"Magic Wand"-Type Plugin for 16-bit images

[Ines Pereira]

Hello all,

I am working with 16-bit grayscale images and I would like to be able to
select areas above a certain threshold (to be defined for each image),
without losing the grayscale information (I need to quantify the pixel
intensity of the selected area). I did a quick search over existing plugins
and couldn't find anything that worked with 16-bit images. Do you know of
something that might work or is there anyone who could help me with this?

Thank you,

Inês Pereira
NAS/LEG/NIA/NIH
Phone: [phone]
Fax: [phone]

[dpoburko]

Ines Pereira wrote:

> Hello all,
>
> I am working with 16-bit grayscale images and I would like to be able to
> select areas above a certain threshold (to be defined for each image),
> without losing the grayscale information (I need to quantify the pixel
> intensity of the selected area). I did a quick search over existing plugins
> and couldn't find anything that worked with 16-bit images. Do you know of
> something that might work or is there anyone who could help me with this?
>
> Thank you,
>
> Inês Pereira
> NAS/LEG/NIA/NIH
> Phone: [phone]
> Fax: [phone]O
>  

One approach would be to threshold your 16-bit images, then use the
Analyze>Analyze Particles function. Hopefully you will be able to adjust
the parameters for Analyze Particles so that ImageJ will create ROI
around the objects that you want to measure. Be sure to select the "Add
to Manager" option to add the ROIs to the ROI manager. Now select your
original 16-bit image and hit "Show All" on the ROI manager to
effectively transfer the ROIs to the 16-bit image. Now run measure to
measure whichever metrics you want for each ROI. Piece o' cake. I do
this almost daily in an automated fashion to analyze fluorescent
puncta/dots from 16-bit images.

Hope that helps,
Damon

--

Damon Poburko, PhD
Postdoctoral Research Fellow
Stanford University School of Medicine
Dept. of Molecular & Cellular Physiology
279 Campus Dr., Beckman B103, Stanford, CA 94305
Ph: 650 725 7564, fax: [phone]

[Ines Pereira]

Thank you for the replies. I have tried this method and it worked well,
however, the intensity measure was in a scale of 0-255 (8-bit). Is there a
way around that?
Thanks once again,
Inês

On Mon, Jul 20, 2009 at 12:42 PM, Damon Poburko <[hidden email]>wrote:

> Ines Pereira wrote:
> > Hello all,
> >
> > I am working with 16-bit grayscale images and I would like to be able to
> > select areas above a certain threshold (to be defined for each image),
> > without losing the grayscale information (I need to quantify the pixel
> > intensity of the selected area). I did a quick search over existing
> plugins
> > and couldn't find anything that worked with 16-bit images. Do you know of
> > something that might work or is there anyone who could help me with this?
> >
> > Thank you,
> >
> > Inês Pereira
> > NAS/LEG/NIA/NIH
> > Phone: [phone]
> > Fax: [phone]O
> >
> One approach would be to threshold your 16-bit images, then use the
> Analyze>Analyze Particles function. Hopefully you will be able to adjust
> the parameters for Analyze Particles so that ImageJ will create ROI
> around the objects that you want to measure. Be sure to select the "Add
> to Manager" option to add the ROIs to the ROI manager. Now select your
> original 16-bit image and hit "Show All" on the ROI manager to
> effectively transfer the ROIs to the 16-bit image. Now run measure to
> measure whichever metrics you want for each ROI. Piece o' cake. I do
> this almost daily in an automated fashion to analyze fluorescent
> puncta/dots from 16-bit images.
>
> Hope that helps,
> Damon
>
> --
>
> Damon Poburko, PhD
> Postdoctoral Research Fellow
> Stanford University School of Medicine
> Dept. of Molecular & Cellular Physiology
> 279 Campus Dr., Beckman B103, Stanford, CA 94305
> Ph: 650 725 7564, fax: [phone]
>

[dpoburko]

Hi Ines,

I'm not sure why your intensity measurements would be on an 8-bit scale
if your images are 16-bit.  As long as you have selected your 16-bit
image before pressing measure, the measured values should be 16-bit. Can
you verify that under Analyze>Set Measurements you have the "Limit to
Threshold" option unchecked? Which version of ImageJ are you running?

D


Ines Pereira wrote:

> Thank you for the replies. I have tried this method and it worked well,
> however, the intensity measure was in a scale of 0-255 (8-bit). Is there a
> way around that?
> Thanks once again,
> Inês
>
> On Mon, Jul 20, 2009 at 12:42 PM, Damon Poburko <[hidden email]>wrote:
>
>  
>> Ines Pereira wrote:
>>    
>>> Hello all,
>>>
>>> I am working with 16-bit grayscale images and I would like to be able to
>>> select areas above a certain threshold (to be defined for each image),
>>> without losing the grayscale information (I need to quantify the pixel
>>> intensity of the selected area). I did a quick search over existing
>>>      
>> plugins
>>    
>>> and couldn't find anything that worked with 16-bit images. Do you know of
>>> something that might work or is there anyone who could help me with this?
>>>
>>> Thank you,
>>>
>>> Inês Pereira
>>> NAS/LEG/NIA/NIH
>>> Phone: [phone]
>>> Fax: [phone]O
>>>
>>>      
>> One approach would be to threshold your 16-bit images, then use the
>> Analyze>Analyze Particles function. Hopefully you will be able to adjust
>> the parameters for Analyze Particles so that ImageJ will create ROI
>> around the objects that you want to measure. Be sure to select the "Add
>> to Manager" option to add the ROIs to the ROI manager. Now select your
>> original 16-bit image and hit "Show All" on the ROI manager to
>> effectively transfer the ROIs to the 16-bit image. Now run measure to
>> measure whichever metrics you want for each ROI. Piece o' cake. I do
>> this almost daily in an automated fashion to analyze fluorescent
>> puncta/dots from 16-bit images.
>>
>> Hope that helps,
>> Damon
>>
>> --
>>
>> Damon Poburko, PhD
>> Postdoctoral Research Fellow
>> Stanford University School of Medicine
>> Dept. of Molecular & Cellular Physiology
>> 279 Campus Dr., Beckman B103, Stanford, CA 94305
>> Ph: 650 725 7564, fax: [phone]
>>
>>    

[Ines Pereira]

Once again, thank you for the quick reply. I'm sorry about the confusion, I
was clicking "apply" in the Threshold window and that was changing the image
to 8-bit. I have been able to select the areas I'm interested in and get a
measurement in 16-bit.
Thank you for all your help!
Inês Pereira


On Mon, Jul 20, 2009 at 3:10 PM, Damon Poburko <[hidden email]>wrote:

> Hi Ines,
>
> I'm not sure why your intensity measurements would be on an 8-bit scale
> if your images are 16-bit.  As long as you have selected your 16-bit
> image before pressing measure, the measured values should be 16-bit. Can
> you verify that under Analyze>Set Measurements you have the "Limit to
> Threshold" option unchecked? Which version of ImageJ are you running?
>
> D
>
>
> Ines Pereira wrote:
> > Thank you for the replies. I have tried this method and it worked well,
> > however, the intensity measure was in a scale of 0-255 (8-bit). Is there
> a
> > way around that?
> > Thanks once again,
> > Inês
> >
> > On Mon, Jul 20, 2009 at 12:42 PM, Damon Poburko <[hidden email]
> >wrote:
> >
> >
> >> Ines Pereira wrote:
> >>
> >>> Hello all,
> >>>
> >>> I am working with 16-bit grayscale images and I would like to be able
> to
> >>> select areas above a certain threshold (to be defined for each image),
> >>> without losing the grayscale information (I need to quantify the pixel
> >>> intensity of the selected area). I did a quick search over existing
> >>>
> >> plugins
> >>
> >>> and couldn't find anything that worked with 16-bit images. Do you know
> of
> >>> something that might work or is there anyone who could help me with
> this?
> >>>
> >>> Thank you,
> >>>
> >>> Inês Pereira
> >>> NAS/LEG/NIA/NIH
> >>> Phone: [phone]
> >>> Fax: [phone]O
> >>>
> >>>
> >> One approach would be to threshold your 16-bit images, then use the
> >> Analyze>Analyze Particles function. Hopefully you will be able to adjust
> >> the parameters for Analyze Particles so that ImageJ will create ROI
> >> around the objects that you want to measure. Be sure to select the "Add
> >> to Manager" option to add the ROIs to the ROI manager. Now select your
> >> original 16-bit image and hit "Show All" on the ROI manager to
> >> effectively transfer the ROIs to the 16-bit image. Now run measure to
> >> measure whichever metrics you want for each ROI. Piece o' cake. I do
> >> this almost daily in an automated fashion to analyze fluorescent
> >> puncta/dots from 16-bit images.
> >>
> >> Hope that helps,
> >> Damon
> >>
> >> --
> >>
> >> Damon Poburko, PhD
> >> Postdoctoral Research Fellow
> >> Stanford University School of Medicine
> >> Dept. of Molecular & Cellular Physiology
> >> 279 Campus Dr., Beckman B103, Stanford, CA 94305
> >> Ph: 650 725 7564, fax: [phone]
> >>
> >>
>

[Mario Guarracino]

Dear Inês,
Yawi3D is a 3D magic wand for ImageJ, that works on 16-bit image stacks,
producing 3D ROIs. Of course, you can use it on a single image, getting one
ROI. It gives some basic statistical measurements and histograms for the 3D
ROIs. It has been used for segmenting lung fibrosis in CT images, although
it implements a general purpose algorithm.

The source code is available here:
https://sourceforge.net/projects/yawi3d/files/

and release notes can be found here:
https://sourceforge.net/project/shownotes.php?group_id=109017&release_id=697
281

Hope it helps.

Mario



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Ines
Pereira
Sent: Monday, July 20, 2009 4:06 PM
To: [hidden email]
Subject: "Magic Wand"-Type Plugin for 16-bit images

Hello all,

I am working with 16-bit grayscale images and I would like to be able to
select areas above a certain threshold (to be defined for each image),
without losing the grayscale information (I need to quantify the pixel
intensity of the selected area). I did a quick search over existing plugins
and couldn't find anything that worked with 16-bit images. Do you know of
something that might work or is there anyone who could help me with this?

Thank you,

Inês Pereira
NAS/LEG/NIA/NIH
Phone: [phone]
Fax: [phone]

[Michael Schmid]

Hi Ines,

maybe your image has a calibration function that maps 0-65535 onto 0-255?
Also check for the number of decimals in Analyze>Set Measurements

Two further possibilities:
- Thresholding, then Edit>Selection>Create Selection
- The Versatile Wand plugin.
  http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start

By moving the sliders of the threshold panel, you have only 8 bits
accuracy; but the numeric values entered with "Set" have full accuracy
(even though the red area in the display may be affected by rounding
errors - they are based on the 8-bit image used for display, not on the
original image data).

Michael
___________________________________________________________________

On Mon, July 20, 2009 19:51, Ines Pereira wrote:

> Thank you for the replies. I have tried this method and it worked well,
> however, the intensity measure was in a scale of 0-255 (8-bit). Is there a
> way around that?
> Thanks once again,
> Inês
>
> On Mon, Jul 20, 2009 at 12:42 PM, Damon Poburko
> <[hidden email]>wrote:
>
>> Ines Pereira wrote:
>> > Hello all,
>> >
>> > I am working with 16-bit grayscale images and I would like to be able
>> to
>> > select areas above a certain threshold (to be defined for each image),
>> > without losing the grayscale information (I need to quantify the pixel
>> > intensity of the selected area). I did a quick search over existing
>> plugins
>> > and couldn't find anything that worked with 16-bit images. Do you know
>> of
>> > something that might work or is there anyone who could help me with
>> this?
>> >
>> > Thank you,
>> >
>> > Inês Pereira
>> > NAS/LEG/NIA/NIH
>> > Phone: [phone]
>> > Fax: [phone]O
>> >
>> One approach would be to threshold your 16-bit images, then use the
>> Analyze>Analyze Particles function. Hopefully you will be able to adjust
>> the parameters for Analyze Particles so that ImageJ will create ROI
>> around the objects that you want to measure. Be sure to select the "Add
>> to Manager" option to add the ROIs to the ROI manager. Now select your
>> original 16-bit image and hit "Show All" on the ROI manager to
>> effectively transfer the ROIs to the 16-bit image. Now run measure to
>> measure whichever metrics you want for each ROI. Piece o' cake. I do
>> this almost daily in an automated fashion to analyze fluorescent
>> puncta/dots from 16-bit images.
>>
>> Hope that helps,
>> Damon
>>
>> --
>>
>> Damon Poburko, PhD
>> Postdoctoral Research Fellow
>> Stanford University School of Medicine
>> Dept. of Molecular & Cellular Physiology
>> 279 Campus Dr., Beckman B103, Stanford, CA 94305
>> Ph: 650 725 7564, fax: [phone]
>>
>