Avizo lab: Segment and measure Aspirin pills

Date: Jan 22, Jan 27

Dataset: aspirin pill

pdf: AvizoClassI&II.pdf

Work on pills dataset

  • open aspirin pill raw dataset, data range, histogram
  • visualize: orthoslice, volume rendering, isosurface (rendering)
  • pre-processing: image filtering
    • median filter
    • bilateral filter
  • create binary data:
    • segmentation - threshold tool
    • interactive threshold + fill holes/closing
  • separate objects into labels
    • image morphology – erosion – does not work well – too much connection
    • fast watershed algorithm - separate objects – works but requires extended license
    • manual segmentation - threshold - 3D lassol/2D brush to remove connecting voxels
    • Advanced: distance map + H-maxima + marker based watershed
    • Advanced: distance map + Hierarchial watershed
  • label individual pills and measure:
    • connected components: produce regions (label) dataset, and component spreadsheet
    • Labeling, filter by measure
    • label analysis and analysis filter – require extended license

More stuff


  • selection in two slices: brush, magic wand, blow, etc
  • interpolate selection
  • multiple materials in the same label field


  • clipping plane / slice
  • generate surface and surface view
  • Mask by label
  • compare two orthoslices ( for two different dataset ):
    • make sure two orthoslices have the same orientation and slice number
    • show/hide one of them to switch between the two
  • orthoslice with color wash ( compare two dataset ):
    • add orthoslice to one dataset
    • click triangle from orthoslice, select color wash
    • in “data” port of colorwash, choose the second dataset
    • choose average weight sum, and change the weight slider


  • Arithmetic
  • Extract Subvolume


  • line probe defined by two points
  • surface measurement