Posted by
George McNamara on
URL: http://confocal-microscopy-list.275.s1.nabble.com/software-tp590473p590474.html
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocalHi Carl,
One of the earliest commercial software packages for doing this is
Meyer Instruments In-Focus,
http://www.meyerinst.com/html/oem/in-focus/default.htm (see
especially the 4 PDFs at bottom), which can optionally run a Leica
stereomicroscope Z-motor (ran inside Image Pro+, check with them on
whether it can be automated to churn through a bizillion Z-series).
Meyer also has a leica stereomicroscope turret for putting the macro
lens directly under one of the stereo lenslets, to generate vertical
views (and could have 2 macro lenses on the scope - a handy feature
since duplicated by various stereo manufacturers). One of the faculty
members at my place told me that Zeiss AxioVision has a software
module for aligning slices on a conventional stereo Z-series (she
also pointed out that the fly specimen used on the Meyer web site was
severely desiccated).
In addition to the other listserv responses, check out
http://www.dipteristsforum.org.uk/deepfocus/DeepFocus.pdf and
Goldsmith 2000 Image Analysis & Stereology, Deep Focus,
http://www.wise-t.com/ias/article.php?id=29&year=2000&issue=11
(free access for both Goldsmith and a 2007 article - maybe we should
all be publishing here).
Reindeer Graphics, the makers of the Fovea Pro plugin for Photoshop
also offer Focus Extender,
http://www.reindeergraphics.com/index.php?option=com_content&task=view&id=29&Itemid=52
The principle of all (or at least most) of these packages is the
same: run a variance filter on each plane in the stack; go through
the computed variance stack to find the highest variance plane for
each "sub-image"; use that sub-image as the result. Some of the
better software must keep track of adjacent sub-images and blend
results to make the result look nicer. Sadly, most vendors do not
implement the direct outputting of the variance data (MetaMorph may
still lack a variance command for example) or the plane number of the
selected sub-image.
George
p.s. Meyer's In-Focus worked much better than MetaMorph (version
5.0), circa 2003.
At 07:34 PM 10/5/2007, you wrote:
>Search the CONFOCAL archive at
>
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal>
>Dea all,
>Does anyone know of software that selects only in focus portions of
>an image and discards the out-of-focus parts. We need to get clear
>views of a curved surface (the fly eye) with a 10x objective using
>reflected light. Only thin optical slices are in focus at this mag,
>but if we could put together the portions that are in focus over the
>entire depth of the specimen, we could rebuild a clean image of the
>structure. This wouild be a used in an assay screening a bizillion
>flies, so SEM is not really practical.
>thanks,
>Carl
>
>Carl A. Boswell, Ph.D.
>Molecular and Cellular Biology
>University of Arizona
>520-954-7053
>FAX 520-621-3709
George McNamara, Ph.D.
University of Miami, Miller School of Medicine
Image Core
Miami, FL 33010
[hidden email]
[hidden email]
305-243-8436 office
http://home.earthlink.net/~pubspectra/http://home.earthlink.net/~geomcnamara/http://www.sylvester.org/health_pro/shared_resources/index.asp (see
Analytical Imaging Core Facility)