ANNULAR ROI

[PabloSAguilar]

Hi there,
I´d like to define annular ROIs, preferentially both: circular and ellipsoidal,
any help will be appreciated!
thanks!
Pablo

[Jean-Yves Tinevez-2]

On Mar 26, 2010, at 2:14 PM, Pablo Aguilar wrote:

> Hi there,
> I´d like to define annular ROIs, preferentially both: circular and  
> ellipsoidal,
> any help will be appreciated!
> thanks!


Hi Pablo.

Try this:
        draw a circle ROI on your image
        in the menu Edit > Selection, select "Make Band..."
Et voila!

Best
jyt


--
Jean-Yves Tinevez
PFID - Imagopole
Institut Pasteur
25-28, rue du Docteur Roux
75724 Paris cedex 15
France
tel: [phone]

[Jean-Yves Tinevez-2]

On Mar 26, 2010, at 2:34 PM, Pablo S. Aguilar wrote:

> awesome! thanks.
> on more question:
> do you know how can I get a "plot profile" from there. I mean, how  
> to plot the intensity all around the annulus.
> thanks again,
> Pablo

Hi Pablo,

It is not doable ou of the box for the kind of ROI you get when using  
the "Make Band..." plugin.
You will have to develop something to do it.

Do I guess correctly that you want to plot the profile of a membrane  
marker around a cell, averaged over a few pixel thickness?

Best
jy

[Jean-Yves Tinevez-2]

On Mar 26, 2010, at 2:42 PM, Pablo S. Aguilar wrote:

>>
>> Hi Pablo,
>>
>> It is not doable ou of the box for the kind of ROI you get when  
>> using the "Make Band..." plugin.
>> You will have to develop something to do it.
>>
>> Do I guess correctly that you want to plot the profile of a  
>> membrane marker around a cell, averaged over a few pixel thickness?
>>
> THAT IS EXACTLY WHAT I WANT TO DO, using a line I get high  
> variability, perhaps there is a line thickness set that I can apply?
> cheers and thanks
> Pablo
>

Yes, you can.
But you will have to drop the oval roi.

- Right-click on the line tool and select "segmented lines"
- Outline the border of your cell - because it is a line ROI, you  
don't get a closed shape
- by default, the profile take a line of 1px,
- to change that, double-click on the Line tool, a slider appear  
allowing to select the line ROI thickness
- the plot profile tool will make an average around this.

Tell us if it works
best
jy


--
Jean-Yves Tinevez
PFID - Imagopole
Institut Pasteur
25-28, rue du Docteur Roux
75724 Paris cedex 15
France
tel: [phone]