Segmenting and counting pixels along rays

[Kustaa Nyholm]

Hi,


I need to estimate the maximum x-ray attenuation of a various
human body parts.

For that purpose I've downloaded the CT/DICOM datasets of the visible
human project.

Now I would like to segment / classify each pixel as bone / soft tissue /
air
and then count the number of each class along all the rays that pass
through the center of the body and collect the maximums for each image.

As this is only for rough estimate I could do with counting the
the segmented pixel values along vertical/horizontal lines and
recording the maximum counts for each image.

I'm an old hand with Java so I can program my way out of this but
surely this is not a unique requirement and thus I'm sure ImageJ
and the plugins have something that could get me half way there.

Any pointers, suggestions etc are welcome.

br Kusti

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ignacio Arganda-Carreras]

Hello Kustaa,

Without seeing your images, from what you said it seems you could use my
Advanced Weka Segmentation plugin.

Let me know if you have questions about it.

Cheers!

ignacio

On Mon, Dec 17, 2012 at 5:43 AM, Kustaa Nyholm
<[hidden email]>wrote:

> Hi,
>
>
> I need to estimate the maximum x-ray attenuation of a various
> human body parts.
>
> For that purpose I've downloaded the CT/DICOM datasets of the visible
> human project.
>
> Now I would like to segment / classify each pixel as bone / soft tissue /
> air
> and then count the number of each class along all the rays that pass
> through the center of the body and collect the maximums for each image.
>
> As this is only for rough estimate I could do with counting the
> the segmented pixel values along vertical/horizontal lines and
> recording the maximum counts for each image.
>
> I'm an old hand with Java so I can program my way out of this but
> surely this is not a unique requirement and thus I'm sure ImageJ
> and the plugins have something that could get me half way there.
>
> Any pointers, suggestions etc are welcome.
>
> br Kusti
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html