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Basically what I am trying to achieve is overlay one stack with another, in a layer that maybe displayed or not. I know it is possible to overlay 2D images but is there a function to overlay stacks.

I have a stack in .raw format containing a 3D uCT scan and another stack in .raw format containing regions of interest. I want to overlay the ROIs onto the stack for all slices, but each slice is different. Is there a way to do this in ImageJ?

Thank you

William Grimes
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1 Answers1

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You can use the command Image / Color / Merge channels. For example, load the two images, assign the uCT to the gray channel and the rois to the red channel.

lib
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  • Oh really, sorry if this is a very basic question I am new to ImageJ. I got an error saying: 'The source images must have the same bit depth.' – William Grimes Jul 08 '13 at 07:43
  • One is 16-bit and another is 32-bit, do you know how I can convert one stack from 16-bit to 32-bit and vice versa. Thanks – William Grimes Jul 08 '13 at 07:44
  • when you open the image, you see in the title bar if ti's 8-bit, 16 bit...etc. Just select a window and use the command Image - Type to change the pixel depth – lib Jul 08 '13 at 07:44
  • I see, that is surprisingly straight forward. Now I have merged the colour channels as suggested and it is almost what I want, however both images are greyscale and I want them to remain when I merge channels one becomes red and the other green. This obfuscates the image somewhat, is there a way to keep the original colours? Also I would like it to be an overlay in the sense that a layer can be shown or hidden. Thank you – William Grimes Jul 08 '13 at 07:50
  • you can choose the colors, probably you have an image in the green channel instead of the gray channel. But you cannot have both in grayscale. I'm sorry I don't have a suggestion for hiding the overlay. But you can select "keep the source images", so that you have both the original images and the merged one. – lib Jul 08 '13 at 07:53
  • Okay, thank you very much for that, it is a big step in the right direction. I am now wondering if ImageJ is suitable for this kind of 3D imaging task or if other software would be more suitable. – William Grimes Jul 08 '13 at 08:41