Re: Objects Counter can't find any objects on my screen?
Posted by esumft on Nov 26, 2014; 9:55pm
URL: http://imagej.273.s1.nabble.com/Objects-Counter-can-t-find-any-objects-on-my-screen-tp5010585p5010652.html
URL: http://imagej.273.s1.nabble.com/Objects-Counter-can-t-find-any-objects-on-my-screen-tp5010585p5010652.html
​Dear Thomas,
The method you suggested works, however, it is not scaled to the DICOM header information (I'm getting intensity mean values of around 32,000 when it should be more like 250). Is there a way to do this? Have I missed something?
From: Thomas Boudier [via ImageJ] <ml-node+[hidden email]>
Sent: 26 November 2014 02:56
To: Griffiths, Elliott
Subject: Re: Objects Counter can't find any objects on my screen?
Sent: 26 November 2014 02:56
To: Griffiths, Elliott
Subject: Re: Objects Counter can't find any objects on my screen?
Dear Elliot,
It seems taht your image is 16 bits but signed, with negative values, so
threshold algorithm may not work properly with this kind of data. I then
advise you to :
1/ duplicate your original image
2/ convert the copy to 8-bits
3/ use segmentation from 3DManager
4/ add the segmented image to 3DManager
5/ select original image and perform quantification
Hope this helps
Thomas
On 25/11/14 19:31, esumft wrote:
> I must add, if I convert the image to 8-bit grayscale it works. But, it
> changes the values of the intensity (this is calibrated with a DICOM header)
> so the readings I get from the 3DObjectsDetector will be wrong?
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Objects-Counter-can-t-find-any-objects-on-my-screen-tp5010585p5010617.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
--
/***************************************************************/
Thomas Boudier, Associate Professor, UPMC,
Université Pierre et Marie Curie, Paris, France.
BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
It seems taht your image is 16 bits but signed, with negative values, so
threshold algorithm may not work properly with this kind of data. I then
advise you to :
1/ duplicate your original image
2/ convert the copy to 8-bits
3/ use segmentation from 3DManager
4/ add the segmented image to 3DManager
5/ select original image and perform quantification
Hope this helps
Thomas
On 25/11/14 19:31, esumft wrote:
> I must add, if I convert the image to 8-bit grayscale it works. But, it
> changes the values of the intensity (this is calibrated with a DICOM header)
> so the readings I get from the 3DObjectsDetector will be wrong?
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Objects-Counter-can-t-find-any-objects-on-my-screen-tp5010585p5010617.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
--
/***************************************************************/
Thomas Boudier, Associate Professor, UPMC,
Université Pierre et Marie Curie, Paris, France.
BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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