questions about grid stitching

[Aryeh Weiss]

I have two questions about this plugin:

First - I have a set of XYZ stacks that I am stitching.

I would like the stitching to be done only in the xy directions, but not
in Z. That is, even if the stitcher thinks that a stack should be
shifted in Z, I do not want that to happen. I though that selecting the
"Ignore Z- stage position" would do this, but it turns out that even
with that option stacks are shifted in the Z direction.

Is there a way to prevent this. I have the ROIs in the ROI manager, but
I do not want to write my own fusion program to fuse the stacks.

Second - when I select "downsample tiles", the stitching does something
strange. It puts all of my grid of tiles in on row. When I do nto
down-sample, with all else the same, it works as expected. Do I
misunderstand what the downsample option does? I was trying ot use it to
same space on a really large stitched image.

Tnx in advance for your help,

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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

[ctrueden]

Hi Aryeh,

> I would like the stitching to be done only in the xy directions, but not
in Z.

Did you try this?
http://imagej.net/Image_Stitching#I_want_to_ignore_the_movement_of_tiles_in_Z

> Second - when I select "downsample tiles", the stitching does
> something strange. It puts all of my grid of tiles in on row.

Sounds like a bug. You can file an issue here:
   https://github.com/fiji/Stitching/issues

It would be helpful to list the settings you used which produced the
problem.

Sorry to say I might not have time to investigate the issue right away.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Aug 10, 2016 at 1:54 PM, Aryeh Weiss <[hidden email]> wrote:

> I have two questions about this plugin:
>
> First - I have a set of XYZ stacks that I am stitching.
>
> I would like the stitching to be done only in the xy directions, but not
> in Z. That is, even if the stitcher thinks that a stack should be shifted
> in Z, I do not want that to happen. I though that selecting the "Ignore Z-
> stage position" would do this, but it turns out that even with that option
> stacks are shifted in the Z direction.
>
> Is there a way to prevent this. I have the ROIs in the ROI manager, but I
> do not want to write my own fusion program to fuse the stacks.
>
> Second - when I select "downsample tiles", the stitching does something
> strange. It puts all of my grid of tiles in on row. When I do nto
> down-sample, with all else the same, it works as expected. Do I
> misunderstand what the downsample option does? I was trying ot use it to
> same space on a really large stitched image.
>
> Tnx in advance for your help,
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Aryeh Weiss]

HI Curtis

Thank you for your reply.

On 10/08/2016 10:14 PM, Curtis Rueden wrote:
> Hi Aryeh,
>
> > I would like the stitching to be done only in the xy directions, but
> not in Z.
>
> Did you try this?
> http://imagej.net/Image_Stitching#I_want_to_ignore_the_movement_of_tiles_in_Z
>
Perfect. Thank you for pointing this out.
> > Second - when I select "downsample tiles", the stitching does
> > something strange. It puts all of my grid of tiles in on row.
>
> Sounds like a bug. You can file an issue here:
> https://github.com/fiji/Stitching/issues
>
> It would be helpful to list the settings you used which produced the
> problem.
>
Done.
> Sorry to say I might not have time to investigate the issue right away.
>
No problem. Your efforts are greatly appreciated.

Best regards
--aryeh

> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Aug 10, 2016 at 1:54 PM, Aryeh Weiss <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     I have two questions about this plugin:
>
>     First - I have a set of XYZ stacks that I am stitching.
>
>     I would like the stitching to be done only in the xy directions,
>     but not in Z. That is, even if the stitcher thinks that a stack
>     should be shifted in Z, I do not want that to happen. I though
>     that selecting the "Ignore Z- stage position" would do this, but
>     it turns out that even with that option stacks are shifted in the
>     Z direction.
>
>     Is there a way to prevent this. I have the ROIs in the ROI
>     manager, but I do not want to write my own fusion program to fuse
>     the stacks.
>
>     Second - when I select "downsample tiles", the stitching does
>     something strange. It puts all of my grid of tiles in on row. When
>     I do nto down-sample, with all else the same, it works as
>     expected. Do I misunderstand what the downsample option does? I
>     was trying ot use it to same space on a really large stitched image.
>
>     Tnx in advance for your help,
>
>     --aryeh
>
>     --
>     Aryeh Weiss
>     Faculty of Engineering
>     Bar Ilan University
>     Ramat Gan 52900 Israel
>
>     Ph:  972-3-5317638
>     FAX: [phone]
>
>     --
>     ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>     <http://imagej.nih.gov/ij/list.html>
>
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


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