Re: Adjust resolution of "plot lanes" command

Posted by Luke Goodsell on Feb 24, 2010; 5:45pm
URL: http://imagej.273.s1.nabble.com/Adjust-resolution-of-plot-lanes-command-tp3689205p3689210.html

Sorry, Michael, that doesn't help. I close off the peak (as in the
attached "Picture 2.png"), double-click the wand tool, chose
"4-connected" and hit ok, and select the region under the peak ,but it
still selects the whole plot (as in the attached "Picture 1.png").
What am I doing wrong?

On Wed, Feb 24, 2010 at 5:38 PM, Michael Schmid <[hidden email]> wrote:

> Hi Luke
>
> set the Wand Options to "4-connected" (double click the Wand tool).
>
> Michael
> ________________________________________________________________
>
> On 24 Feb 2010, at 18:34, Luke Goodsell wrote:
>
>> Thanks for the response. This comes close to achieving what I'm after.
>> After setting it to vertical, with no grid lines and inverting my
>> image, I can see the kind of graph I'm after. However, when I try to
>> close a peak with the line tool and then use the wand tool to select
>> the area under the peak, the line I drew disappears and the wand tool
>> selects the entire plot (as in the attached image. Is it possible to
>> manually close a peak and then have ImageJ tell me the bound area?
>>
>> Many thanks,
>> Luke
>>
>> On Wed, Feb 24, 2010 at 4:21 PM, Gluender <[hidden email]> wrote:
>>>
>>> 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>
>>>
>