3D segmentation protocol

[Timothy J Gallaher]

Hello, 

I am new to 3D image analysis so I have a very basic question. I apologize in advance but I need your help...

 

I have a z-stack of confocal images with a single channel. I would like to process it/them into a 3D surface which I can then use to visualize the objects shape, calculate surface area and volume and ultimately print it on a 3D printer and make an animation. 

Can ICY do this?

Is there a simple beginners step by step protocol that I can follow? 

I have spent the day trying to implement Active Contours, Active cells and other add-ons but I think I am missing some fundamental steps. 

Any help that the community can provide is greatly appreciated and I am sure it would help others. Even if you just point me to the latest and greatest website or youtube tutorial It would be a great help.

Thank you

Tim

[Stephane]

Hi Tim,

Did you tried to use IsoSurface plugin ? Or just doing segmentation (Threshold, HK-Means... plugins)  then use the obtained ROI for 3D analysis (as area, surface...) and even 3D visualization. The thing is that print it on a 3D printer is a different matter and would probably require another software... I don't know if VTK export can be useful for that (but i doubt it can).

Best,

- Stephane