xy-coordinates for freehand selection

[Rune Jakobsen]

Just recently discovered ImageJ as fantastic program for handling  
images. I am using the selection tool to trace and measure xy-
coordinates for subtle lines in x-rays . This works but I wonder if  
theres is anyway that you can get the xy-coordinates from a freehand  
(or even a segmented line) selection into a text/xls.file? I am using  
the xy-coordinates in matlab to determine the shortest distance  
between to traced lines on a x-ray - so if anyone know if this is a  
feature already build into ImageJ - or if something like that exist  
as a plugin - that would off course be even better.
Thank you in advance.

Rune Jakobsen

[Volker Baecker]

Either File>SaveAs>XY Coordinates... or the Path Writer plugin should do
the job.
Look at
http://rsb.info.nih.gov/ij/docs/menus/file.html#saveas
Cheers,
Volker

Rune Jakobsen a écrit :

> Just recently discovered ImageJ as fantastic program for handling
> images. I am using the selection tool to trace and measure
> xy-coordinates for subtle lines in x-rays . This works but I wonder if
> theres is anyway that you can get the xy-coordinates from a freehand
> (or even a segmented line) selection into a text/xls.file? I am using
> the xy-coordinates in matlab to determine the shortest distance
> between to traced lines on a x-ray - so if anyone know if this is a
> feature already build into ImageJ - or if something like that exist as
> a plugin - that would off course be even better.
> Thank you in advance.
>
> Rune Jakobsen
>
> --passerelle antivirus du campus CNRS de Montpellier
> --
>
>

--
passerelle antivirus du campus CNRS de Montpellier
--

[Rune Jakobsen]

Thank you - very easy and probably something that I should have  
discovered my self.

Another question - is there a way to save selections onto the image  
(merge the selection into the image) - so that when opened again the  
selection will be visible.

Rune

Den 1. aug. 2006 kl. 23.39 skrev Rasband Wayne:

>
> On Aug 1, 2006, at 10:50 PM, Rune Jakobsen wrote:
>
>> Just recently discovered ImageJ as fantastic program for handling  
>> images. I am using the selection tool to trace and measure xy-
>> coordinates for subtle lines in x-rays . This works but I wonder  
>> if theres is anyway that you can get the xy-coordinates from a  
>> freehand (or even a segmented line) selection into a text/
>> xls.file? I am using the xy-coordinates in matlab to determine the  
>> shortest distance between to traced lines on a x-ray - so if  
>> anyone know if this is a feature already build into ImageJ - or if  
>> something like that exist as a plugin - that would off course be  
>> even better.
>> Thank you in advance.
>
> Use the File>Save As>XY Coordinates command.
>
> -wayne

[Michael Cammer]

Reminder:

If a section of a freehand selection is perfectly horizontal or vertical,
only the beginning and end points of that part of the line is saved.  If
you need the individual points along the line, you have to calculate them
yourself.

-mc

At 09:45 AM 08/02/06 +0200, you wrote:

>Either File>SaveAs>XY Coordinates... or the Path Writer plugin should do
>the job.
>Look at
>http://rsb.info.nih.gov/ij/docs/menus/file.html#saveas
>Cheers,
>Volker
>
>Rune Jakobsen a écrit :
>>Just recently discovered ImageJ as fantastic program for handling images.
>>I am using the selection tool to trace and measure xy-coordinates for
>>subtle lines in x-rays . This works but I wonder if theres is anyway that
>>you can get the xy-coordinates from a freehand (or even a segmented line)
>>selection into a text/xls.file? I am using the xy-coordinates in matlab
>>to determine the shortest distance between to traced lines on a x-ray -
>>so if anyone know if this is a feature already build into ImageJ - or if
>>something like that exist as a plugin - that would off course be even better.
>>Thank you in advance.
>>
>>Rune Jakobsen
>>
>>--passerelle antivirus du campus CNRS de Montpellier
>>--
>>
>
>--
>passerelle antivirus du campus CNRS de Montpellier
>--

____________________________________________________________________________
Michael Cammer   Analytical Imaging Facility   Albert Einstein Coll. of Med.
URL:  http://www.aecom.yu.edu/aif/ 

[Thomas Boudier-2]

Rune Jakobsen a écrit :
> Thank you - very easy and probably something that I should have
> discovered my self.
>
> Another question - is there a way to save selections onto the image
> (merge the selection into the image) - so that when opened again the
> selection will be visible.
>
> Rune

Hi Rune,

You can "draw" the selection, maybe is that's u want, else u have to  
save separately your image and your selection.

Thomas

>
> Den 1. aug. 2006 kl. 23.39 skrev Rasband Wayne:
>
>>
>> On Aug 1, 2006, at 10:50 PM, Rune Jakobsen wrote:
>>
>>> Just recently discovered ImageJ as fantastic program for handling
>>> images. I am using the selection tool to trace and measure
>>> xy-coordinates for subtle lines in x-rays . This works but I wonder
>>> if theres is anyway that you can get the xy-coordinates from a
>>> freehand (or even a segmented line) selection into a text/xls.file?
>>> I am using the xy-coordinates in matlab to determine the shortest
>>> distance between to traced lines on a x-ray - so if anyone know if
>>> this is a feature already build into ImageJ - or if something like
>>> that exist as a plugin - that would off course be even better.
>>> Thank you in advance.
>>
>> Use the File>Save As>XY Coordinates command.
>>
>> -wayne
>
> .
>

--
/*****************************************************/
 Thomas Boudier, MCU Université Pierre et Marie Curie
 Imagerie Intégrative,Institut Curie - INSERM U759.
 Tél : [phone]  Fax : [phone]
/*****************************************************/


 

[Gabriel Landini]

On Wednesday 02 August 2006 16:43, Rune Jakobsen wrote:
> Another question - is there a way to save selections onto the image
> (merge the selection into the image) - so that when opened again the
> selection will be visible.

The following is is very ugly :-) and non-standard, but it is better than
nothing:

You can decode the ROI into a string and insert it as metadata of a tiff file.
You then will need another macro that reads the metadata and creates the ROI.
I used a similar method to store LUTs in a stack (so each image has a LUT
associated).

Perhaps the easiest is to save the ROI via the ROI manager with a same name as
the image, so you can process any image and you can derive the name of the
roi straightforwardly.

Cheers

Gabriel