Plot Profile axis

[Chao-Yin Chen]

I have collected LSM images with three different dyes.  The Image J
opens the file into three separate windows (Red, Green and Blue). I
would like to be able to see the Plot Profile of the same region in
each channel (a line across a cell).  Is there a way to make this
easier than making sure I draw the line in the same XY coordinate in
each window.  I tried merging the images before performing the Plot
Profile but can't get the information for individual channels.  Any
suggestion will be greatly appreciated.

Thanks,

Chao


Chao-Yin Chen
Associate Adjunct Professor
Department of Pharmacology
University of California, Davis
Phone: [phone]
Fax; 530-752-7710
e-mail: [hidden email]
web: http://www.ucdmc.ucdavis.edu/pharmacology 

[Jonathan Hilmer]

Perhaps I don't fully understand your question, but wouldn't it be
possible to make them into a stack, then perform the plotting once for
each layer in the stack?

Keep in mind that regardless how you get the plots, by default their
vertical axes will be different.  That issue has been addressed
previously in the mailing list: search for posts by Schechinger,
Mutterer, and myself to find a few of the discussions.  In particular,
this was brought up by Mutterer and might be just the thing for you,
though I haven't tried it personally:
http://rsbweb.nih.gov/ij/macros/SinglePanelGelAnalyzer.txt


Jonathan Hilmer



On 5/14/07, Chao-Yin Chen <[hidden email]> wrote:

> I have collected LSM images with three different dyes.  The Image J
> opens the file into three separate windows (Red, Green and Blue). I
> would like to be able to see the Plot Profile of the same region in
> each channel (a line across a cell).  Is there a way to make this
> easier than making sure I draw the line in the same XY coordinate in
> each window.  I tried merging the images before performing the Plot
> Profile but can't get the information for individual channels.  Any
> suggestion will be greatly appreciated.
>
> Thanks,
>
> Chao
>
>
> Chao-Yin Chen
> Associate Adjunct Professor
> Department of Pharmacology
> University of California, Davis
> Phone: [phone]
> Fax; 530-752-7710
> e-mail: [hidden email]
> web: http://www.ucdmc.ucdavis.edu/pharmacology

[Chao-Yin Chen]

Perhaps I did not have the right search words.  I spent a few days
trying to find this on the archive with no success.  Thanks for the
suggestions.  This could work well with a stack of images.  The other
option provided by Jim Quinn (see below) did exactly what I wanted to do.

Use "macro record" to see what coordinates you are
selecting.  Then use a macro with the same coords
on all the images.

Thanks again for the suggestions.

Chao


At 01:42 PM 5/15/2007, you wrote:

>Perhaps I don't fully understand your question, but wouldn't it be
>possible to make them into a stack, then perform the plotting once for
>each layer in the stack?
>
>Keep in mind that regardless how you get the plots, by default their
>vertical axes will be different.  That issue has been addressed
>previously in the mailing list: search for posts by Schechinger,
>Mutterer, and myself to find a few of the discussions.  In particular,
>this was brought up by Mutterer and might be just the thing for you,
>though I haven't tried it personally:
>http://rsbweb.nih.gov/ij/macros/SinglePanelGelAnalyzer.txt
>
>
>Jonathan Hilmer
>
>
>
>On 5/14/07, Chao-Yin Chen <[hidden email]> wrote:
>>I have collected LSM images with three different dyes.  The Image J
>>opens the file into three separate windows (Red, Green and Blue). I
>>would like to be able to see the Plot Profile of the same region in
>>each channel (a line across a cell).  Is there a way to make this
>>easier than making sure I draw the line in the same XY coordinate in
>>each window.  I tried merging the images before performing the Plot
>>Profile but can't get the information for individual channels.  Any
>>suggestion will be greatly appreciated.
>>
>>Thanks,
>>
>>Chao
>>
>>
>>Chao-Yin Chen
>>Associate Adjunct Professor
>>Department of Pharmacology
>>University of California, Davis
>>Phone: [phone]
>>Fax; 530-752-7710
>>e-mail: [hidden email]
>>web: http://www.ucdmc.ucdavis.edu/pharmacology
>
>Chao-Yin Chen
>Associate Adjunct Professor
>Department of Pharmacology
>University of California, Davis
>Phone: [phone]
>Fax; 530-752-7710
>e-mail: [hidden email]
>web: http://www.ucdmc.ucdavis.edu/pharmacology 

[karo03]

Try..
RGB Merge the three channels
RGB Profiles will plot for one line the three profiles (plugin)
Regards
Karsten
Am 15.05.2007 um 07:28 schrieb Chao-Yin Chen:

> I have collected LSM images with three different dyes.  The Image J  
> opens the file into three separate windows (Red, Green and Blue). I  
> would like to be able to see the Plot Profile of the same region in  
> each channel (a line across a cell).  Is there a way to make this  
> easier than making sure I draw the line in the same XY coordinate  
> in each window.  I tried merging the images before performing the  
> Plot Profile but can't get the information for individual  
> channels.  Any suggestion will be greatly appreciated.
>
> Thanks,
>
> Chao
>
>
> Chao-Yin Chen
> Associate Adjunct Professor
> Department of Pharmacology
> University of California, Davis
> Phone: [phone]
> Fax; 530-752-7710
> e-mail: [hidden email]
> web: http://www.ucdmc.ucdavis.edu/pharmacology