Adjust resolution of "plot lanes" command

[Luke Goodsell]

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

[Gluender-3]

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>

[Luke Goodsell]

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>
>

[Gluender-3]

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>

[Luke Goodsell]

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>
>

[Michael Schmid]

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>
>>

[Luke Goodsell]

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>
>>>
>

[Gluender-3]

Luke,

ok, what you want is a bit unusual, but if you are happy with that
kind of measure, you may try to really "draw" a line to close peaks.

1.
Choose the straight line tool and draw the closing line that appears
as a line selection, i.e. commonly in yellow with three handles that
may serve for fine tuning the line's length, angle and position.

2.
Now choose "Draw" from the "Edit Menu" and the line will be drawn in
the current foreground colour, that in your case should be black.

3.
Click somewhere to deselect or chose "Edit > Selection > Select None"
and you should see the drawn line.

4.
Finally use the wand tool to select the area.

Furthermore, I should recommend to study the ImageJ manual to get an
idea of ImageJ's features.

>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

HTH
--

                   Herbie

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

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

On Feb 24, 2010, at 9:13 AM, Luke Goodsell wrote:

> 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?

The Analyze>Gels>Gel Analyzer Options dialog in the 1.43r12 daily build allows you to enter scale factors for enlarging the plots.

-wayne