Whole z-stack alignment across time? (ie stackreg, but on a z-stack)

Image Analysis
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#1

Hi-
I am looking for a plugin or solution to align a z-stack of images across time. Normally, I use StackReg on a z-projection and that works great. In this case however, I want to have all slices of the stack registered across time (the image is eventually going to Imaris, which uses the z-stack information). For example, I have a 13 z-step by 30 timepoint z-stack, where I want to correct for drift across time in all slices. Doing stackreg on each z-slice independently probably isn’t a great idea as there won’t be much structural information to use toward the edges of the stack. Note that I don’t need something to align slices in z at one time point; essentially what I want is to apply StackReg of the z-projection to each z-level of the stack across time (or some better computational method).Some things I’ve come across so far include:

-correct_3d_drift plugin, which I think theoretically does what I want, though the results on my stack weren’t great for xy drift correction. I may have included too many of the edge z-slices.
-multistackreg. I think this will do what I want as it’s essentially stackreg that saves out the transform, so I could write a macro that uses MultiStackReg on the z-projection to get the transform, then makes substacks at each z-slice of the original z-stack, applies the transform to each one, then re-stacks the slices.
-Poorman3DReg, looks like an old plugin and when I tried it it wouldn’t work on my computer, but theoretically this does what I’ve described with StackReg + apply to each z level.

Any input for existing solutions that would work better (or faster!) than this would be appreciated. Thanks.

1 Like
#2

Hi @fredtbn1gs

I introduce an Image Plugin “CoordinateShift”.
I hope you give it a try.

hwada

#3

Thanks. I’m not sure I understand how to make it do what I’m looking for. If I load a z-stack in the format of say, [t1 (z1-z13)] [t2 (z1-z13)] …[t30 (z1-z13)] it’s straightforward to hyperstack it correctly (c=1, t=30, z=13). Then to do the registration the way I’m looking for I’m not sure what I need to do. I assume click shift, but it’s not clear how to that works on the stack. Is there more documentation somewhere? Thanks.

#4

@fredtbn1gs ,

It’s a feature not described in the video.
I’ll write the procedure I envision, so please try it.

1, open the image as Hyperstack.(czt stacks)

2, click Project-Z button,

3, click Shift button,
if the registration is not good, you can retry, please click “Clear_All” and change Subpixel Value (1 to 10), or change selected ROI region and so on. Then click “Shift” again. *The projection is also canceled, so retry from 2.

4, If the registration is good, click “Split-Z” button. (The projection is released while maintaining the same shift amount for all z.)

I think this will achieve the purpose, how about it?
And, If you will upload a sample data, I can try.

hwada

#5

How is the shift calculated in your plugin? Is it using stackreg or something similar?

#6

Were you able to align your images?

I’m not sure what method stackreg is using, but it’s probably a different methdo. The accuracy seems to be higher in StackReg, but our method seems to be faster if the image is well aligned with our method.

hwada