multiple ROI

[AJBell]

I am able to use the threshold tool to define multiple ROI (cells) within
my image. Is there a way to perform individual measurements and plot
profiles on each ROI, without manually outlining each cell?

On average I have between 5 and 15 cells per image and currently about 200
images to process!

Reagrds

Andrew Bell

[Fabrice Senger]

Andrew James Bell a écrit :

> I am able to use the threshold tool to define multiple ROI (cells) within
> my image. Is there a way to perform individual measurements and plot
> profiles on each ROI, without manually outlining each cell?
>
> On average I have between 5 and 15 cells per image and currently about 200
> images to process!
>
> Reagrds
>
> Andrew Bell
>  

After thresholding your image, you may binarize it ( Process __
Binary___Make binary), next you can run Analyze_ Analyze particles, in
the window wich opens you should check "Add to manager", all your ROI's
will then be added to the "ROI manager",
without selecting any ROI you can hit measure, and all the selected
measurment will be performed on the set of ROI's.

If your approach is robust you may record a macro and insert this macro
into the "batch process" macro. Then you can process a whole folder of
files.

Fabrice.

--
Senger Fabrice

[Albert Cardona]

Andrew James Bell wrote:
> I am able to use the threshold tool to define multiple ROI (cells) within
> my image. Is there a way to perform individual measurements and plot
> profiles on each ROI, without manually outlining each cell?
>
> On average I have between 5 and 15 cells per image and currently about 200
> images to process!
>  


ShapeROI, which handles ROIs with separated regions, does not currently
provide a way to iterate over each region (but it easily could; it's
just not implemented).

Since you are using the Threshold to define ROIs, use the "Analyze -
Analyze Partices" first, with the desired output as separate ROIs (aka
"outlines" and tick on the checkbox "add to manager"). Then from the ROI
Manager that opens push "Measure" to measure all ROIs. Be sure to select
the proper image first, as others may have opened as a result of the
particle analysis.

Albert

--
Albert Cardona
http://albert.rierol.net

[AJBell]

Thanks for that, it is working fine.

Is there a plug-in or a method to have ImageJ draw a line along the major
axis for each ROI to enable image profiling? I'd rather not have to draw
each line by hand!

Andrew Bell

[Fabrice Senger]

Andrew James Bell a écrit :
> Thanks for that, it is working fine.
>
> Is there a plug-in or a method to have ImageJ draw a line along the major
> axis for each ROI to enable image profiling? I'd rather not have to draw
> each line by hand!
>
> Andrew Bell
>  
If you go on the imageJ site and to news there is an interesting macro
by Jerome Mutterer.
So when in analyze particles you choose ellipse as depiction you can
have aswell a depiction of Feret diameters

Fabrice.

--
Senger Fabrice

[Emilio Miguelanez Martin]

Hi,

On the same subject, I would like create a plugin that can draw several
ROIs on the same image. ROIs are made of X,Y points extracted from a
file.

Any ideas?


Cheers,
Emilio


On Mon, 2009-02-23 at 15:31 +0100, Senger Fabrice wrote:

> Andrew James Bell a écrit :
> > Thanks for that, it is working fine.
> >
> > Is there a plug-in or a method to have ImageJ draw a line along the major
> > axis for each ROI to enable image profiling? I'd rather not have to draw
> > each line by hand!
> >
> > Andrew Bell
> >  
> If you go on the imageJ site and to news there is an interesting macro
> by Jerome Mutterer.
> So when in analyze particles you choose ellipse as depiction you can
> have aswell a depiction of Feret diameters
>
> Fabrice.
>