3D using Stack Focusser?

Posted by Joel Sheffield on Apr 21, 2011; 7:23pm
URL: http://imagej.273.s1.nabble.com/3D-using-Stack-Focusser-tp3684866.html

Colleagues,

Here's an interesting challenge.  As I understand it, both the 3D Viewer or
the 3D rotation utility built into ImageJ work on some form of an algorithm
in which the relative positions of the slices in a stack are shifted
relative to each other, and then a Maximum projection is generated, creating
a new view through the shifted stack.  We have been looking at the DIC
stacks that are generated either with confocal or manual DIC systems, which
also have optical slices.  However, when we try a standard Max projection,
the resultant is a mess, since the criteria for inclusion are not intensity,
but contrast.  On the other hand, we have been able to use the Stack
Focuser  plugin to create "flattened" images of these stacks so that all
components remain in focus.  I am wondering if it is possible to use an
image shift algorithm similar to the one for transparent fluorescent objects
to generate a rotating, or at least a simple stereo view of such DIC
samples.

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Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs