Plot profiles of multiple ROI's on the same graph, with color coding for each ROI???

[John Clark]

I just installed the ImageJ package, and my first little 'get to know it' project, has presented me with a problem.

I'd like to plot the profiles of several ROI's, on the same graph, and color code each profile plotted. I often do this in
SCILAB, but that is a 'scripting' environment. Whereas ImageJ has more image processing functionality via the
UI. But there didn't seem to be a way to do this from the UI.

I searched but questions about multiple ROI's don't seem to answer this simple question.

So is there an example script that I can use to do this?

John Clark.

[Philippe GENDRE]

Hello John,

I don't know what kind of ROI you need to plot. For my own use I have
modified the "Roi Manager" java file according to plot several line Rois (up
to four) on the same plot with different colors (see attached plot).  I can
send to you the bin or src corresponding file or the modified ij.jar if you
prefer.

Best regards,

Philippe

2011/4/27 John Clark <[hidden email]>

> I just installed the ImageJ package, and my first little 'get to know it'
> project, has presented me with a problem.
>
> I'd like to plot the profiles of several ROI's, on the same graph, and
> color code each profile plotted. I often do this in
> SCILAB, but that is a 'scripting' environment. Whereas ImageJ has more
> image processing functionality via the
> UI. But there didn't seem to be a way to do this from the UI.
>
> I searched but questions about multiple ROI's don't seem to answer this
> simple question.
>
> So is there an example script that I can use to do this?
>
> John Clark.
>

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

> I just installed the ImageJ package, and my first little 'get to know it' project, has presented me with a problem.
>
> I'd like to plot the profiles of several ROI's, on the same graph, and color code each profile plotted. I often do this in
> SCILAB, but that is a 'scripting' environment. Whereas ImageJ has more image processing functionality via the
> UI. But there didn't seem to be a way to do this from the UI.
>
> I searched but questions about multiple ROI's don't seem to answer this simple question.
>
> So is there an example script that I can use to do this?

You can plot multiple line and/or rectangular selections on the same graph using the ROI Manager's More>>Multi Plot command, which was added in the 1.45g daily build. You can upgrade by using the Help>Update ImageJ command and selecting "daily build" from the drop down menu.

-wayne

[John Clark]

On Apr 28, 2011, at 5:27 PM, Rasband, Wayne (NIH/NIMH) [E] wrote:

>> I just installed the ImageJ package, and my first little 'get to know it' project, has presented me with a problem.
>>
>> I'd like to plot the profiles of several ROI's, on the same graph, and color code each profile plotted. I often do this in
>> SCILAB, but that is a 'scripting' environment. Whereas ImageJ has more image processing functionality via the
>> UI. But there didn't seem to be a way to do this from the UI.
>>
>> I searched but questions about multiple ROI's don't seem to answer this simple question.
>>
>> So is there an example script that I can use to do this?
>
> You can plot multiple line and/or rectangular selections on the same graph using the ROI Manager's More>>Multi Plot command, which was added in the 1.45g daily build. You can upgrade by using the Help>Update ImageJ command and selecting "daily build" from the drop down menu.

Thanks, that worked and was rather painless...

John Clark.

[dpoburko]

On 4/28/2011 5:27 PM, Rasband, Wayne (NIH/NIMH) [E] wrote:

>> I just installed the ImageJ package, and my first little 'get to know it' project, has presented me with a problem.
>>
>> I'd like to plot the profiles of several ROI's, on the same graph, and color code each profile plotted. I often do this in
>> SCILAB, but that is a 'scripting' environment. Whereas ImageJ has more image processing functionality via the
>> UI. But there didn't seem to be a way to do this from the UI.
>>
>> I searched but questions about multiple ROI's don't seem to answer this simple question.
>>
>> So is there an example script that I can use to do this?
> You can plot multiple line and/or rectangular selections on the same graph using the ROI Manager's More>>Multi Plot command, which was added in the 1.45g daily build. You can upgrade by using the Help>Update ImageJ command and selecting "daily build" from the drop down menu.
>
> -wayne

Hi Wayne,

   I love the idea of multiplot. Would it be possible in the future to
remove the constraints requiring rectangle or line selections (to
include ovals and freehand ROIs) and to increase the number of ROIs that
can be plotted. It seems like there is a limit of 6 ROIs that multiplot
can handle. I would often like to plot 100+.

Many thanks,
Damon



--
Post Doctoral Fellow
Tsien Lab, Molecular&  Cellular Physiology
Stanford University

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

>   I love the idea of multiplot. Would it be possible in the future to
> remove the constraints requiring rectangle or line selections (to
> include ovals and freehand ROIs) and to increase the number of ROIs that
> can be plotted. It seems like there is a limit of 6 ROIs that multiplot
> can handle. I would often like to plot 100+.

In the latest 1.45g daily build, the ROI Manager's More>>Multi Plot command plots oval and freehand ROIs by using the new Edit>Selection>Area to Line command, which converts area selections to line selections. There is also no longer a limit on the number of selections that can be plotted.

-wayne

[Philippe GENDRE]

Dear Imagej list,

Another suggestion regarding Multi Plot : it will be good for some users to
have the opportunity to draw multiple plots with zaxisprofiler.

Best regards,

Philippe

2011/4/29 Rasband, Wayne (NIH/NIMH) [E] <[hidden email]>

> >   I love the idea of multiplot. Would it be possible in the future to
> > remove the constraints requiring rectangle or line selections (to
> > include ovals and freehand ROIs) and to increase the number of ROIs that
> > can be plotted. It seems like there is a limit of 6 ROIs that multiplot
> > can handle. I would often like to plot 100+.
>
> In the latest 1.45g daily build, the ROI Manager's More>>Multi Plot command
> plots oval and freehand ROIs by using the new Edit>Selection>Area to Line
> command, which converts area selections to line selections. There is also no
> longer a limit on the number of selections that can be plotted.
>
> -wayne
>

[Posthume]

Hi Philippe,

I'd be very interested in looking at your code. Would it be possible for you to post it please?

Regards.
Michael.