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Re: Adjust resolution of "plot lanes" command

Posted by Gluender-3 on Feb 24, 2010; 4:21pm
URL: http://imagej.273.s1.nabble.com/Adjust-resolution-of-plot-lanes-command-tp3689205p3689212.html

Luke,

it's much clearer now: you're concerned about the amplitude (gray-value).

I'm not familiar with the built in gel-analysis
but it should be based on profile plots. That
said, I recommend to do the following:

1.
Go to menu item "Edit > Options > Profile Plot
Options" set the desired window dimensions of the
plot window. In your case set Height to perhaps
your screen height or even higher.

2.
Make a suitable rectangular selection for the lane of interest.

3.
Go to menu item "Analyze > Plot Profile"

Is the plot you get better?

Now you may even have a look at the amplitude
values, if you click "List" in the plot window.

>Hi Herbie, thanks for your response.
>
>The 'resolution' I'm referring to is that of the graph images produced
>by the 'plot lanes' operation. The width is the same as that of
>selection height on my image, which is fine, but the height is a
>constant value with the height of the peaks scaled according to the
>highest peak. However, I'm using chemiluminescence and a 16bit tif, so
>my peak heights can vary considerably. When I try to quantify a small
>peak, I cannot accurately draw the baseline on the peak as it is only
>a couple of pixels high. Zooming in on the graph just magnifies the
>pixels of the graph, offering no increase in accuracy.
>
>I would like to be able to increase the (seemingly hard-coded) height
>of the graphs produced to be more useful for 16 bit images. Is this
>possible?
>
>Many thanks,
>Luke
>
>On Wed, Feb 24, 2010 at 2:47 PM, Gluender <[hidden email]> wrote:
>>  Luke,
>>
>>  not quite sure what the real problem is...
>>
>>  First, there is the spatial resolution of your images.
>>  This resolution will determine most of your post-processing. If it is to
>>  low, then you have to increase it by scanning/capturing parts.
>>  Do you scan the lanes or do you use a camera?
>>
>>  Second, there is the spatial resolution of your profile graphs (x-axis).
>>  This resolution at best can be the same as the spatial resolution of your
>>  images.
>>  It may however be smaller. You may change it in Menu-Item "Profile Plot
>>  Options".
>>
>>  Finally there is the amplitude (gray-value) resolution of your images as
>>  well as your profile plots (y-axis). 8 bits means 255 values different zero
>>  and under all circumstances your profile graph can't show more. Plot
>>  amplitude resolution may also be changed in Menu-Item "Profile Plot
>>  Options".
>>
>>  That said you may give us a little more information about your desires.
>>
>>>  Hi,
>>>
>>>  I am trying to quantify my westerns but am having difficulty because
>>>  the resolution of the graphs output by the "plot lanes" command is too
>>>  low. I have a number of bands of a wide range of concentrations so the
>>>  smallest bands have small peaks in the graphs, making it impossible to
>>>  place the baseline accurately. I assumed the zoom tool would help, but
>>>  that just, err, makes the pixels bigger - sorry, I don't know how to
>>>  describe it. I also tried using multiple selections in the same lane,
>>>  but then the areas of the graphs are not comparable because they have
>>>  been scaled differently. I've attached an example of the graphs I get.
>>>
>>>  I searched Google and the mailing list archives, and I saw at least
>>>  one person mention this as a side issue, but no one addressed it.
>>>
>>>  Is it possible to change the resolution/size of the graphs output by
>>>  the "plot lanes" command so that I can zoom in and accurately define
>>>  the baseline?
>>>
>>>  Many thanks,
>>>  Luke
>>>
>>>  Content-Type: image/png; name="Picture 1.png"
>>>  Content-Disposition: attachment; filename="Picture 1.png"
>>>  X-Attachment-Id: f_g627gugk0
>>>
>>>  Attachment converted: Download:Picture 1 3.png (PNGf/«IC») (0001832A)
>>
>>  Best
>>  --
>>
>>                   Herbie
>>
>>          ------------------------
>>          <http://www.gluender.de>
>>

HTH
--

                   Herbie

          ------------------------
          <http://www.gluender.de>