-manager?
>
> Here is an example macro:
>
> // ROI-xor Demo
> newImage("Test", "8-bit ramp", 256, 256, 1);
> makeOval(52, 59, 128, 128);
> roiManager("Add");
> run("Enlarge...", "enlarge=-16");
> roiManager("Add");
> roiManager("Select", newArray(0,1));
> roiManager("XOR");
> roiManager("Add");
> roiManager("Select", newArray(0,1));
> roiManager("Delete");
> roiManager("Show All with labels");
>
> Regards
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::::::::::::
> Am 23.07.18 um 09:00 schrieb Straub, Volko A. (Dr.):
>> Dear All,
>>
>>
>> I have encountered a problem using the particle analyzer and I was
>> wondering whether anybody had a suggestion for a solution.
>>
>> I am trying to create ring-like ROIs to measure the intensity around a
>> central region. I can create the ring-like ROIs by first creating a
>> selection of the central regions using the particle analyzer and then use
>> the 'Make Band' function to create rings for each ROI. This is okay, but
>> gets very slow when images are large and contain hundreds or thousands of
>> ROIs.
>>
>> So, instead I tried to use the maximum filter to dilate the ROIs and then
>> subtract the original ROIs. This produces the desired rings, which can be
>> analysed with the particle analyzer. This works and inspecting the
>> measurement in the results table shows the expected results. 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 issue has previously been discussed on the mailing list
>> (
http://imagej.1557.x6.nabble.com/ROI-with-holes-Particle-Analyzer-vs-ROI-Manager-td5009887.html)
>> and the suggested solution was to use the 'Limit to Threshold' option in
>> measurements. That works okay for the binary images of the rings, however
>> I can't get this to work if I want to use the ROIs to measure the pixel
>> intensity on another image. I also tried to use the redirect option in
>> "Set Measurements", but I don't seem to get this to work either.
>>
>>
>> I attach a small sample image and some macro to illustrate the issue. The
>> image contains three nuclei. I am trying to measure the intensity of the
>> ring around the nuclei. The first three ROIs are created using the 'Make
>> Band' function, while ROIs 4-6 are created by dilation and subsequent
>> subtraction of the original image. Both approaches produce the same
>> results for measurements on the binary 'Border' image (compare results
>> 1-3 and 4-6). However, using the ROIs to measure the intensity of the
>> ROIs on the original image ('Test') produces different results for the
>> ROIs created using the 'Make Band' function (1-3) and the ROIs created by
>> dilation and subsequent subtraction (4-6) as these ROIs contain the whole
>> area and not just the ring.
>>
>>
>> Sorry for the lengthy email. I hope that this makes sense and would be
>> very grateful for any suggestions.
>>
>> Thanks,
>>
>> Volko
>>
>>
>>
>> Test Macro:
>>
>>
>> image=getTitle();
>> run("Duplicate...", "title=Nuclei");
>> setAutoThreshold("Default dark no-reset");
>> setOption("BlackBackground", true);
>> run("Convert to Mask");
>>
>> run("Set Measurements...", "area mean center limit redirect=None
>> decimal=1");
>> run("Analyze Particles...", "display clear add");
>> for(i=0;i<roiManager("count");i++){
> > roiManager("Select", i);
>> run("Make Band...", "band=2");
>> roiManager("Update");
>> };
>>
>> run("Select None");
>> run("Duplicate...", "title=Border");
>> run("Maximum...", "radius=2");
>> imageCalculator("Subtract", "Border","Nuclei");
>> run("Analyze Particles...", "display add");
>>
>> setThreshold(100,255);
>>
>> roiManager("multi-measure append");
>> selectWindow("Test");
>> roiManager("multi-measure append");
>>
>>
>>
>>
>> ImageJ - ROI with holes / Particle Analyzer vs. ROI
>> Manager<
http://imagej.1557.x6.nabble.com/ROI-with-holes-Particle-Analyzer-vs-ROI-Manager-td5009887.html>>> imagej.1557.x6.nabble.com
>> ROI with holes / Particle Analyzer vs. ROI Manager. Dear all, the
>> Particle Analyzer can "exclude" holes when measuring particles, gives
>> reasonable results on my data.
>>
>>
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html