Avizo lab – Introduction

Date: Jan 13, 2016

Reading: Avizo User’s guide

Topics

  • Avizo versions : Lite, Standard, Extended
  • User’s guide : get started, tutorials: Visualizing and Processing 2D and 3D Images
  • Import data : formats
  • Export data : formats
  • Avizo project: save and collaborate
  • Data properties : Lattice info, data info, voxel size - Crop - Transform Editor
  • Modules:
    • Display modules : orthoslice, isosurface, volume rendering, surface view
      • Image Stack
      • ROI
      • Colormap
    • Compute modules : resample, extract subvolume, arithmetic
    • Geometry transform modules : affine, shear, register two volumes
    • Image Processing modules : filter, morphology, separation
    • Image segmentation: threshold, label, watershed
    • Measure and Analyze: Histogram, Line probe
    • Module Help
  • Menu and Toolbars

Practice

Open data/tutorial/chocolate-bar.am

  • from the data property and segmentation view, describe the data value distribution.
  • line probe, and histogram, to confirm the data value distribution
  • orthoslice
  • volume rendering, edit the colormap to better view the data
  • ROI
  • extract subvolume to fit the same ROI
  • isosuface
  • threshold from segmenation tools
  • generate surface and surface view
  • connected components and label analysis
  • watershed segmentation
  • export data
  • save snapshots, save project