Gel analyzer - lane profiles

[Knauf, Anke (NIH/NIAID) [F]]

Hi,

I was wondering if anyone could explain how the Gel Analyzer plugin actually generates the lane profiles? How does it convert the 2dim data from the blot into a 1dim intensity profile? Does this involve an intensity sum over all pixels in the lane, or is it a maximum projection or something else?

Thanks,
Anke.

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[Rasband, Wayne (NIH/NIMH) [E]]

On May 28, 2014, at 11:16 AM, Knauf, Anke (NIH/NIAID) [F] wrote:

> Hi,
>
> I was wondering if anyone could explain how the Gel Analyzer plugin actually generates the lane profiles? How does it convert the 2dim data from the blot into a 1dim intensity profile? Does this involve an intensity sum over all pixels in the lane, or is it a maximum projection or something else?

The Gel Analyzer sums the pixel values along each line in the lane. The following macro duplicates what it does.

-wayne

   getSelectionBounds(xbase, ybase, width, height);
   values = newArray(height)
   for (y=ybase; y<ybase+height; y++) {
      sum = 0;
      for (x=xbase; x<xbase+width; x++)
         sum += getPixel(x,y);
      values[y-ybase] = sum/width;
   }
   Plot.create("Profile", "X", "Y", values)

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