Re: Clean-up ROIs

Posted by Peter Haub on Jan 20, 2020; 6:28am
URL: http://imagej.273.s1.nabble.com/Clean-up-ROIs-tp5022832p5022847.html

Hi Philippe,

assuming an 8bit image with black background (=0) and bright object
pixels (=255) which are representing your ROI, try the following macro
to delete the 'connector' pixels (the pixels which are only connected at
their corners):

run("Convolve...", "text1=[0 1 0\n1 4 1\n0 1 0\n] normalize");
setThreshold(150, 255);
setOption("BlackBackground", true);
run("Convert to Mask");

By the way,
if you implement Michaels solution, you can use the coordinates of the
'Ultimate points' of a binary image as starting point x, y of the wand tool.


Regards,
Peter


On 19.01.2020 19:03, CARL Philippe (LBP) wrote:

> Dear Gabriel, Michael and Peter,
> Thanks a lot for your replies and lightings on my question.
> Peter, I tried to follow your suggested recipie, but unless I missed something, I wasn't able to reach the wished results.
> Thus I will finally implement (in java) the solution proposed by Michael which I validated by a use "by hand".
> Very nice end of weekend for everybody!
> My best regards,
> Philippe
>
> ----- Le 17 Jan 20, à 15:25, Michael Schmid [hidden email] a écrit :
>
> Hi Philippe,
>
> if you convert the rois to a mask, you can use the wand tool in
> 4-connected mode to select only the core.
>
> You will need to find an initial pixel for the wand.
>
> Among all pixels contained in the roi, I would try to use the pixel
> closest to the roi center as a starting position for the wand.
> This staring position will not work if you have crescent-shaped
> particles and the center happens to be at a small 'side particle' on the
> concave side of the crescent. If this can happen, you will have to try
> all different starting positions in the roi and see which one gives the
> largest area (for each roi tried, change the value of the mask to
> something else than 255 inside the roi, then you know that you don't
> need to try that point again).
>
> Java method:
> (new Wand(ip)).autoOutline(startX, startY, /*tolerance=*/0,
> Wand.FOUR_CONNECTED)
>
> Best,
>
> Michael
> ________________________________________________________________
>
> On 17.01.20 15:02, CARL Philippe (LBP) wrote:
>> Dear all,
>> Please find under the following link:
>> http://punias.free.fr/ImageJ/Clean_up_ROIs.jpg
>> a picture of two ROIs.
>> The ROI on the left had been obtained through a threshold process followed by an Analyze particles.
>> As the right ROI is obtained by a "by hand cleaning" of the right one.
>> My question is whether there may be a way to perform such a "cleaning" automatically?
>> I thank you very much in advance for your lighting on this.
>> My best regards,
>> Philippe
>>
>> Philippe CARL
>> Laboratoire de Bioimagerie et Pathologies
>> UMR 7021 CNRS - Université de Strasbourg
>> Faculté de Pharmacie
>> 74 route du Rhin
>> 67401 ILLKIRCH
>> Tel : [phone]
>>
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