Using overlays on image channels

[edsimmons]

Hi IJ list,

I wonder if someone could help, please?

I'm trying to work out how best to use overlays on an image with two channels. I'm using Micro-manager to acquire images (displayed as greyscale channels that the user can choose between, not a composite image) and I would like to draw on the overlays of individual channels of the same image.

Is this something that is possible to do with IJ directly or do I need to code this myself?

I recall that it can be made to work the way I want with stacks of images (eg each image in the stack has it's own overlay) but I can't make this happen using channels.

Any help gratefully receieved - thanks in advance.

Best regards,
Ed

[Rasband, Wayne (NIH/NIMH) [E]]

On May 20, 2013, at 7:45 AM, edsimmons wrote:

> Hi IJ list,
>
> I wonder if someone could help, please?
>
> I'm trying to work out how best to use overlays on an image with two
> channels. I'm using Micro-manager to acquire images (displayed as greyscale
> channels that the user can choose between, not a composite image) and I
> would like to draw on the overlays of individual channels of the same image.
>
> Is this something that is possible to do with IJ directly or do I need to
> code this myself?

You can add overlays to multichannel images. Here are JavaScript and macro examples that create a 2 channel, 10 frame hyperstack and then add an overlay containing a rectangle that is displayed on channel 1 of all 10 frames, a rectangle that is only displayed on channel 1 of frame 1, a circle that is displayed on channel 2 of all 10 frames and a circle that is only displayed only on channel 2 of frame 2.

-wayne

  // This script demonstrates how to create a two
  // channel hyperstack and add an overlay to it.
  channels = 2;
  slices = 1;
  frames = 10;
  imp = IJ.createHyperStack("Test", 500, 500, channels, slices, frames, 8);
  imp.setMode(CompositeImage.GRAYSCALE);
  overlay = new Overlay();
  // add rectangle that will be displayed on channel 1 of all 10 frames
  rect1 = new Roi(100, 100, 100, 100);
  rect1.setPosition(1, 1, 0);
  overlay.add(rect1);
  // add rectangle that will be displayed on channel 1 of 1st frame
  rect2 = new Roi(100, 250, 100, 100);
  rect2.setPosition(1, 1, 1);
  overlay.add(rect2);
  // add circle that will be displayed on channel 2 of all 10 frames
  circle1 = new OvalRoi(250, 100, 100, 100);
  circle1.setPosition(2, 1, 0);
  overlay.add(circle1);
  // add circle that will be displayed on channel 2 of 2nd frame
  circle2 = new OvalRoi(250, 250, 100, 100);
  circle2.setPosition(2, 1, 2);
  overlay.add(circle2);
  imp.setOverlay(overlay);
  imp.show();


  // This macro demonstrates how to create a two
  // channel hyperstack and add an overlay to it.
  // It requires the ImageJ 1.47r daily build.
  requires("1.47r");
  channels = 2;
  slices = 1;
  frames = 10;
  newImage("Test", "8-bit black", 500, 500, channels, slices, frames);
  Stack.setDisplayMode("grayscale");
  // add rectangle that will be displayed on channel 1 of all 10 frames
  makeRectangle(100, 100, 100, 100);
  Overlay.addSelection;
  Overlay.setPosition(1, 1, 0)
  // add rectangle that will be displayed on channel 1 of 1st frame
  makeRectangle(100, 250, 100, 100);
  Overlay.addSelection;
  Overlay.setPosition(1, 1, 1)
  // add circle that will be displayed on channel 2 of all 10 frames
  makeOval(250, 100, 100, 100);
  Overlay.addSelection;
  Overlay.setPosition(2, 1, 0)
  // add circle that will be displayed on channel 2 of 2nd frame
  makeOval(250, 250, 100, 100);
  Overlay.addSelection;
  Overlay.setPosition(2, 1, 2);
  Overlay.show;
  run("Select None");

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[Jan Eglinger]

Dear all,

On 21.05.2013 6:31 PM, Rasband, Wayne (NIH/NIMH) [E] wrote:
> You can add overlays to multichannel images. Here are JavaScript and macro examples that create a 2 channel, 10 frame hyperstack and then add an overlay containing a rectangle that is displayed on channel 1 of all 10 frames, a rectangle that is only displayed on channel 1 of frame 1, a circle that is displayed on channel 2 of all 10 frames and a circle that is only displayed only on channel 2 of frame 2.

Thanks, Wayne, for this illustrative code.
Just a note for *Fiji* users: in order for the Javascript example to
work in Fiji, you have to add:

importClass(Packages.ij.gui.Overlay);

to the begining of the code.

Jan

>
>   // This script demonstrates how to create a two
>   // channel hyperstack and add an overlay to it.
>   channels = 2;
>   slices = 1;
>   frames = 10;
>   imp = IJ.createHyperStack("Test", 500, 500, channels, slices, frames, 8);
>   imp.setMode(CompositeImage.GRAYSCALE);
>   overlay = new Overlay();
>   // add rectangle that will be displayed on channel 1 of all 10 frames
>   rect1 = new Roi(100, 100, 100, 100);
>   rect1.setPosition(1, 1, 0);
>   overlay.add(rect1);
>   // add rectangle that will be displayed on channel 1 of 1st frame
>   rect2 = new Roi(100, 250, 100, 100);
>   rect2.setPosition(1, 1, 1);
>   overlay.add(rect2);
>   // add circle that will be displayed on channel 2 of all 10 frames
>   circle1 = new OvalRoi(250, 100, 100, 100);
>   circle1.setPosition(2, 1, 0);
>   overlay.add(circle1);
>   // add circle that will be displayed on channel 2 of 2nd frame
>   circle2 = new OvalRoi(250, 250, 100, 100);
>   circle2.setPosition(2, 1, 2);
>   overlay.add(circle2);
>   imp.setOverlay(overlay);
>   imp.show();
>

... [show rest of quote]

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[edsimmons]

Rasband, Wayne (NIH/NIMH) [E] wrote

  imp.setMode(CompositeImage.GRAYSCALE);
  overlay = new Overlay();
  // add rectangle that will be displayed on channel 1 of all 10 frames
  rect1 = new Roi(100, 100, 100, 100);
  rect1.setPosition(1, 1, 0);
  overlay.add(rect1);
 

Thanks Wayne, very nice example.

Please could you steer me towards the Java API equivalent of imp.setMode(CompositeImage.GRAYSCALE);?

I've tried looking at the ImagePlus and Stack api docs, but not found the way to actually do it to the imageplus i'm trying to work with.

Thanks,
Ed

[John Hayes]

Hi Ed,

I believe you are looking for CompositeImage::setMode.

Best,

John

Le 24 mai 2013 à 13:06, edsimmons a écrit :

> Rasband, Wayne (NIH/NIMH) [E] wrote
>>  imp.setMode(CompositeImage.GRAYSCALE);
>>  overlay = new Overlay();
>>  // add rectangle that will be displayed on channel 1 of all 10 frames
>>  rect1 = new Roi(100, 100, 100, 100);
>>  rect1.setPosition(1, 1, 0);
>>  overlay.add(rect1);
>>
>
> Thanks Wayne, very nice example.
>
> Please could you steer me towards the Java API equivalent of
> imp.setMode(CompositeImage.GRAYSCALE);?
>
> I've tried looking at the ImagePlus and Stack api docs, but not found the
> way to actually do it to the imageplus i'm trying to work with.
>
> Thanks,
> Ed
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Using-overlays-on-image-channels-tp5003054p5003107.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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