Registration, xy-drift correction and pixel values

[PabloSAguilar]

Hi there,

I have time series where there is a XY-drift over time. To align the time slices I tried:
-TurboReg
-Image Stabilizer
-Register Virtual Stack Slices

In all three cases the drift was nicely corrected, objects look static, but the resulting intensity pixel values are changed.
Since I need to use the registered images for intensity quantification I'd like to know if any of you
knows how to perform registration with these (or other) plugins keeping original pixel values,
thanks!
Pablo

[Saalfeld, Stephan]

Hi Pablo,

I guess you want it to interpolate by nearest neighbor instead of
n-linear or other interpolation schemes.  The plugin

http://fiji.sc/Transform_Virtual_Stack_Slices

can read transformations previously calculated by

http://fiji.sc/Register_Virtual_Stack_Slices

and it has a checkbox to toggle interpolation, uncheckit to have
nearest-neighbor (only pre-existing intensity values).  Keep in mind
that his measn that you cannot correct for sub-pixel drift (the
transformation is sub-pixel, but the rendered result is either on one or
the other pixel.

Best,
Stephan


On Tue, 2014-03-25 at 05:54 -0700, PabloSAguilar wrote:

> Hi there,
>
> I have time series where there is a XY-drift over time. To align the time
> slices I tried:
> -TurboReg
> -Image Stabilizer
> -Register Virtual Stack Slices
>
> In all three cases the drift was nicely corrected, objects look static, but
> the resulting intensity pixel values are changed.
> Since I need to use the registered images for intensity quantification I'd
> like to know if any of you
> knows how to perform registration with these (or other) plugins keeping
> original pixel values,
> thanks!
> Pablo
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Registration-xy-drift-correction-and-pixel-values-tp5007073.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--

Stephan Saalfeld, Ph.D.
Group Leader
Janelia Farm Research Campus
19700 Helix Drive | Ashburn, VA 20147
Phone: [phone] | Fax: [phone]
[hidden email]

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[PabloSAguilar]

Thanks a lot Stephan!
Pablo