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Stephen,

We do this all the time to make animations and 3D reconstructions.

However, I do not use Macs so some of my suggestions may not work.
Why don't you use Photoshop for the whole process? We put all the images on
separate layers and then adjust the opacity of the layers while aligning
them. You can move the layers and rotate them quite easily.

We then save all the layers as images and convert them to animations using
Macromedia's Fireworks. I think Adobe ImageReady would do the same job and
is closely integrated with Photoshop.

Amira has a utility to align images but it is expensive for what you want
and I am not aware of a Mac version.

Hope that helps.

John




Dr. John Cork
Associate Professor of Anatomy,
Computer Imaging Lab.,
Dept. of Cell Biology & Anatomy,
LSUHSC, New Orleans, LA 70112

Tel (504) 568 7177  Fax (504) 568 4392

-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]] On
Behalf Of Stephen C. Kempf
Sent: Tuesday, January 18, 2005 3:15 PM
To: [log in to unmask]
Subject: Image registration

Search the CONFOCAL archive at
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This is not exactly a confocal question, but I suspect some of the
readers
of our list may have some useful suggestions.

I have a series of standard light microscope images of stained serial
plastic sections of a larva I am interested in. I would like to assemble
these into a quicktime movie so that I can easily track organ systems
through the larva.

In order to do this, I have to rotate and adjust the position  of each
image relative to one I choose as the "key" image so that all the images
are in proper registration with each other.

I currently do this by using two programs, Web painter and Photoshop.
Web
painter allows me to assemble all the images into a series of sequential
frames such that the "previous" or "next" frame can be layered onto the
currently viewed frame as a transparent image that they call an "onion
skin". This allows me to determine what has to be done to the current
image to get it in registration with the previous or next image. Once
all
the registration is completed, the entire sequence can be converted to a
quicktime movie.

Unfortunately, making rotation adjustments doesn't work very well in
WebPainter, so I transfer the image to photoshop, rotate it there, then
transfer it back to WebPainter and check to see if the rotation is
correct
or if further adjustment is needed. If so, I repeat the process.

This, of course, is rather tedious and time consuming.

I would be very interested in any suggestions on a better way to do all
this. My lab is MacIntosh OS X based, so programs for the Mac would be
most useful.

Thank you for any suggestions,

Steve Kempf

Stephen C. Kempf
E-mail: [log in to unmask]
Associate Professor
Tel: 334-844-3924
Fax: 334-844-4065
Faculty Director, AU Hybridoma Facility
Department of Biological Sciences
331 Funchess Hall
Auburn University, AL  36849