Straightening a segmented line

[Rafael Carazo-Salas-2]

Dear NIH Image users ,

I am analyzing 2D images which contain mostly background and some
'fluorescence lines' which represent the signal .  Although the lines are
mostly straight the do bend often and so to analyze them I use the Segmented
Line Selection , followed by the Plot Profile tool .  This gives me the
fluorescence per pixel for the whole segmented line selected and this data
can then be saved as a table .

I would like to do something slightly more sophisticated .  I would like to
:  1) create a segmented line selection , then 2) open a new window as wide
as the total segmented line length , and then 3) 'paste' the fluorescence
intensity information from my segmented line in this new window (in a
nutshell , I want to straighten the segmented line and create a new
straightened line window with the fluorescence information in each pixel of
it) .

If this is not too confusing would any of you have ideas about this ? I have
written a macro fo this but it seems to complicated to be the most efficient
way to accomplish this thing .

Thank you very much in advance !  Cheers ,





Rafael



_____________________________________________________________________

Rafael Edgardo Carazo Salas, Ph.D.
Cell Cycle Laboratory
Cancer Research UK, London Research Institute
44 Lincoln's Inn Fields
London WC2A 3PX, UNITED KINGDOM
Tel ::: [phone]
Fax ::: [phone]
_____________________________________________________________________

[Liu, Dongfang (NIH/NIAID) [F]]

could you share your macro with us?
Thank you very much.

Best regards

> ----------
> From: Rafael Carazo-Salas
> Reply To: List IMAGEJ
> Sent: Monday, April 24, 2006 2:06 PM
> To: List IMAGEJ
> Subject: Straightening a segmented line
>
> Dear NIH Image users ,
>
> I am analyzing 2D images which contain mostly background and some
> 'fluorescence lines' which represent the signal .  Although the lines are
> mostly straight the do bend often and so to analyze them I use the Segmented
> Line Selection , followed by the Plot Profile tool .  This gives me the
> fluorescence per pixel for the whole segmented line selected and this data
> can then be saved as a table .
>
> I would like to do something slightly more sophisticated .  I would like to
> :  1) create a segmented line selection , then 2) open a new window as wide
> as the total segmented line length , and then 3) 'paste' the fluorescence
> intensity information from my segmented line in this new window (in a
> nutshell , I want to straighten the segmented line and create a new
> straightened line window with the fluorescence information in each pixel of
> it) .
>
> If this is not too confusing would any of you have ideas about this ? I have
> written a macro fo this but it seems to complicated to be the most efficient
> way to accomplish this thing .
>
> Thank you very much in advance !  Cheers ,
>
>
>
>
>
> Rafael
>
>
>
> _____________________________________________________________________
>
> Rafael Edgardo Carazo Salas, Ph.D.
> Cell Cycle Laboratory
> Cancer Research UK, London Research Institute
> 44 Lincoln's Inn Fields
> London WC2A 3PX, UNITED KINGDOM
> Tel ::: [phone]
> Fax ::: [phone]
> _____________________________________________________________________
>
>

[Kurt De Vos]

Hi Rafael,
You could use the straighten plugin
kurt de vos

On 24 Apr 2006, at 19:06, Rafael Carazo-Salas wrote:

> Dear NIH Image users ,
>
> I am analyzing 2D images which contain mostly background and some
> 'fluorescence lines' which represent the signal .  Although the  
> lines are
> mostly straight the do bend often and so to analyze them I use the  
> Segmented
> Line Selection , followed by the Plot Profile tool .  This gives me  
> the
> fluorescence per pixel for the whole segmented line selected and  
> this data
> can then be saved as a table .
>
> I would like to do something slightly more sophisticated .  I would  
> like to
> :  1) create a segmented line selection , then 2) open a new window  
> as wide
> as the total segmented line length , and then 3) 'paste' the  
> fluorescence
> intensity information from my segmented line in this new window (in a
> nutshell , I want to straighten the segmented line and create a new
> straightened line window with the fluorescence information in each  
> pixel of
> it) .
>
> If this is not too confusing would any of you have ideas about  
> this ? I have
> written a macro fo this but it seems to complicated to be the most  
> efficient
> way to accomplish this thing .
>
> Thank you very much in advance !  Cheers ,
>
>
>
>
>
> Rafael
>
>
>
> _____________________________________________________________________
>
> Rafael Edgardo Carazo Salas, Ph.D.
> Cell Cycle Laboratory
> Cancer Research UK, London Research Institute
> 44 Lincoln's Inn Fields
> London WC2A 3PX, UNITED KINGDOM
> Tel ::: [phone]
> Fax ::: [phone]
> _____________________________________________________________________

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