Posted by
Thomas Boudier on
URL: http://imagej.273.s1.nabble.com/3DObject-Counter-Surface-Map-tp5008891p5008893.html
Hi Nadia,
3D object counter should display both volume and surface from the detected
objects, do not forget to adjust brightness in order to see all labelled
objects. The surface should represent the boundary of your objects, you
can then binarize this image (threshold) and then add it or use color
merge to see the contours superimposed on your original images. You may
also want to have a look to 3DManage that does the job for you :
http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:startBest,
Thomas
> Dear ImageJ Users,
> Im trying to use the 3d object counter to analyse mitochondria. While the
> plug in seems to run through its steps just fine, the generated surface
> map at the end looks nothing like what I would expect looking at the
> thresholded image. Instead of displaying the rendered surfaces (which I
> need so I can compare the analysis/segmentation with my original image) it
> just has tiny dots, similar to what I would expect for the "centroids" to
> look like.
>
> Have I misunderstood the descriptions of the various maps generated? How
> can I be confident that the analysis has picked up the mitochondria
> correctly if I cant compare the final segmented "image" with the original?
>
> Thanks, Nadia
>
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--
Thomas Boudier, Associate Prof. UPMC,
IPAL UMI 2955, Singapore.
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