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

Posted by Ines Pereira on Jul 20, 2009; 9:16pm
URL: http://imagej.273.s1.nabble.com/Magic-Wand-Type-Plugin-for-16-bit-images-tp3691703p3691708.html

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]
> >>
> >>
>