ROI analysis of image stack

[Mazaheri Tehrani, Yousef/Medical Physics]

A question regarding ROI analysis of Image Stack:

I would like to draw ROI's, slice-by-slice, on an image stack and then
convert to mask (i.e. fill inside, clear outside).
Is there a plugin, or batch mode way to do this?

Also, when using multi measure plugin, the slice number is not recorded,
and hence the slice location of each ROI is subsequently lost. Is there
a way to register the slice for each ROI and retrieve later?

Thanks
Yousef

 
     =====================================================================
     
     Please note that this e-mail and any files transmitted with it may be
     privileged, confidential, and protected from disclosure under
     applicable law. If the reader of this message is not the intended
     recipient, or an employee or agent responsible for delivering this
     message to the intended recipient, you are hereby notified that any
     reading, dissemination, distribution, copying, or other use of this
     communication or any of its attachments is strictly prohibited.  If
     you have received this communication in error, please notify the
     sender immediately by replying to this message and deleting this
     message, any attachments, and all copies and backups from your
     computer.

[Robert Dougherty]

Yousef,

In Analyze/Set Measurements..., you can select "Slice Number" to get Multi
Measure or other things that use Measure to record the slice number.

Bob

Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Mazaheri Tehrani, Yousef/Medical Physics
> Sent: Thursday, January 12, 2006 3:05 PM
> To: [hidden email]
> Subject: ROI analysis of image stack
>
> A question regarding ROI analysis of Image Stack:
>
> I would like to draw ROI's, slice-by-slice, on an image stack and then
> convert to mask (i.e. fill inside, clear outside).
> Is there a plugin, or batch mode way to do this?
>
> Also, when using multi measure plugin, the slice number is not recorded,
> and hence the slice location of each ROI is subsequently lost. Is there
> a way to register the slice for each ROI and retrieve later?
>
> Thanks
> Yousef
>
>
>      =====================================================================
>
>      Please note that this e-mail and any files transmitted with it may be
>      privileged, confidential, and protected from disclosure under
>      applicable law. If the reader of this message is not the intended
>      recipient, or an employee or agent responsible for delivering this
>      message to the intended recipient, you are hereby notified that any
>      reading, dissemination, distribution, copying, or other use of this
>      communication or any of its attachments is strictly prohibited.  If
>      you have received this communication in error, please notify the
>      sender immediately by replying to this message and deleting this
>      message, any attachments, and all copies and backups from your
>      computer.

[Robert Dougherty]

This does not quite work due to an incompatibility between the Slice feature
of Measurements and Multi Measure.  I'm updating Multi Measure to fix this
and also incorporate many enhancements from Ulrik Stervbo.

Bob

> In Analyze/Set Measurements..., you can select "Slice Number" to get Multi
> Measure or other things that use Measure to record the slice number.
>
> Bob

[Wayne Rasband]

> A question regarding ROI analysis of Image Stack:
>
> I would like to draw ROI's, slice-by-slice, on an image stack
> and then convert to mask (i.e. fill inside, clear outside).
> Is there a plugin, or batch mode way to do this?

You can do this by adding the ROIs to the ROI Manager and then running
this macro:

   n = roiManager("count");
   for (i=0; i<n; i++) {
      roiManager('select', i);
      run("Clear Outside", "slice");
      run("Fill", "slice");
   }

Install the ROI Manager macro set at

     http://rsb.info.nih.gov/ij/macros/RoiManagerMacros.txt

and you will be able to add an ROI to the ROI Manager and advance to
the next slice by pressing "5".

-wayne

[Mazaheri Tehrani, Yousef/Medical Physics]

Bob:

I greatly appreciate your help.
Thanks
Yousef

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Robert Dougherty
Sent: Friday, January 13, 2006 12:41 PM
To: [hidden email]
Subject: Re: ROI analysis of image stack


This does not quite work due to an incompatibility between the Slice
feature of Measurements and Multi Measure.  I'm updating Multi Measure
to fix this and also incorporate many enhancements from Ulrik Stervbo.

Bob

> In Analyze/Set Measurements..., you can select "Slice Number" to get
> Multi Measure or other things that use Measure to record the slice
> number.
>
> Bob


 
     =====================================================================
     
     Please note that this e-mail and any files transmitted with it may be
     privileged, confidential, and protected from disclosure under
     applicable law. If the reader of this message is not the intended
     recipient, or an employee or agent responsible for delivering this
     message to the intended recipient, you are hereby notified that any
     reading, dissemination, distribution, copying, or other use of this
     communication or any of its attachments is strictly prohibited.  If
     you have received this communication in error, please notify the
     sender immediately by replying to this message and deleting this
     message, any attachments, and all copies and backups from your
     computer.