stitching/registration

[Harald Hausen]

Is there a straightforward ImageJ tool for combining two confocal stacks, which overlap in z-direction?

To reduce intensity drop along z-axis we are imaging thick samples by recording first a stack A from the top down to ca. 2/3 of sample thickness. Then we turn the sample upside down and start imaging a stack B in the very same manner. As a result we get two image stacks (A and B) overlapping in z-direction. Is there a an ImageJ tool, which is able to combine such data into one smooth image stack?

Harald



 

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[Jitte Groothuis]

Hi Harald,

I use Stephan Preibisch' Pairwise Stitching plugin for the same purpose.

This works very well for any translation in x,y, *and* z. Unfortunately I
have not found a decent automated solution for any rotation of the sample,
so this is done manually for rotation around Z (for some samples I'm able
to hit it in 5', for others it's a painstaking process).

Keep in mind that one of your stacks will have to be reversed and flipped
to have the same orientation as the other (and make sure that the channel
order is still correct afterwards; in my case I have to use Arrange
Channels to switch the order back around).

Good luck,
Jitte

Jitte Groothuis, MSc

PhD Candidate

Wageningen UR

Laboratory for Entomology

P.O. Box 16, 6700 AA Wageningen

Wageningen Campus, building 107 (Radix)

Droevendaalsesteeg 1, 6708 PB Wageningen.

Tel. [phone] (desk)

Websites: LinkedIn <http://www.linkedin.com/pub/jitte-groothuis/41/36/376>
 / ResearchGate <http://www.researchgate.net/profile/Jitte_Groothuis/>


On 17 July 2014 13:33, Harald Hausen <[hidden email]> wrote:

> Is there a straightforward ImageJ tool for combining two confocal stacks,
> which overlap in z-direction?
>
> To reduce intensity drop along z-axis we are imaging thick samples by
> recording first a stack A from the top down to ca. 2/3 of sample thickness.
> Then we turn the sample upside down and start imaging a stack B in the very
> same manner. As a result we get two image stacks (A and B) overlapping in
> z-direction. Is there a an ImageJ tool, which is able to combine such data
> into one smooth image stack?
>
> Harald
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Stephan Preibisch]

Hi,

you can try out Plugins>Registration>Descriptor-based registration. For the rigid model you can specify an approximate rotation around an axis that it will take into account. If you use anything else than a Translation Model, make sure the calibration (voxel size in x,y,z) are correct.

Cheers,
Stephan

On Jul 17, 2014, at 9:12 , Jitte Groothuis <[hidden email]> wrote:

> Hi Harald,
>
> I use Stephan Preibisch' Pairwise Stitching plugin for the same purpose.
>
> This works very well for any translation in x,y, *and* z. Unfortunately I
> have not found a decent automated solution for any rotation of the sample,
> so this is done manually for rotation around Z (for some samples I'm able
> to hit it in 5', for others it's a painstaking process).
>
> Keep in mind that one of your stacks will have to be reversed and flipped
> to have the same orientation as the other (and make sure that the channel
> order is still correct afterwards; in my case I have to use Arrange
> Channels to switch the order back around).
>
> Good luck,
> Jitte
>
> Jitte Groothuis, MSc
>
> PhD Candidate
>
> Wageningen UR
>
> Laboratory for Entomology
>
> P.O. Box 16, 6700 AA Wageningen
>
> Wageningen Campus, building 107 (Radix)
>
> Droevendaalsesteeg 1, 6708 PB Wageningen.
>
> Tel. [phone] (desk)
>
> Websites: LinkedIn <http://www.linkedin.com/pub/jitte-groothuis/41/36/376>
> / ResearchGate <http://www.researchgate.net/profile/Jitte_Groothuis/>
>
>
> On 17 July 2014 13:33, Harald Hausen <[hidden email]> wrote:
>
>> Is there a straightforward ImageJ tool for combining two confocal stacks,
>> which overlap in z-direction?
>>
>> To reduce intensity drop along z-axis we are imaging thick samples by
>> recording first a stack A from the top down to ca. 2/3 of sample thickness.
>> Then we turn the sample upside down and start imaging a stack B in the very
>> same manner. As a result we get two image stacks (A and B) overlapping in
>> z-direction. Is there a an ImageJ tool, which is able to combine such data
>> into one smooth image stack?
>>
>> Harald
>>
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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