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NIH Imaging software

Carlisle Landel landel at helios
Fri Jul 22 10:46:04 EST 1994

In article <CtCIGA.F2M at demon.co.uk>,
Anthony Tomlinson  <anthony at pplros.demon.co.uk> wrote:
>I am interested in any software for the Mac that can calibrate
>gels/autorads so that molecular weights are calculated from band
>mobilities using MW markers present on the image.  This is so that I can
>eliminate my own incompetence with a ruler from data I am collecting from
>repeated reprobings of a single Southern blot.  Somebody out there is
>going to reply: "Use GelReader!" to which I reply "How?!"  I can't get it
>to work, even when I follow the instructions to the letter.  Generating
>the template seems to be the problem; if anyone has specific tips on
>that, I'll be eternally grateful.
>Anthony Tomlinson.

Somebody in my lab found a message in bionet.software from
mangalam at SALK-SC2.SDSC.EDU (Harry Mangalam) describing bugs
in GelReader.  Basically, the trick is that you *must* have 
a lane of standards on each side of your samples for the thing
to work.

I've tried using it, and it is still a bit buggy, mostly in that
I have a hard time getting it to see all my bands:  if there are
a bunch of small faint bands, upping the sensitivity of the image
capture program causes the bright large bands to run together, so
that the program can't differentiate them, while not doing so
causes it to miss the faint ones.  Also, if you have bands that
are close together (eg the top of a 1 kb ladder), it seem to want
to assign differing numbers of bands to the ladder each time it looks
at it, which is definitely a pain when you are setting up your file
of size markers.

So I was wondering, does anybody know of a program out there that will
take manually entered restriction fragment size data and assemble it
into a map for you?  I'm busy slogging through some mapping of
some cosmids, and since GelReader isn't working for me (too many bugs
in my hands) I thought I'd try something else.


Carlisle Landel

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