Image analysis on Unix - SUMMARY

Martin Ligr martin.ligr at po.uni-stuttgart.de
Sun Jun 23 15:33:14 EST 1996


Dr. Ernst Molitor <ernst at mibi03.meb.uni-bonn.de>,
Ken Clark <kwc at ibc.wustl.edu>, and
Reece Kimball Hart <reece at dasher.wustl.edu>
recomended DNA/DUI package, which can be found at:

http://www.ibc.wustl.edu/bcl/dnagui/dnagui_home.html

Dr. Ernst Molitor <ernst at mibi03.meb.uni-bonn.de> wrote this summary
about DUI:
I'd suggest to look into DNA-GUI, a most impressive program written by
people at the Biomedical Computer Laboratory, Washington State
University.  While not intended for use with sequencing gels, it is
very well suited for other gels. The program takes TIF-images (so
you'll need a video camera with equipment to store the pictures in
one of the large number of graphics formats, most of which can be
converted to TIF, or a scanner to convert conventional pictures into 
TIF files) and allows to process them in a very convenient manner. 

DNA-GUI needs two (or three) standard lanes (with one each on the left
and right margin of the gel); it detects the bands in the standard
lanes (manual corretions are possible) and normalizes the gel as
needed (that is, minor distortions that invariably occur every then
and now will be corrected). Next, the bands in the other lanes are
assigned by the program (again, with options for manual
correction). All bands detected (or marked manually) are saved,
ordered by the molecular weights calculated by DNA-GUI (from the
marker data it needs) for further use.
------
robert at BIO1.LAN.MCGILL.CA <robert at BIO1.LAN.MCGILL.CA> wrote:
Although I haven't tried it, NIH Image is supposed to run well under
Executor, which is a 
Mac emulator for Unix. I believe that Executor is public domain (I came
across it in a 
Compuserve library).
------
Joe Smith <jes at presto.med.upenn.edu> wrote:
NIH Image is reported to run on Executor, a Mac emulator, but that's
only for x86 PCs (DOS, Windows, OS/2, Linux & Nextstep).  See
<http://www.ardi.com> if this sounds feasible.  Perhaps there is a Mac
emulator for SGI.

Xv is a free Unix/X image viewer that can do simple image processing
(contrast, de-speckle, sharpen) but doesn't do any quantitation.

Image Magick is another free image viewer that can do simple image
adjustments.

AVI is a large commercial package that does everything.  Yes,
_everything_.  It's expensive but they do have more reasonable
academic licenses.

There are several general-purpose image processing libraries also, but
no simple application similar to NIH-image that I know of.
------
broveak at slip.net <broveak at slip.net>
I believe the BioImage software runs on Sun workstations.
Are you wedded to Unix?  Hitachi Software has a Mac image analysis
package
that is being used pretty heavily for sequencing gels and in the
forensics
area.  It was image the gel directly using fluorescents.
------

Thanks to all who responded, and special thanks to Ken Clark who has
helped me a great deal during the instalation of DUI.

Martin Ligr




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