Re: what's the best way to process 3D image data in ImageJ

Posted by Michael Doube-4 on
URL: http://imagej.273.s1.nabble.com/what-s-the-best-way-to-process-3D-image-data-in-ImageJ-tp5013349p5013427.html

Dear Shameem,

On 30/06/15 12:54, Shameem Sampath wrote:
> Hi List,
> Coincidentally, I have a related query regarding analysing CAT scan Dicom images of knees in ImageJ.
> Is there a way to measure trabecular orientation in the xyz planes?

Trabecular orientation is usually measured using the mean intercept length (MIL) method, although in greyscale images, Fourier-based (autocorrelation) methods can work as well.

The bigger problem you have is that if you have clinical CT images, you have relatively low resolution in the axial (z) direction compared to the in-plane resolution of the slices (xy) and trabecular size (in humans, no greater than 500µm diameter). Typical pixel spacings are something like 100-500 µm in xy and 500-2000µm in z. True resolution is usually somewhat less than that. Usually, z slice-spacing is 10-20× greater than xy pixel spacing. So that means it's very difficult to resolve the z element of any 3D trabecular orientation vector.

If you really need trabecular orientation, you must have isotropic pixel spacing (same in x, y and z), otherwise your measurement is likely to be confounded by its interaction with pixel spacing.

Best regards,

Michael

> Regards,
> Shameem Sampath
> The Bluespot Knee Clinic

<http://www.rvc.ac.uk>

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