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This particular dataset was BioRad multiphoton, but I think the question
is general since most systems can save in TIFF format.
Sarah
-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]] On
Behalf Of Haydar, Tarik
Sent: Tuesday, May 11, 2004 9:03 AM
To: [log in to unmask]
Subject: Re: 3D montage clarification
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What system was used to take the z-stacks?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Tarik Haydar, Ph.D.
Center V-Neuroscience, Suite 5346
Children's Research Institute, CNMC
Assistant Professor of Pediatrics and Pharmacology
George Washington University School of Medicine
111 Michigan Ave., N.W.
Washington, D.C. 20010
p:202-884-2383
f:202-884-4988
e:[log in to unmask]
-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]] On
Behalf Of Locknar, Sarah A
Sent: Tuesday, May 11, 2004 8:56 AM
To: [log in to unmask]
Subject: Re: 3D montage clarification
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OK, I guess my first message was not clear. The data is several
z-stacks that we want to align in x, y, and z. Currently she makes
projections of each (losing the z-information) and makes a montage in
photoshop. We're looking for a way to PRESERVE the z-information so the
entire combined data set can be rotated in 3-dimensions. I guess this
would be the equivalent of "stitching" in 3-D. Does that help? Any new
ideas? Thanks again- Sarah
-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]] On
Behalf Of Joel Sheffield
Sent: Monday, May 10, 2004 4:52 PM
To: [log in to unmask]
Subject: Re: 3D montage
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It sounds to me as if you want to make a 3d rendering of a stack. In
ImageJ, and several other image processing programs, it is possible to
set a level of transparency and then "stack" the images in such a way
that the composite can be rotated. There are several levels of this
kind of processing. You can construct what is conceptually a set of
plexiglas sheets each of which has an image on it. Then, you can take
this "stacked" structure and rotate it.
Alternatively, you can select some level of intensity, and draw
polygons that connect all areas in the stack, and then fill in the
polygons to create a surface. This process is generally called Volume
rendering. Again, there is a plugin in Imagej that does a remarkable
job of this.
Joel Sheffield
>
> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-
> bin/wa?S1=confocal Hi Sarah, I"m not clear what is being asked
> here.The original meaning of "montage" meant showing an image stack
> presented in a series of rows and/or columns, yes? In that case,
> MetaMorph and ImageJ do this readily. Compix, on the other hand, uses
> the term to mean a projection, or making a single imageby combingall
> the images in the stack.Are you asking can one make a montage of
> several image stacks, with each stack representing one frame in the
> montage? Thanks, Carl
>
>
>
> Carl Boswell
> Dept. of Molecular and Cellular Biology
> Univ. of Arizona
> 520-626-8469
> 520-621-3709 FAX
> ----- Original Message -----
> From: Locknar, Sarah A
> To: [log in to unmask]
> Sent: Monday, May 10, 2004 12:15 PM
> Subject: 3D montage
>
> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-
> bin/wa?S1=confocal Hi- Does anyone know of a program that will create
> a 3D montage of image stacks? The only thing I can think of right now
> is for the user to create montages in photoshop, save each montage
> slice as a tiff and then open them as a stack in some 3D rendering
> program. Any ideas about an easier way to do this? Thanks- Sarah
>
> ----------------------------------------------------------------------
> ----------------- Sarah Locknar, Ph.D. Director, Neuroscience COBRE
> Imaging / Physiology Core College of Medicine, University of Vermont
> E015 Given Building 89 Beaumont Ave. Burlington, VT 05405 802-656-0413
> 802-656-8704 (fax)
> ----------------------------------------------------------------------
> -----------------
>
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[log in to unmask]
(215) 204 8839, fax (215) 204 0486
http://astro.temple.edu/~jbs
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