Avizo Lab - Simple Segmentation

date: Jan 15, 2016 data: Chocolate_bar.am

Topics

  • data import/export :

    • volume to raw
    • surface to obj – later after we created labels

  • segmentation:

    Here I choose to segment one material at a time, with different label fields. Somehow multiple materials inside same label field behave strangely in Avizo 9 – they want to exclude with each other, which is fine, but sometimes a material completely disappears, after I worked on another material – lock didn’t seem to help

    Note: It’s important to distinguish between selection and materials

    • the outer layer
      • add a new label field
      • threshold with higher data value range, apply to all slices
      • add selection to material
      • smooth labels
      • don’t fill holes, we don’t want to include air bubbles, remove island also fill some holes - confusing
    • filling
      • add a new label field
      • threshold with medium data range, apply to all slices
      • add selection to material, enable 3D view
      • smooth labels, check slices, smooth again until all big noises are gone
      • but we also included air bubbles inside the filling - now need to remove them
      • now do threshold again, with low data range, this selects air
      • under selection, use the “substract” tool to substract selection from current material
      • we end up with filling with no air bubbles
    • air bubble
      • add a new label field
      • threshold with medium to high data range, apply to all slices – now this selects the whole bar
      • add selection to material
      • fill holes
      • now the material include air bubbles
      • do a same threshold as before, apply to all slices – again we select the whole bar without air bubbles
      • under selection, use the “substract” tool to substract selection from current material
      • we end up with air bubbles only

  • from label field, -> Measure and Analyze -> material statistics, set original gray-scale data as field, apply.

    • We want to look for mean, standard deviation, min-max. These indicators tell us about the data value distribution

      statistics
      material mean std
      outlayer 1176 140
      filling 715 74
      airbubble 198 116

  • create surface model, surface view, export surface to external data format: stl, obj, iv

  • visually check the air bubble distribution

  • count air bubbles with connected components, generate regions label field, label analysis (individual measures)

  • can we filter the results? Analysis filter

Practice:

Re-generate the project from scratch. Practice segmenatoin skills. Find different ways to segment your materials