Stacks or Overlays

[amsmota]

Hi all.

I like to do something like this:

1- open imageA
2- select a ROI from it
3- cut it from imageA
4- create a Image1 as a "FillOutside" - so I can get image1 with the same size as A with only the ROI and filled with a transparent color
5- repeat 2,3,4 a number of times
6- with all those image1...imageN create a stack/overlay that when put together will look the same as imageA

So, what's the best way to achieve this? Is it with stacks or overlays? Is there something like this already done?

Cheers.

[Christophe CHAMOT-2]

  Hi alone,

Give a try with this macro  code:


//----------------------------------------------------------------------------
waitForUser("Draw your ROI and hit t\nthen press OK");
n=roiManager("count");

for(i=0;i<n;i++){
selectImage(1);
roiManager("Select", i);
run("Duplicate...", "title=roi"+i+1);
run("Clear Outside");
}

run("Images to Stack", "method=[Copy (center)] name=Stack title=roi use");
roiManager("reset");
//-----------------------------------------------------------------------------------

Bye,

C.C.

Le 20/10/2010 13:34, amsmota a écrit :

> Hi all.
>
> I like to do something like this:
>
> 1- open imageA
> 2- select a ROI from it
> 3- cut it from imageA
> 4- create a Image1 as a "FillOutside" - so I can get image1 with the same
> size as A with only the ROI and filled with a transparent color
> 5- repeat 2,3,4 a number of times
> 6- with all those image1...imageN create a stack/overlay that when put
> together will look the same as imageA
>
> So, what's the best way to achieve this? Is it with stacks or overlays? Is
> there something like this already done?
>
> Cheers.

--
Christophe CHAMOT
Responsable Technique PLATIM
IFR128 BioSciences Lyon-Gerland
04.72.72.87.62
www.ifr128.prd.fr/PLATIM

[Zachary Freyberg]

Dear all,
I've been trying to add text to individual slices in a stack that I've  
made with little success.  Though I've been able to add numbers to the  
frames using the Label command which add progressively incrasing  
numbers for every frame, I would also like to add specific text every  
5 frames. What would be the best way to do so and do I needa specific  
plug-in for this? Any help is greatly appreciated!

Best regards,
Zach Freyberg

[BenTupper]

Hi,

On Oct 21, 2010, at 7:55 AM, Zachary Freyberg wrote:

> Dear all,
> I've been trying to add text to individual slices in a stack that  
> I've made with little success.  Though I've been able to add numbers  
> to the frames using the Label command which add progressively  
> incrasing numbers for every frame, I would also like to add specific  
> text every 5 frames. What would be the best way to do so and do I  
> needa specific plug-in for this? Any help is greatly appreciated!


If you would like to add text to each image you can use the macro  
command drawText(). For example...

run("Bat Cochlea Volume (19K)");
for (i = 1; i < nSlices; i+=5){
        setSlice(i);
        drawString("S="+i, 50,50);
}

Cheers,
Ben

[amsmota]

Interesting. I'm not using macros, I'm coding everything in Java, but this gave me some good points.

Cheers.

[Knecht, David]

You can do that with label using the text instead of number mode.  You can specify the frame or frame range and interval for any text label to put different labels on different frames.  Is it the same text every 5 frames or new text each time?  If the later, then you will need to specify each frame/frame range for each text label.  Dave

On Oct 21, 2010, at 7:55 AM, Zachary Freyberg wrote:

> Dear all,
> I've been trying to add text to individual slices in a stack that I've  
> made with little success.  Though I've been able to add numbers to the  
> frames using the Label command which add progressively incrasing  
> numbers for every frame, I would also like to add specific text every  
> 5 frames. What would be the best way to do so and do I needa specific  
> plug-in for this? Any help is greatly appreciated!
>
> Best regards,
> Zach Freyberg

Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)

[Christophe CHAMOT-2]

  In fact, it does the job you asked for. I can translate as plugin if
your more comfortable with …

Le 21/10/2010 15:28, amsmota a écrit :
> Interesting. I'm not using macros, I'm coding everything in Java, but this
> gave me some good points.
>
> Cheers.

--
Christophe CHAMOT
Responsable Technique PLATIM
IFR128 BioSciences Lyon-Gerland
04.72.72.87.62
www.ifr128.prd.fr/PLATIM

[amsmota]

*Hi again.

Thanks for your pointers and code. As it's normal in these kind of things,
my app grow much more complex than my first idea, so I had to write lots of
more functionalities, but your pointers were a good starting point.

Cheers.


*
* Melhores cumprimentos / Beir beannacht / Best regards
**_____________________________________________________________*
*António Manuel dos Santos Mota
Contacts: http://card.ly/amsmota
**_____________________________________________________________*

On 22 October 2010 16:30, Christophe CHAMOT
<[hidden email]>wrote:

>  In fact, it does the job you asked for. I can translate as plugin if your
> more comfortable with …
>
> Le 21/10/2010 15:28, amsmota a écrit :
>
>> Interesting. I'm not using macros, I'm coding everything in Java, but this
>>
>> gave me some good points.
>>
>> Cheers.
>>
>
> --
> Christophe CHAMOT
> Responsable Technique PLATIM
> IFR128 BioSciences Lyon-Gerland
> 04.72.72.87.62
> www.ifr128.prd.fr/PLATIM
>