Saving everything as an image

Hi, sorry for bothering for such a small problem, but I’m not familiar with ImageJ.

I used the multi-point tool to point some regions, so I can see the points and the numbers for each region, and I would like to save it just like that.
That sounds simple but I can’t, taking a screenshot or using the “Capture Screen” utility gives a bad resolution.

I tried to make an overlay and then flatten it. I can save it with the native resolution, but the points are smaller, and I don’t have the numbers anymore.
I would like to have the numbers automatically done just like it’s done when I’m using the multi point tools.

Thank you for your help, I’m pretty sure the answer will be obvious for you but I haven’t found how to do it.

Double-click on the multi-point tool to open the options dialog.

Adjust some options and then use the flatten action.

I was able to create an image with numbers, etc. without any problem.

As an alternative you can use the ROI manager and add the point to the ROI Manager. See this thread:

Thank you for your answer.

Yes, this is what I did.
But once I flatten it, the extra large circles that I did look very smaller, same for the numbers, I don’t know why.

Hard to say. Are you working on a multi monitor setup?

Just a guess: do you have a high dpi display and the ImageJ application is scaled by default so that the resulting image is maybee an unscaled result?

What happens if you use another computer?

Yes I am.

I work with 2448x3264 px images, so maybe you’re right, ImageJ might consider it as a 1920x1080.
How can I scale it ? If I do scale (Ctrl + E) the scale seems to be ok.

No that is not the case if you flatten the image you get the 100% original sized copy image not a scaled down version whatever zoom you applied. Even the markers won’t be changed in size.

Maybee you can send a screenshot before and after the flattening?

(The key shortcut ‘Ctrl+5’ gives you the 100% size display).

Your workflow should be (and nothing else!):

Multipoint tool->Flatten image

Well, once I do the multipoint tool, if I do the flattening (ctrl + shift + f to make sure that we talk about the same one), I have an error saying “overlay or multi-channel image required”. So what I do is just adding the selection to an overlay (ctrl + b), and then flatten it.

Here are the screens of before and after the flattening.
Before with extra large red circles :

After :


Ok I used another ImageJ distribution. However if I flatten the image on Windows (Ctrl+b) it works fine, too.
I will try this on Linux, too (your screenshot suggests Linux OS).

Yes I am using Debian.

I will try that on my Windows PC at home, and see if there is a change.

I could reproduce this feature on Linux and Windows by scaling an image (leaf.jpg) which exceeds the monitor resolution and is displayed as 33,3% (see below):

It does not happen if the image is displayed as 100% or if I zoom a tiny image (blobs.gif).

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Yes, I guess this is intended behavior, but @Wayne might want to comment this.

In any case, you can work around it by first scaling the image to the desired size to be displayed, and then adding the overlay and flatten.

If you display the image at 100% first the flatten will work as expected.

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Ok thank you.
So what I would like to do is to save what is displayed with the points at 33.3%.

Because you are right, if I zoom at 100%, I see the exact same thing that I have once that I flatten.

But I didn’t manage to do what you did with the points 1 and 2 on the leaf, that’s the size I would like to have instead of the other small ones that I get.

This should do it:

  • Image > Scale… with X Scale and Y Scale set to 0.33
  • Create your multi-point selection
  • Image > Overlay > Add Selection… (not required when working with a single plane 8-bit image)
  • Image > Overlay > Flatten

This works, thank you a lot.

But by doing that, the resolution is also reduced by 3, so the easiest way to have the same result is just to use the “Capture Screen” utility.

If there’s any way to do the same thing and keep the native resolution, let me know.

You can of course use a macro to loop over all the coordinates to label and draw a circle and a label:

run("Leaf (36K)"); // open a sample image for illustration

makeOval(320, 100, 30, 30);
setForegroundColor(255, 0, 0);
run("Line Width...", "line=10");
run("Draw", "slice");
run("Select None");

setFont("SansSerif" , 48, "bold antialiased");
drawString("1", 350, 170);

run("Out [-]");
run("Out [-]"); // zoom out to illustrate how it displays at lower zoom levels

The Flatten command in the latest ImageJ daily build (1.51d3) works better with multi-points selections (currently only “Circle” type) on large images, such as the 4000x4000 Nile Bend sample image.