Dear Prof. Peng,

      I am a master student major in clinical medicine, My study focused on the visualization of head and neck anatomy. To build a natural digital anatomy model, I have tried 3D doctor, mimics, amira and finally found the great software Vaa3D. Because I am not familiar with the computer language and some complicated process, I have to ask for help here,even some questions maybe easy for professionals.
Let me introduce my problems:
1. Several methods are used for biomedical image segmentation in software Amira,such as Interactive Image Segmentation,Threshold Segmentation,region growing,brush and lasso Segmentation.However,I found Cell- segmentation and label objects in Vaa3d with default plug-in.I wonder if there are other segmentation methods available and how can I find it?
2.How to put or paste the source codes from the official website into the software and run it normally?
3. If we can volume rendering the targets segmented but not ROI using true color or surface rendering targets segmented by true color other than pseudo color?

Best regards,
Jun Tian

For your questions:
1. Vaa3d has some other related plugins (e.g. cell_counting, image_thresholding, shape-analysis). They are all under "Plug-In" menu. Also, there are some basic functions under "Image/Data" --> "intensity" menu.

2. Do you want to build Vaa3D from the source code? If in this case, please check the instruction from https://github.com/Vaa3D/Vaa3D_Wiki/wiki/Vaa3D-Wiki. On the right side menu, you can find different instructions based on your platform (Windows, Linux, or Mac).

3. Please provide us an example image.  

Zhi

Dear Zhi,

            Thanks for your answer. An example image have uploaded,how to segmentation like this image?Where is the undo function of the software?
 

Best regards,
Jun Tian

Thanks for sending the image. Could you please also indicate which part you want to segment? Or provide the labeled image.

I want to segmentate the cartilage.Could you tell me the segmentation process?   thanks！

I want to segment the cartilage.Could you tell me the segmentation process? thanks！

Dear ALL,

Thanks very much for this wonderful tool. I am a new user of Vaa3D and have learned this software for several weeks, but I cannot find the Region growing and Global alignment functions of the software. There are so many plugins in this software and I don't know which one is suitable for me. So could you please give me some suggestions about my concern?
Thanks very very much and I am looking forward to hearing from you soon.

Best regards,
Jun Tian

Jun,

Depending on how you would like to segment, you may need to develop some small tools based on existing modules of Vaa3D or its plugin to segment the regions you like. We  do not maintain a current readily useful plugin for your image, unfortunately. But if you want to try some variants of methods, I think tools such as the the grayscale distance transform plugin can be used followed by a simple threshold, and you should be able to produce meaningful results. Then you can refine the boundary of the segmentation a little bit by using a deformable model.


-Hanchuan



Originally posted by jun tian:

Dear Prof. Peng,
Thanks for your answer. The following questions are still bothering me.
1.What should I do if I want to customize some small tools based on existing modules of Vaa3D or its plugin to segment the interesting regions? I can not design these small     tools by ourselves.
2.Whether the area segmented in one channel can be copy to other two channels directly for final blending three channels other than segmentation in other two channels separately which might result in that the same object are segmented differently and then the blending model have much redundant colour dots. If we can find a simple way to solve the problem, it is easily to get a true color rendering model after segmentation just based on one optimal channel.Image as follows:
So could you please give me some suggestions about my concerns?
Thanks very very much and I am looking forward to hearing from you soon.

Best regards,
Jun tian