how to combine several volumes into a single volume or save to a single .tif file?

[David Romano]

Hi everyone,

I'm new to ImageJ and am struggling to understand how to use it correctly:
I have several .tif files corresponding to volumes of identical dimensions,
and I can view them all simultaneously by loading them into the 3D Viewer
plugin, but I can't figure out how to save the result as a single .tif
file.   (Can one merge multiple volumes into a single volume somehow?)

I'd be grateful for any help with this question!

Thanks in advance,
David Romano

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[John Dunsmuir]

David,
           I use the 3D viewer menu item View->Take Snapshot.  You may need to update to the latest version of the viewer.  The Image->Stacks->Tools menus has several options for combining stacks.

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[David Romano]

Thank you, John; I tried your suggestions, but am still stumped:  For me,
'Take Snapshot' produces a 2D image, like a screenshot of what I see in the
3D Viewer window, but I'm trying to see if I can produce a single 3D volume
that corresponds to the multi-volume image I see in the 3D Viewer window.

I had also thought the items under Image->Stacks and Image->Hyperstacks
might be useful, but after spending a lot of time investigating them, I
can't get any of them to merge volumes.  From the User's Guide, the item
that seems the closest to what I'm looking for is
Image>Stacks>Tools>Insert, but when I insert, say, image1.tif into
image2.tif, this just overwrites image1.tif onto image2.tif (as images, not
files) rather than merging the images.  (For my purposes it would be fine
if only the nonzero voxels from image1.tif were overwritten onto
image2.tif.)

I also tried to use Process>Multiple Image Processor, but I get an error.

Any further thoughts, suggestion, or comments are welcome.

Thanks agian,
David

On Sat, Jun 8, 2013 at 6:26 PM, John Dunsmuir <[hidden email]> wrote:

> David,
>            I use the 3D viewer menu item View->Take Snapshot.  You may
> need to update to the latest version of the viewer.  The
> Image->Stacks->Tools menus has several options for combining stacks.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[John Dunsmuir]

David,
         I understand what you are trying to do a bit better now and I can't offer any help.  Maybe one of the authors will pick up this thread.

Regards,

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[David Romano]

Thanks, John, I appreciate your willingness to help; I think part of the
problem is just me not knowing enough about the philosophy behind ImageJ.

Best,
David

On Sun, Jun 9, 2013 at 5:58 PM, John Dunsmuir <[hidden email]> wrote:

> David,
>          I understand what you are trying to do a bit better now and I
> can't offer any help.  Maybe one of the authors will pick up this thread.
>
> Regards,
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Cammer, Michael]

It sounds like what you want to do is Image > Merge Channels... on the stacks before running the 3D visualization routine.

_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of John Dunsmuir [[hidden email]]
Sent: Sunday, June 09, 2013 8:58 PM
To: [hidden email]
Subject: Re: how to combine several volumes into a single volume or save to a single .tif file?

David,
         I understand what you are trying to do a bit better now and I can't offer any help.  Maybe one of the authors will pick up this thread.

Regards,

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[David Romano]

I'm not quite sure what a channel is, but this seems to help quite a bit!
The resulting composite image keeps the colors of the originals as long as
I display the composite as a volume, and, in contrast to when I tried
before to create surfaces from multiple images, the composite really is
treated as a single volume.  The only thing I'm not quite sure how to do
now is retain the original colors even after creating a surface.

Thanks, Michael!

David

On Sun, Jun 9, 2013 at 7:18 PM, Cammer, Michael
<[hidden email]>wrote:

> It sounds like what you want to do is Image > Merge Channels... on the
> stacks before running the 3D visualization routine.
>
> _________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] on behalf of John
> Dunsmuir [[hidden email]]
> Sent: Sunday, June 09, 2013 8:58 PM
> To: [hidden email]
> Subject: Re: how to combine several volumes into a single volume or save
> to a single .tif file?
>
> David,
>          I understand what you are trying to do a bit better now and I
> can't offer any help.  Maybe one of the authors will pick up this thread.
>
> Regards,
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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