ImageJ FIJI - is there a way to have concentric circles show up on crosshairs on every frame in stack without re-doing it on each frame?

ImageJ FIJI - is there a way to have concentric circles show up on crosshairs on every frame in stack without re-doing it on each frame? please help I am new at this and don’t think I can re-do the concentric circles on each frame because I have thousands! please help
thank you!!!

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Hey @Fekmouse,

can you share an example or screenshot? It’s a bit hard to imagine what you are trying to achieve without seeing it :wink:

Cheers,
Robert

Yes thank you! here is what it looks like when I manually do it:

and then…

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when I advance to the next frame and the crosshairs move (linked to gaze tracker) then the concentric circles need to be re-done by measuring the horizontal length of the crosshair and then going under PlugIns and Concentric Circles and entering the calculated radii…

Hi
@Fekmouse
You should watch this thread.
The question was about two concentric circles.

You can be more specific about the radius. With an annotated image …
Regards

oh wow. that is super complicated and not sure that I something that I can figure out…the radius of the foveola is 5.315 pixels and the radius of the fovea is 25.25 pixels.

I think I may just trace the concentric circles on a piece of clear plastic and then hold it over the crosshairs on my screen instead of re-doing it on every frame and I can still get the answers I need :slight_smile: the good ole fashioned way! lol if anyone can help though, please let me know because would still be interested! thank you and stay safe and wash hands and do not touch face amid COVID. this is a very helpful video here about how to not catch it - take care! his video from a NY (Cornell) doctor prepared for his family members is incredibly informative and I recommend watching it ALL the way through.

https://vimeo.com/399733860

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There are therefore two positions:

  • The initial position (your 1st photo where the circles are centered on the cross)
    -a final position where the cross has moved and the two circles must follow and be centered on the cross.
    Exact?
    If this is how it should happen then you can drop an image (on the forum) which has the cross and not the circles.

Screen Shot 2020-04-04 at 5.01.19 PM

that would be amazing. here is a photo of the crosshairs without the circles. would be amazing if the circles could follow the cross hairs centered on the cross through each frame since I have thousands of frames. thank you!!!

hi M
the emails are not going through :slight_smile:

Hi @Fekmouse

Please, follow the steps:

  • open an image (one copy; no original)
  • copy and paste the macro in: Plugin -> New —> macro
  • run
macro "Concentric circles"
{
// Start macro
requires("1.52u");
setBackgroundColor(0,0,0);
setOption("BlackBackground",true);
img=getImageID();
setBatchMode(true);
selectImage(img);
run("Duplicate...", "title=1");
close("\\Others");
run("Duplicate...", "title=2");
run("8-bit");
run("Gaussian Blur...", "sigma=3");
setAutoThreshold("Intermodes");
//run("Threshold...");
//setThreshold(0, 183);
run("Convert to Mask");
run("Fill Holes");
run("Set Measurements...", "area centroid center bounding add redirect=None decimal=4");
run("Analyze Particles...", "size=4000-Infinity display exclude add");
iR=5.315;
oR=25.25;
roiManager("Select", 0);
roiManager("Measure");
a=getResult("XM",0);
b=getResult("YM",0);
print(a);
oX=a-oR;
print("oX=",oX);
oY=b-oR;
iX=a-iR;
iY=b-iR;
roiManager("reset");
makeOval(oX, oY, oR*2, oR*2);
roiManager("Add");
makeOval(iX, iY, iR*2, iR*2);
roiManager("Add");

selectWindow("1");
roiManager("Set Color", "red");
roiManager("Set Line Width", 2);
roiManager("Show All without labels");
setBatchMode(false);
close("Results");close("Log");
exit("Completed");
// Macro end
}

Can you tell me about your results, if you don’t mind.
Regards

Hi - when you say open an image (one copy; no original) - what does that mean? I open the original video with all of the 3,000+frames in it and then go to plugin and new and macro and run? thanks!

Hello @Fekmouse
This macro works for one (1) image.
For several images it is a little more complicated.
I need to know the names + numbering of the images.
Have you tested for an image (a copy)?
Is it okay?

hi
I have not tried it yet - I am on a very tight deadline unfortunately and so I have developed a work around. I will trace the concentric circles for each of the 8 videos onto a clear plastic square and without changing zoom etc, will just hold that on the laptop screen over the crosshair to assess each image :slight_smile:

thank you so much for all of your help! In the future, it would be awesome if the software had that capability so the concentric circles do not need to be redrawn and placed on each frame when you have thousands of frames. really really appreciated all of your help!!!

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