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I'm trying to find out a way to merge two stacks together. For example I'm taking some 60X images about the soma of a neuron and then I'll take another stack at 60X for the basal dendrite. Then how can I combine them together?

Daniele Piccolo
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5 Answers5

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Combining stacks

Probably what you want is to create a composite image, with each image stack forming one of the channels in a combined multichannel image. You can do this using the Merge Channels command:

Merge Channels

Just open each image stack separately, then run Image > Stack > Merge Channels..., assigning each image stack to the desired channel. The result will be a composite of each respective plane.

Alternately, if what you mean is to merge each plane in some mathematical way (though I am guessing not), the Image Calculator command can combine two stacks using various operations:

Image Calculator

Image registration/alignment

I am also guessing your images will need to be coregistered first, especially since you tagged this question with alignment.

The Fiji distribution of ImageJ has several nice tools for that, including:

See the Fiji wiki for other options, too.

ctrueden
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  • Are you aware of any ImageJ plugin that allows one to manually (e.g., with the mouse) coregister two stacks and the resample one stack into the geometry of the other? I am tired of trying bazillions of automatic registration algorithms that don't work well enough in the end, when I just need to rigidly align two stack. – bers Sep 08 '17 at 15:24
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    @bers The "Align Image by line ROI" plugin is a manual registration method that does just that for two images. https://imagej.net/Align_Image_by_line_ROI – ctrueden Sep 08 '17 at 21:24
  • Yes - I need stacks, however ☺️ – bers Sep 09 '17 at 06:54
  • @bers Do you want to align them slice by slice? Or do you need a "3D line" which crosses planes? – ctrueden Sep 21 '17 at 10:46
  • Well, aligning two lines in 3D is kind of ill-posed because you can still rotate freely around the line; but yes, I am looking for interactive 3D registration with ability to translate along and rotate around all 3 axes. – bers Sep 21 '17 at 12:34
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    @bers Perhaps [this thread](http://forum.imagej.net/t/manual-registration-of-spim-data/2755/2) on the ImageJ Forum is helpful. – ctrueden Sep 23 '17 at 08:48
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    this certainly looks helpful. Since I have found a workable solution with MITK in the meantime, I will not go through the hassle of trying to understand how to open actual data in SIPM now ;) but it's good to know that I can if I need to. Thanks! – bers Sep 25 '17 at 11:21
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after you open all the "mini stacks" you have, go to: Image>Stack>Tools>Concatenate

Chen Arazi Haroush
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I am not sure what you mean by combine.

The merge channels creates a composite with the soma stack in one color and the dendrite in another.

If you want to make it so that the dendrite is next to the soma (to make a stitched mosaic), you can use the "Combine" command under Stacks. You have to make sure the dimensions of the edges that you use to combine are the same. That is, you an combine a 512x512 image and a 512 x 128 image vertically, and you can combine 512x512 and 128x512 images horizontally.

If you want to add on the second stack at the end of the first stack, use "Concatenate", also under stacks.

Im Age J
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Overlaying fluorscence and DIC

  1. Open the images in ImageJ
  2. Adjust the contrast if neceesary: Image/Adjust/BrightnessConstrast
  3. Change or check all Images are in 8-bit format. Image/Type/8-bit
  4. Image/Color/Merge Channels and the Merge Channels box will appear
  5. Select the fluorescent images in the appropriate R, G and B channels and the DIC or similar image in gray channel. Select “Create Composite” and click “OK”
  6. Click on the new ‘composite’ image to activate it
  7. Image/Type/RGB Color
  8. Save it as “Tiff” file
Aline
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I guess what you want to do is the following : screenshot_Fiji

Hugo Trentesaux
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