selection

[Naoki Irie-2]

I want to select a region of doughnut-like shape within my image.
However, since the selection I want to make is irregular shape, it is
difficult to
make a proper selection by using [Edit -> selection -> Make Band...]
command.

Is there any way that I can un-select the portion of field from an
already selected field?

thank you for your help.

[Wayne Rasband]

> I want to select a region of doughnut-like shape within
> my image. However, since the selection I want to make is
> irregular shape, it is difficult to make a proper selection
> by using [Edit -> selection -> Make Band...]
> command.
>
> Is there any way that I can un-select the portion of field
> from an already selected field?

You can make a doughnut-like selection by creating a selection and  
then creating a second one with the alt key down, which will be  
subtracted from the first.

-wayne

[michael shaffer]

 
Wayne writes ...
RE:
> > [...].
> >
> > Is there any way that I can un-select the portion of field from an
> > already selected field?
>
> You can make a doughnut-like selection by creating a
> selection and then creating a second one with the alt key
> down, which will be subtracted from the first.


  What if there are ^many^ holes?

Genuinely, Michael Shaffer  :o)

SEM/MLA Research Coordinator
     [phone] (ofc)
     [phone] (lab)
     [phone] (FAX)
     http://www.mun.ca/creait/maf/
     http://www.esd.mun.ca/epma/ 

Inco Innovation Centre
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[Gabriel Landini]

On Monday 24 April 2006 10:48, michael shaffer wrote:
>   What if there are ^many^ holes?

You press alt key every time to make a new hole.

G.

[Andre Klarsfeld]

Dear ImageJ co-users,

I asked a few weeks ago whether ImageJ could consider that such a ³holed²
region of interest is indeed a single ROI. That would allow the ³revert to
previous ROI² command to recall it, rather than the last ³hole² that was
punched into it.
(same question with multipartite ROI¹s drawn by adding discontinuous
selections while pressing the Shift key).

Maybe someone answered my query without my noticing it ?

Thank you for your help.
André

-----------------------------------------------
André Klarsfeld
"Génétique moléculaire des rythmes circadiens"
UPR 2216 Neurobiologie génétique et intégrative
CNRS, Institut de neurobiologie Alfred Fessard
F-91198 GIF/YVETTE Cedex
Tel : [phone]
Fax : [phone]
NOTE : skip the initial zero from outside France.
Web : http://www.inaf.cnrs-gif.fr/ngi/rouyer/index.html


Le 24/04/06 13:23, « Gabriel Landini » <[hidden email]> a écrit :

> On Monday 24 April 2006 10:48, michael shaffer wrote:
>> >   What if there are ^many^ holes?
>
> You press alt key every time to make a new hole.
>
> G.

[vytas-2]

If you use the ROI manager to ADD the complex ROI, you can restore it by
dbl-click

At 07:22 AM 4/24/2006, you wrote:

>Dear ImageJ co-users,
>
>I asked a few weeks ago whether ImageJ could consider that such a ³holed²
>region of interest is indeed a single ROI. That would allow the ³revert to
>previous ROI² command to recall it, rather than the last ³hole² that was
>punched into it.
>(same question with multipartite ROI¹s drawn by adding discontinuous
>selections while pressing the Shift key).
>
>Maybe someone answered my query without my noticing it ?
>
>Thank you for your help.
>André
>
>-----------------------------------------------
>André Klarsfeld
>"Génétique moléculaire des rythmes circadiens"
>UPR 2216 Neurobiologie génétique et intégrative
>CNRS, Institut de neurobiologie Alfred Fessard
>F-91198 GIF/YVETTE Cedex
>Tel : [phone]
>Fax : [phone]
>NOTE : skip the initial zero from outside France.
>Web : http://www.inaf.cnrs-gif.fr/ngi/rouyer/index.html
>
>
>Le 24/04/06 13:23, « Gabriel Landini » <[hidden email]> a écrit :
>
> > On Monday 24 April 2006 10:48, michael shaffer wrote:
> >> >   What if there are ^many^ holes?
> >
> > You press alt key every time to make a new hole.
> >
> > G.

Vytas Bindokas, Ph.D.
Research Assoc. / Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
Dept Neurobiol Pharmacol Physiol MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room 1007 (CLSC)

773-702-4875

email [hidden email]
  web site for LMCF:
http://digital.bsd.uchicago.edu/index.html 



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[michael shaffer]

 
Gabriel writes ...

> On Monday 24 April 2006 10:48, michael shaffer wrote:
> >   What if there are ^many^ holes?
>
> You press alt key every time to make a new hole.

  Ooops! ... I was trying to make a point, and others may have missed it as
well.  What you are suggesting cannot be automated.  What would be ideal
would to create a ROI, or many ROIs based on a binary image generated by a
variety of means.  For example, I'd at least like to create ROIs based after
thresholding, but there seems to be no way to "select" and work with what is
(or isn't) masked(?)

genuinely  :o)
michael shaffer

SEM/MLA Research Coordinator
[phone] (ofc)
[phone] (lab)
[phone] (FAX)
    <http://www.mun.ca/creait/maf/>
    <http://www.esd.mun.ca/epma/>

Inco Innovation Centre
c/o Memorial University
230 Elizabeth Avenue
P.O. Box 4200
St. John's, NL A1C 5S7

[Wayne Rasband]

> I asked a few weeks ago whether ImageJ could consider that
> such a “holed” region of interest is indeed a single ROI. That
> would allow the “revert to previous ROI” command to recall it,
> rather than the last “hole” that was punched into it.
> (same question with multipartite ROI’s drawn by adding
> discontinuous selections while pressing the Shift key).

The Edit>Selection>Restore Selection command will work as expected with
composite ROIs in ImageJ 1.37e.

-wayne

[Joachim Wesner]

Hi there,

by the way, I see another issue with multipart ROIs, if you try to add
ellipses or rectangles, the Shift key acts both as "add ROI" and as "keep
circle/square" indicator, so one can only add
true circles and squares!?

Am I missing something here? is there a trick to work around?

Joachim



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> I asked a few weeks ago whether ImageJ could consider that
> such a “holed” region of interest is indeed a single ROI. That
> would allow the “revert to previous ROI” command to recall it,
> rather than the last “hole” that was punched into it.
> (same question with multipartite ROI’s drawn by adding
> discontinuous selections while pressing the Shift key).

The Edit>Selection>Restore Selection command will work as expected with
composite ROIs in ImageJ 1.37e.

-wayne

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[Wayne Rasband]

> by the way, I see another issue with multipart ROIs, if you try to
> add ellipses or rectangles, the Shift key acts both as "add ROI"
> and as "keep circle/square" indicator, so one can only add
> true circles and squares!?
>
> Am I missing something here? is there a trick to work around?

Release the shift key after you start adding the selection.

-wayne

[Joachim Wesner]

AHA! Thanx!!!!!!!!!


JW



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> by the way, I see another issue with multipart ROIs, if you try to
> add ellipses or rectangles, the Shift key acts both as "add ROI"
> and as "keep circle/square" indicator, so one can only add
> true circles and squares!?
>
> Am I missing something here? is there a trick to work around?

Release the shift key after you start adding the selection.

-wayne



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[Gabriel Landini]

On Monday 24 April 2006 16:35, michael shaffer wrote:
>   Ooops! ... I was trying to make a point, and others may have missed it as
> well.  What you are suggesting cannot be automated.

How about this:

makeRectangle(50, 30, 264, 253);
setKeyDown("alt");
makeRectangle(75, 69, 86, 101);
makeRectangle(209, 149, 75, 108);
setKeyDown("none");

Cheers,

G.

[Wayne Rasband]

>   Ooops! ... I was trying to make a point, and others may
>   have missed it as well.  What you are suggesting cannot be
>   automated.  What would be ideal would to create a ROI, or
>   many ROIs based on a binary image generated by a variety
>   of means.  For example, I'd at least like to create ROIs
>   based after thresholding, but there seems to be no way to
>   "select" and work with what is (or isn't) masked(?)

One way to convert a thresholded image to a set of ROIs is to check
"Record Starts" in the particle analyze and then use doWand(x,y) to
generate ROIs from the recorded coordinates. Here are some macros that
demonstrate this technique:

   http://rsb.info.nih.gov/ij/macros/CircularParticles.txt
   http://rsb.info.nih.gov/ij/macros/ConvertMaskToCompositeROI.txt
   http://rsb.info.nih.gov/ij/macros/ConvexHull.txt
   http://rsb.info.nih.gov/ij/macros/FeretsDiameter.txt
   http://rsb.info.nih.gov/ij/macros/LabelParticlesWithArea.txt
   http://rsb.info.nih.gov/ij/macros/RoiManagerAddParticles.txt

-wayne