image segmentation feature size

[Nicole Chen]

Hello,

I'm working on 3D reconstruction for microstructure. I tried with the pipeline "image segmentation", it can calculate the size for features. I'm wondering how it counts the feature size. 

When I set "scalar tolerance" in the filter "segment features", for example, I set it as 10, does it mean that the pixels in the range of 10 are counted as a feature?

When it was visualized in Paraview, what did the different colors mean for FeatureIds, and what does the number on the color bar mean?

I attach the screenshot from Paraview, and two slices from my stack.

Thank you very much!

Best,

Nicole

[Michael Jackson]

Segmentation using a Scalar: if you put in a Tolerance of “10” that means all pixels that are identified as the same feature will be within a range of “10” in the pixel value. This could mean that one feature has pixel values from 88 to 98 and another could have a range of 196 to 206. 

Each “feature” that gets created will have a unique integer value. ParaView is just coloring by those features. Nothing. It will help you “see” the individual grains better in the visualization.

--
Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

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[Michael Jackson]

Dear Nicole,

   1: Calculate volume Fraction of pixels < value use the “Compute Volume Fractions of Ensembles” filter. In order to do this correctly you will also need to run the “Create Ensemble Info” filter BEFORE the “Compute Volume Fractions of Ensembles” filter. Create 2 phases. The values will not matter really. What this filter is going to do is make sure the proper attribute matrix is created. In order to actually look at that data you will need to export the values to a file, for example a simple CSV File.

  2: After you have segmented the features, you can run the "Compute Feature Sizes”. In order to color by those sizes you will need to run the “Create Element Array from Feature Array” filter.

I have included a pipeline that works for a stack of images. You may need to adjust the threshold values for the 3D stack. 

This pipeline works with DREAM3D-NX RC-12 which can be downloaded from https://www.dream3d.io

--
Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

On Jul 17, 2024 at 09:12:15, Chen Ruomeng <crmen...@outlook.com> wrote:

Hi Mike,

 

Thanks for your explaination!

 

Is there any filters in Dream 3D to calculate the volume fraction for the pixels  segmented by thresholding (for example, calculate the volume fraction of pixel value <50)? And is it possible to calculate the size of volume of different features and visualize with different colors?

 

Best,

Nicole

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