ImageJ interaction: ROI Manager etc.

[karo03]

Hi, I am just exploring the niceties of ImageJ interactive abilities:  
Some questions for clarification

Using the ROI Manger with display, the numbers in the display usually  
don't correspond with the numbers of the ROI's in the list, at least  
after having deleted any object from the list. Is that intended?

Using the Wand on a mask image clicking into the background will  
select the next most connected object on the right. Is that intended?

Having a list of objects in the ROI manager, I would like to correct  
one selected, either cut it into two or change it and than update it  
in the ROI manager. My quite complicated way was:
        1. Select the object
        2. Change the mask image by drawing, deleting, etc.
        3. Remove the selection
        4. Multiple object select by doWand with shift if there are more  
than one object after correction
        5. Add the object(s) to ROI Manager
        6. Find the formerly selected object and delete it in the ROI list
Another again complicated method is:
        1. correct the mask image
        2. (re)run analyze particles...
        3. control the objects
        4. if necessary go to 1.
Is there any idea to improve this proceeding?

Thanks in advance
Karsten

[Michael Schmid]

On 5 Jul 2007, at 09:41, Karsten Rodenacker wrote:

> Using the ROI Manger with display, the numbers in the display  
> usually don't correspond with the numbers of the ROI's in the list,  
> at least after having deleted any object from the list. Is that  
> intended?
Hmm, the rois are not numbered in the roi manager, but have names  
that relate to their y and x coordinates. The labels are the position  
in the list of rois and updated correctly, as far as I see (ImageJ  
1.38v; maybe you have an earlier version?)

> Using the Wand on a mask image clicking into the background will  
> select the next most connected object on the right. Is that intended?
It has been like this since the early days of ImageJ and I think  
everyone is used to it by now, even though it is different from the  
Wand of other programs.

> Having a list of objects in the ROI manager, I would like to  
> correct one selected, either cut it into two or change it and than  
> update it in the ROI manager. My quite complicated way was:
> 1. Select the object
> 2. Change the mask image by drawing, deleting, etc.
> 3. Remove the selection
> 4. Multiple object select by doWand with shift if there are more  
> than one object after correction
> 5. Add the object(s) to ROI Manager
> 6. Find the formerly selected object and delete it in the ROI list
> Another again complicated method is:
> 1. correct the mask image
> 2. (re)run analyze particles...
> 3. control the objects
> 4. if necessary go to 1.
> Is there any idea to improve this proceeding?

What about this:
  1. select all items in ROI manager
  2. ROI Manager More>>Combine (may be slow with many particles)
  3. Create Mask
  4. correct whatever you like (draw, delete, fill)
  5. run "Analyze Particles" on the mask
  6. delete everything in the ROI Manager
  7. ROI Manager More>>Add Particles

1.-3. is not needed in case you have the mask of all objects already.
---
Michael

[karo03]

Thank you Michael for explanations. Consider my questions as from a  
newbie.

Am 09.07.2007 um 16:19 schrieb Michael Schmid:

> On 5 Jul 2007, at 09:41, Karsten Rodenacker wrote:
>
>> Using the ROI Manger with display, the numbers in the display  
>> usually don't correspond with the numbers of the ROI's in the  
>> list, at least after having deleted any object from the list. Is  
>> that intended?
> Hmm, the rois are not numbered in the roi manager, but have names  
> that relate to their y and x coordinates. The labels are the  
> position in the list of rois and updated correctly, as far as I see  
> (ImageJ 1.38v; maybe you have an earlier version?)
>

I mistook the first four character in the ROI list as number. I have  
the current ImageJ version, that live updater is very helpful.
However, dealing with several hundred particles, it is cumbersome to  
relate the displayed number with the respective ROI.

>> Using the Wand on a mask image clicking into the background will  
>> select the next most connected object on the right. Is that intended?
> It has been like this since the early days of ImageJ and I think  
> everyone is used to it by now, even though it is different from the  
> Wand of other programs.
>
Ok, I did not trust my machine!

>> Having a list of objects in the ROI manager, I would like to  
>> correct one selected, either cut it into two or change it and than  
>> update it in the ROI manager. My quite complicated way was:
>> 1. Select the object
>> 2. Change the mask image by drawing, deleting, etc.
>> 3. Remove the selection
>> 4. Multiple object select by doWand with shift if there are more  
>> than one object after correction
>> 5. Add the object(s) to ROI Manager
>> 6. Find the formerly selected object and delete it in the ROI list
>> Another again complicated method is:
>> 1. correct the mask image
>> 2. (re)run analyze particles...
>> 3. control the objects
>> 4. if necessary go to 1.
>> Is there any idea to improve this proceeding?
> What about this:
>  1. select all items in ROI manager
>  2. ROI Manager More>>Combine (may be slow with many particles)
>  3. Create Mask
>  4. correct whatever you like (draw, delete, fill)
>  5. run "Analyze Particles" on the mask
>  6. delete everything in the ROI Manager
>  7. ROI Manager More>>Add Particles
>
> 1.-3. is not needed in case you have the mask of all objects already.

Thank you, I tried that. This way is similar to applying analyze  
particle... with appropriate options after mask correction.

Regards
Karsten