Problems with Plot lane window

[Olaku, Vivienne]

Hi ImageJ users,

I am new to using the Analyze-Gel for measuring the band intensities in western blots. I mark each lane from left to right with the Select First Lane and then Select Next Lane. However once I go to "Plot Lanes" the figure comes up extremely narrow and long, each lane is shown in the plot one under the other (I typically have 4 lanes). I see only part of the plot (even the word Figure in the plot is cut off to Figu). If it helps the pixels in the plot figure are 28x618. I have tried to resize the canvas/size in Image-Adjust-Canvas size and Image-Adjust-Size. The latter just stretches what I already see on the plot.
I have the ImageJ 1.42q for MACS but the I had this problem with the previous version. Please help!

Vivienne

[Jonathan Hilmer]

The problem you see is because GelAnalyzer is expecting the longest
axis of your selection to be x-axis of the resulting plot, and the
shorter axis will be the averaged/summed (can't recall which) data to
generate the y-axis.

The easiest way to solve your problem as you have it here is to make
your selections taller on the original image.  Then everything should
look the way you expect.  That will also make it easier accurately
define baseline.  I would also recommend extending your selections in
the horizontal direction to include as much as the band as possible,
ideally extending directly to the center of area between bands,
between lanes.


Jonathan


On Fri, Oct 9, 2009 at 7:37 AM, Olaku, Vivienne
<[hidden email]> wrote:
> Hi ImageJ users,
>
> I am new to using the Analyze-Gel for measuring the band intensities in western blots. I mark each lane from left to right with the Select First Lane and then Select Next Lane. However once I go to "Plot Lanes" the figure comes up extremely narrow and long, each lane is shown in the plot one under the other (I typically have 4 lanes). I see only part of the plot (even the word Figure in the plot is cut off to Figu). If it helps the pixels in the plot figure are 28x618. I have tried to resize the canvas/size in Image-Adjust-Canvas size and Image-Adjust-Size. The latter just stretches what I already see on the plot.
> I have the ImageJ 1.42q for MACS but the I had this problem with the previous version. Please help!
>
> Vivienne
>

[Robert Baer]

You need to delineate the peak areas by using the line drawing tool and wand
tool from this image, but it is not necessary to have the whole image on the
screen at once.  The way to accomplish your task is to select the hand tool
and move the part of the image of interest onto the screen lane by lane.




----- Original Message -----
From: "Olaku, Vivienne" <[hidden email]>
To: <[hidden email]>
Sent: Friday, October 09, 2009 8:37 AM
Subject: Problems with Plot lane window


Hi ImageJ users,

I am new to using the Analyze-Gel for measuring the band intensities in
western blots. I mark each lane from left to right with the Select First
Lane and then Select Next Lane. However once I go to "Plot Lanes" the figure
comes up extremely narrow and long, each lane is shown in the plot one under
the other (I typically have 4 lanes). I see only part of the plot (even the
word Figure in the plot is cut off to Figu). If it helps the pixels in the
plot figure are 28x618. I have tried to resize the canvas/size in
Image-Adjust-Canvas size and Image-Adjust-Size. The latter just stretches
what I already see on the plot.
I have the ImageJ 1.42q for MACS but the I had this problem with the
previous version. Please help!

Vivienne

[Olaku, Vivienne]

Thanks, I'll give that a try.


-----Original Message-----
From: ImageJ Interest Group on behalf of Robert Baer
Sent: Sat 10/10/2009 6:12 PM
To: [hidden email]
Subject: Re: Problems with Plot lane window
 
You need to delineate the peak areas by using the line drawing tool and wand
tool from this image, but it is not necessary to have the whole image on the
screen at once.  The way to accomplish your task is to select the hand tool
and move the part of the image of interest onto the screen lane by lane.




----- Original Message -----
From: "Olaku, Vivienne" <[hidden email]>
To: <[hidden email]>
Sent: Friday, October 09, 2009 8:37 AM
Subject: Problems with Plot lane window


Hi ImageJ users,

I am new to using the Analyze-Gel for measuring the band intensities in
western blots. I mark each lane from left to right with the Select First
Lane and then Select Next Lane. However once I go to "Plot Lanes" the figure
comes up extremely narrow and long, each lane is shown in the plot one under
the other (I typically have 4 lanes). I see only part of the plot (even the
word Figure in the plot is cut off to Figu). If it helps the pixels in the
plot figure are 28x618. I have tried to resize the canvas/size in
Image-Adjust-Canvas size and Image-Adjust-Size. The latter just stretches
what I already see on the plot.
I have the ImageJ 1.42q for MACS but the I had this problem with the
previous version. Please help!

Vivienne

[Olaku, Vivienne]

Ok Jonathan, I will try that. Thanks a lot.

Vivienne


-----Original Message-----
From: ImageJ Interest Group on behalf of Jonathan Hilmer
Sent: Fri 10/9/2009 5:32 PM
To: [hidden email]
Subject: Re: Problems with Plot lane window
 
The problem you see is because GelAnalyzer is expecting the longest
axis of your selection to be x-axis of the resulting plot, and the
shorter axis will be the averaged/summed (can't recall which) data to
generate the y-axis.

The easiest way to solve your problem as you have it here is to make
your selections taller on the original image.  Then everything should
look the way you expect.  That will also make it easier accurately
define baseline.  I would also recommend extending your selections in
the horizontal direction to include as much as the band as possible,
ideally extending directly to the center of area between bands,
between lanes.


Jonathan


On Fri, Oct 9, 2009 at 7:37 AM, Olaku, Vivienne
<[hidden email]> wrote:
> Hi ImageJ users,
>
> I am new to using the Analyze-Gel for measuring the band intensities in western blots. I mark each lane from left to right with the Select First Lane and then Select Next Lane. However once I go to "Plot Lanes" the figure comes up extremely narrow and long, each lane is shown in the plot one under the other (I typically have 4 lanes). I see only part of the plot (even the word Figure in the plot is cut off to Figu). If it helps the pixels in the plot figure are 28x618. I have tried to resize the canvas/size in Image-Adjust-Canvas size and Image-Adjust-Size. The latter just stretches what I already see on the plot.
> I have the ImageJ 1.42q for MACS but the I had this problem with the previous version. Please help!
>
> Vivienne
>