Ratio image stack alignment

[TimFeinstein]

Hello,

In processing time-lapse images of a ratiometric biosensor, I found that cells sometimes move to a confounding degree.  I split the channels and applied StackReg to each channel separately, but in this case it sometimes results in the two colors diverging over time as the algorithm aligns them separately.  Does anyone know how to either (1) align multicolor 16-bit (hyper)stacks as a unit, or (2) apply an alignment matrix calculated for one stack to one or more subsequent stacks?

Thanks in advance,


Tim

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology


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[Jan Eglinger]

Hi Tim,

The MultiStackReg plugin [1] allows to register multiple stacks (and to
reapply a measured transformation to other stacks).

Here's the link to the current release:
https://github.com/cmci/MultiStackRegistration/releases

And here's a related discussion on the ImageJ forum:
http://forum.imagej.net/t/multistackreg-macro/174?u=imagejan

Jan

[1]: https://github.com/cmci/MultiStackRegistration/


On 15.03.2016 19:08, Feinstein, Timothy N wrote:
> Hello,
>
> In processing time-lapse images of a ratiometric biosensor, I found that cells sometimes move to a confounding degree.  I split the channels and applied StackReg to each channel separately, but in this case it sometimes results in the two colors diverging over time as the algorithm aligns them separately.  Does anyone know how to either (1) align multicolor 16-bit (hyper)stacks as a unit, or (2) apply an alignment matrix calculated for one stack to one or more subsequent stacks?
>
> Thanks in advance,
>
>
> Tim

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