alignment with whole pixel shift

[Glen MacDonald-2]

Hello,
Are there any plugins that will align a time-lapse stack with whole pixel shifts, thereby avoiding interpolation of intensities?   I'm needing to align some time-lapse images in order to measure intensities.  Sub-pixel precision is not necessary.  so far, searching the list server and plugin websites have not provided any answers.

Thanks,
glen


Glen MacDonald
Cellular Morphology Core
Center for Human Development and Disability
Box 357920
University of Washington
Seattle, WA 98195-7920  USA
[phone]
[hidden email]

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[Stephan Saalfeld]

Hi Glen,

to avoid interpolation, just switch it off.  It does not matter whether
an alignment method estimates a sub-pixel translation if only it renders
the result by nearest-neighbor interpolation.  In Fiji's Register
Virtual Stack Slices and Linear Stack Alignment with SIFT, you can
uncheck `interpolation'.

Best,
Stephan





On Wed, 2012-08-15 at 11:37 -0700, Glen MacDonald wrote:

> Hello,
> Are there any plugins that will align a time-lapse stack with whole pixel shifts, thereby avoiding interpolation of intensities?   I'm needing to align some time-lapse images in order to measure intensities.  Sub-pixel precision is not necessary.  so far, searching the list server and plugin websites have not provided any answers.
>
> Thanks,
> glen
>
>
> Glen MacDonald
> Cellular Morphology Core
> Center for Human Development and Disability
> Box 357920
> University of Washington
> Seattle, WA 98195-7920  USA
> [phone]
> [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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

[Glen MacDonald-2]

HI,
that does work.  I had been mostly using StackReg, since it has a simple interface gave consistent results with prior datasets.  But SIFT seems to align these time stacks well.  I will need to become familiar with its parameters.


Thanks,
Glen

> Hi Glen,
>
> to avoid interpolation, just switch it off.  It does not matter whether
> an alignment method estimates a sub-pixel translation if only it renders
> the result by nearest-neighbor interpolation.  In Fiji's Register
> Virtual Stack Slices and Linear Stack Alignment with SIFT, you can
> uncheck `interpolation'.
>
> Best,
> Stephan
>
>
>
>
>
> On Wed, 2012-08-15 at 11:37 -0700, Glen MacDonald wrote:
>> Hello,
>> Are there any plugins that will align a time-lapse stack with whole pixel shifts, thereby avoiding interpolation of intensities?   I'm needing to align some time-lapse images in order to measure intensities.  Sub-pixel precision is not necessary.  so far, searching the list server and plugin websites have not provided any answers.
>>
>> Thanks,
>> glen
>>
>>
>> Glen MacDonald
>> Cellular Morphology Core
>> Center for Human Development and Disability
>> Box 357920
>> University of Washington
>> Seattle, WA 98195-7920  USA
>> [phone]
>> [hidden email]
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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