gel analysis

Posted by Peter Frenzel on
URL: http://imagej.273.s1.nabble.com/gel-analysis-tp3703740.html

Dear List,

I’m analysing DGGE-gels but doing the numerical analysis (baseline
subtraction, peak detection etc) externaly using R
(http://cran.r-project.org/).

ImageJ’s "Analyze-Gels" is great, but has a graphical output and no
(obvious) access to the numerical data.
As a work-around I rotated the gels to orient the lanes horizontally, marked
the first lane with a rectangular ROI, analysed with "Analyze-Plot Profile",
and got the plot values with "List". From here I saved the date to import it
to R. After moving the ROI with the arrow keys, the process was repeated.
In summary, it works, but with many lanes and/or gels it can be quite
tedious.

I would appreciate very much any support to improve the overall procedure.

(i) If the lanes are not perfectly perpendicular to the edge of the image, I
rotate the image accordingly before analysis. The Angle-Tool allows to
measure arbitrary angles, but not directly the deviation of an arbitraty
line from from a horizontal line. A solution like that in Photoshop would be
great (in Photoshop: draw any line with the Measure-Tool, do
Image-Rotate-Arbitrary, and the deviation of the arbitrary from a horizontal
line is offered as default for rotation).

(ii) Making the process of gel analysis faster e.g. by adding a table output
to Analyze-Gels. N.b.: I’m requesting a table of the x/y data and NOT of
peak areas.

Kind regards,

Peter