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Thread Subject:
3D Segmentation Tool?

Subject: 3D Segmentation Tool?

From: Jim O'Doherty

Date: 1 Oct, 2010 12:33:07

Message: 1 of 6

Hello,
Does anybody know of a program on the file exchange or elsewhere that can perform 3D object segmentation from a dataset? I'm beginning to write a tool for it but I've a feeling I might be re-inventing the wheel here!

Jim

Subject: 3D Segmentation Tool?

From: ImageAnalyst

Date: 1 Oct, 2010 13:09:54

Message: 2 of 6

Jim O'Doherty
Depends on how you want to segment it. How about thresholding it
slice by slice? Or were you thinking of some kind of manual way where
you carve out the chunk you want, like a sculptor?

Subject: 3D Segmentation Tool?

From: Sean

Date: 1 Oct, 2010 13:35:45

Message: 3 of 6

"Jim O'Doherty" <jim.o'doherty@nhs.net> wrote in message <i84ke2$hov$1@fred.mathworks.com>...
> Hello,
> Does anybody know of a program on the file exchange or elsewhere that can perform 3D object segmentation from a dataset? I'm beginning to write a tool for it but I've a feeling I might be re-inventing the wheel here!
>
> Jim

I have one that's not publicly available (yet) that may be of use for you. It takes in a binary image volume and allows you to define cut planes to segment objects. You can then view the cut to make sure it's what you want and save it or scrap it. Let me know if this is up your alley and I could email it to you.

Subject: 3D Segmentation Tool?

From: Jim O'Doherty

Date: 1 Oct, 2010 14:10:30

Message: 4 of 6

Thanks for your answers. Slice by slice would be a good way to process since I'm looking at tomographic data. Since it requires use by clinicians then I would need something to be as user friendly as possible!
Defining the cut plane would be probably even more advantageous. Sean, does your program work on DICOM data rather than binary?

Jim

"Sean " <sean.dewolski@nospamplease.umit.maine.edu> wrote in message <i84o3h$os0$1@fred.mathworks.com>...
> "Jim O'Doherty" <jim.o'doherty@nhs.net> wrote in message <i84ke2$hov$1@fred.mathworks.com>...
> > Hello,
> > Does anybody know of a program on the file exchange or elsewhere that can perform 3D object segmentation from a dataset? I'm beginning to write a tool for it but I've a feeling I might be re-inventing the wheel here!
> >
> > Jim
>
> I have one that's not publicly available (yet) that may be of use for you. It takes in a binary image volume and allows you to define cut planes to segment objects. You can then view the cut to make sure it's what you want and save it or scrap it. Let me know if this is up your alley and I could email it to you.

Subject: 3D Segmentation Tool?

From: Sean

Date: 1 Oct, 2010 14:26:24

Message: 5 of 6

> Thanks for your answers. Slice by slice would be a good way to process since I'm looking at tomographic data. Since it requires use by clinicians then I would need something to be as user friendly as possible!
> Defining the cut plane would be probably even more advantageous. Sean, does your program work on DICOM data rather than binary?

The program is GUI-based and is (at least for me ;) ) very user friendly. I designed it so we could have undergrads manually segment images that weren't doable with standard image processing techniques.

It isn't set up for DICOM and I've never used DICOM so I can't really say what modifications would need made. Dirk Jan Kroon has a bunch of DICOM friendly files on the FEX that may be useful to you. One idea would be that you could write a wrapper function to convert DICOM to binary and then back.
For the segmentation is it going to have to be visible in grayscale?

Subject: 3D Segmentation Tool?

From: J Rey

Date: 1 Oct, 2010 21:06:05

Message: 6 of 6

Jim,

It depends on your needs. Please check the ISO2MESH project:
http://iso2mesh.sourceforge.net/

Jose

"Jim O'Doherty" <jim.o'doherty@nhs.net> wrote in message <i84ke2$hov$1@fred.mathworks.com>...
> Hello,
> Does anybody know of a program on the file exchange or elsewhere that can perform 3D object segmentation from a dataset? I'm beginning to write a tool for it but I've a feeling I might be re-inventing the wheel here!
>
> Jim

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