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

Posted by dpoburko on Jul 20, 2009; 7:10pm
URL: http://imagej.273.s1.nabble.com/Magic-Wand-Type-Plugin-for-16-bit-images-tp3691703p3691707.html

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]
>>
>>