NIH Imaging software

[Nigel Eastmond]

Carlisle Landel (landel at helios) wrote:
: 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.

: Thanks,

: Carlisle Landel

Well we have a nice bit of software by BioRad which does that.  The catch is
that it only works for Phosphor images captured on a Pounds Sterling 40,000
machine.