ROI to particle conversion.

[Aryeh Weiss]

Is there a  simple function that will convert a set of entries in the
ROI manager to a set of particles that the particle analyzer can work on.

I can write something to do it, (eg, by setting all of the ROIs to zero
and then thresholding and running the particle analyzer), but I wonder
if there is a built in function or existing plugin to do it.

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

[dscho]

Hi,

On Wed, 29 Dec 2010, Aryeh Weiss wrote:

> Is there a simple function that will convert a set of entries in the ROI
> manager to a set of particles that the particle analyzer can work on.

As far as I can tell, the easiest way to accomplish this is to put the
ROIs into the ROI Manager, select all, and click ROI Manager's 'Measure'
button.

Does this help?

Ciao,
Dscho

[Aryeh Weiss]

On 12/29/10 8:45 PM, Johannes Schindelin wrote:

> Hi,
>
> On Wed, 29 Dec 2010, Aryeh Weiss wrote:
>
>> Is there a simple function that will convert a set of entries in the ROI
>> manager to a set of particles that the particle analyzer can work on.
>
> As far as I can tell, the easiest way to accomplish this is to put the
> ROIs into the ROI Manager, select all, and click ROI Manager's 'Measure'
> button.
>
> Does this help?
>

Thank you -- this is indeed very helpful.
I would also like to make a mask from the ROIs. There is such a command
under edit>selection. However, I cannot make it work on a stack of ROIs.
The ROI manager has the slice info, so it should be possible to have the
create mask command respect the slice info.

Again, one can loop through the ROIs , but I wonder if it is already
built in .

Best regards
--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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

On Dec 29, 2010, at 1:31 PM, Aryeh Weiss wrote:

> Is there a  simple function that will convert a set of entries in the
> ROI manager to a set of particles that the particle analyzer can work on.

You can do this using the ROI Manager's More>>Fill command.

-wayne


> I can write something to do it, (eg, by setting all of the ROIs to zero
> and then thresholding and running the particle analyzer), but I wonder
> if there is a built in function or existing plugin to do it.

[Aryeh Weiss]

On 12/29/10 10:22 PM, Rasband, Wayne (NIH/NIMH) [E] wrote:
> On Dec 29, 2010, at 1:31 PM, Aryeh Weiss wrote:
>
>> Is there a  simple function that will convert a set of entries in the
>> ROI manager to a set of particles that the particle analyzer can work on.
>
> You can do this using the ROI Manager's More>>Fill command.
>

perfect -- thank you.

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]