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

Posted by Michael Schmid on Jul 21, 2009; 8:09am
URL: http://imagej.273.s1.nabble.com/Magic-Wand-Type-Plugin-for-16-bit-images-tp3691703p3691706.html

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]
>>
>