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Clear Outside on multiple ROIs

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Nilwik Rachel (BW)

Jan 24, 2013; 1:55pm

Clear Outside on multiple ROIs

16 posts

Hi all,

I wonder if anyone could help me with the following:

In a multi-channel image, I have created a ROI list in one channel and I use this list to perform analyses in another channel. However, there's much more information in this channel than I need, so I would like to clear everything from this image except for what is within the ROIs in the list.

I have found I could use the function ClearOutside for this, however, it only works for one ROI at a time, which means that all the information of the other ROIs in the list is lost, which is of course not what I want...

So, does anyone know if it is possible to perform this step, or something like it, in multiple ROIs at a time? As far as I can see it would be solved if I can activate all ROIs at a time, but I can't find how to do this. It would also be helpful if I could simply make an overlay that 'covers' everything outside the ROIs in the list, so that only the parts within the ROIs are visible (ie, without changing the image itself).

Many thanks!
Rachel

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Thomas Boudier

Jan 24, 2013; 2:02pm

Re: Clear Outside on multiple ROIs

172 posts

Hi,

RoiManager/More/Combine shoud help.

best,

Thomas

Le 24/01/2013 14:55, Nilwik Rachel (BW) a écrit :

> Hi all,
>
> I wonder if anyone could help me with the following:
>
> In a multi-channel image, I have created a ROI list in one channel and I use this list to perform analyses in another channel. However, there's much more information in this channel than I need, so I would like to clear everything from this image except for what is within the ROIs in the list.
>
> I have found I could use the function ClearOutside for this, however, it only works for one ROI at a time, which means that all the information of the other ROIs in the list is lost, which is of course not what I want...
>
> So, does anyone know if it is possible to perform this step, or something like it, in multiple ROIs at a time? As far as I can see it would be solved if I can activate all ROIs at a time, but I can't find how to do this. It would also be helpful if I could simply make an overlay that 'covers' everything outside the ROIs in the list, so that only the parts within the ROIs are visible (ie, without changing the image itself).
>
> Many thanks!
> Rachel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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/**********************************************************/
Thomas Boudier, MCU Université Pierre et Marie Curie,
Modélisation Cellulaire et Imagerie Biologique (EE1),
IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
Tel : 01 44 27 46 92 Fax : 01 44 27 22 91
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Nilwik Rachel (BW)

Jan 25, 2013; 2:30pm

Re: Clear Outside on multiple ROIs

16 posts

Thanks Thomas, it did! And sorry for bothering you with such an easy question...

Regards, rachel

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Thomas Boudier
Sent: Thursday, January 24, 2013 3:02 PM
To: [hidden email]
Subject: Re: Clear Outside on multiple ROIs

Hi,

RoiManager/More/Combine shoud help.

best,

Thomas

Le 24/01/2013 14:55, Nilwik Rachel (BW) a écrit :

... [show rest of quote]

jumpfunky

Jan 25, 2013; 8:51pm

Re: Clear Outside on multiple ROIs

81 posts

In reply to this post by Nilwik Rachel (BW)

Hi,

select all ROIs in the ROI Manager. Then use "More -> Or (Combine". Now
you can use the function Clear Outside.

Kind Regards
Thorsten

Am Donnerstag, den 24.01.2013, 14:55 +0100 schrieb Nilwik Rachel (BW):I
wonder if anyone could help me with the following:

In a multi-channel image, I have created a ROI list in one channel and I
use this list to perform analyses in another channel. However, there's
much more information in this channel than I need, so I would like to
clear everything from this image except for what is within the ROIs in
the list.

>
> I have found I could use the function ClearOutside for this, however, it only works for one ROI at a time, which means that all the information of the other ROIs in the list is lost, which is of course not what I want...
>
> So, does anyone know if it is possible to perform this step, or something like it, in multiple ROIs at a time? As far as I can see it would be solved if I can activate all ROIs at a time, but I can't find how to do this. It would also be helpful if I could simply make an overlay that 'covers' everything outside the ROIs in the list, so that only the parts within the ROIs are visible (ie, without changing the image itself).
>
> Many thanks!
> Rachel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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