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Sarah,
I will again point out that the latest release of Image-Pro Plus includes a
new Automatic Tiling module which can uses Fouier analysis or user defined
shifts to align images into a tile. It would be very easy to develop a
macro which calculates the alignment based on a known goos section (such as
the middle plane of the stack) and then iterates through the the planes
generateing a new set of montage images (one of each plane of the original z
Stacks). This method is based on the assumption that all of the stacks have
the same number of z planes in the same positions. It could be adapted
(with some book keeping) to match up planes in the same positions, if the
stacks have different numbers of planes, but I would recommend that you take
the simple step during image acquisition to insure that the only variation
from one stack to the next is its XY position. Links to our web sites are
in my signature.
Chris Tully
Senior Technical Services Engineer and Quality Assurance Analyst
Media Cybernetics, Inc. "From Images to Answers"
8484 Georgia Avenue, Suite 200
Silver Spring, MD 20910
Tel: +1 (301) 495-3305 ext. 3 Fax: +1 (301) 495-5964
E-mail: [log in to unmask]
Websites: http://www.MediaCy.com
http://Support.MediaCy.com
http://www.Solutions-Zone.com
http://Shop.MediaCy.com
-----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: [CONFOCAL] 3D montage clarification
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
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
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
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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