Manual moving of a stack

Hi all,

I am a biologist that is fairly new in ImageJ or FIJI.

Is it possible to move a stack manually?

I have some stacks from different sources that I combine altogether, so that the new stack consists of 4 color channels. However, one of the stacks seems not well-aligned to the others.
The problem does not seem to be solved with StackReg or other related plugins. So, my idea is to move this stack manually following X-Y coordinate of the reference stack. Is it possible?

I will appreciate any answer.

Thank you very much in advance.


Hi @royan

I am going to introduce our plugin “CoordinatShift”.
It can shift stack image by manually.
Please try it.


Hi @hwada

Thank you very much for your answer.

Doesn’t it require more than 1 frame stack image? I have tried it, but it shows a messege window stating that I need a stack image that has more than 1 frame. My stack consists of 4 dimensions only (X, Y, Z, and C), without T dimension. Do you know what the problem is?

Thank you.

Hi @royan

Since this plug-in shifts with respect to the T-axis, it is necessary to convert the dimension to be operated manually into the frame (T-axis).
If you want to align the color channel, you need to create an image with the channel converted to a frame.
*You should be able to use “concatenate” after loading each channel’s stack.
Image > Stacks > Tools > Concatenate


Thank you very much for your suggestion, @hwada.

I tried to modify your step a little bit accordingly. So what I did is to split the channels, and then convert the Z axis of one channel, which I would like to shift, into T axis. And then I used your plugin to shift the coordinate of the image, and convert it back to Z axis again thereafter. Finally, I merge the channels altogether, and it succeeded. Eventhough it cannot be shifted following the other channels alignment, it is fine and still works perfectly.

Thank you very much for your plugin, @hwada. It’s really helpful!