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Hanchuan Peng edited this page Apr 12, 2016 · 4 revisions



Vaa3D is a handy, fast, and versatile 3D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions for 3D real-time interactive visualization and 3D image analysis.

Data Types

  • 3D color image stacks
    • Tiff stack (.tif, .tiff)
    • Zeiss LSM (.lsm)
    • MRC (used for electron microscopy images) (.mrc)
    • Vaa3D's raw file (.v3draw, .raw, *.v3dpbd, *.vaa3dpbd) (The PBD files are compressed raw files)
    • Any other image formats (e.g. jpeg, PNP, BMP, ...) supported by LOCI Bioinformats Java library (through a Vaa3D-bioformats plugin, see the plugin pages)
  • 5D time series of color image stacks
    • Each time point saved as a separate file (end with suffix like 000.tif, 001.tif, ...)
    • Each time point saved as a single slice of a 3D image stack of whatever formats Vaa3D supports (e.g. tiff, or Vaa3D's raw)
  • 3D irregular shaped surfaces
    • Wavefront .OBJ files
    • Vaa3D’s surface format (.v3ds)
  • 3D neuron structures or any relational data that can be described as a graph
    • SWC file (.swc)
    • Enhanced SWC file (*.eswc)
  • 3D point cloud
    • .apo file (a simple CSV format with fixed number of columns)
  • 3D landmarks
    • .marker (indeed a simple CSV format)
    • .csv
  • Linker files
    • linker files (.ano) that enables opening many data files of different types easily
    • atlas files (.atlas) for managing colocalized/registered image files

3D Real-Time Interactive Visualization

  • Intentisity projections
    • MIP (Maximal intensity projection)
    • mIP (minimal intensity projection)
  • Alpha blending
  • Cross-sectional view
  • Surface rendering
  • Volume 3D cut
  • Surface 3D cut
  • Frontal cut (with arbitrary cutting plane)
  • Color-mapping of voxels and recoloring of surface objects
  • Global and local 3D viewers for any image (Hierarchical rendering).
  • Dynamics local 3D viewer generation
    • Based on region of interest
    • Based on one-mouse-stroke defined 3D region of interest
    • Based on local 3D window around a marker
    • Based on object manager specified multiple markers
  • 3D pinpointing
    • 1-mouse click define any 3D location in 3D image based on automatically determined 3D location (including depth, etc) and color channel
    • 2-mouse click define any 3D location without ambiguity
    • 3-mouse click define any 3D location without ambiguity
  • 3D curving
    • 1-mouse/pen stroke generation of a 3D curve in space
    • Multiple mouse/pen stroke to generate a 3D curve
    • Multile mouse/pen stroke to refine a 3D curve
  • 3D direct zoom or jump
    • 1-mouse click zoom/jump of local 3D viewer
    • 1-mosue/pen stroke zoom/jump in 3D directly!
  • Animation and movie making
  • Tri-view window for google-map style navigation of image content
  • Dual looking-glasses for comparing any two locations in a 3D image
  • real time 4D (multi-color channels) blending
    • max blending
    • sum blending
    • mean-value blending
    • OIT (order independent blending)
  • Co-localizing and comparing many images easily in tri-views
  • Real time generation of surface objects
    • 3D surface mesh generation
      • Marching cube
      • Marching tetrahedron
      • Label field image (mask image)
      • Range surface (surface for an intensity range)
    • 3D neuron tracing
      • GD tracing
      • paint-and-trace
      • Intelligent editing
      • Scene-locked editing ...
    • 3D landmarking
  • Switching the relative 3D depth (layer) relationships of volumetric data and surface objects
  • Transparency of surface objects
  • Localization of mesh grid location of surface objects
  • Annotation of image contents or surface objects directly in 3D space
  • Quantitative measurement of image content and surface objects in 3D
  • Built-in landmarker manager, surface object manager, and atlas viewer to manage a large database of heterogeneous data.
  • Powerful plugin interface that especially supports real-time 3D data pushing!
  • Others you can explore and find out!

3D Image Analysis Functions

  • Quantitative measurements (3D point/location, 3D line, or 3D curve) directly in 3D
  • 3D annotation, landmarking, data management
  • Multiple image 3D colocalization, blending
  • Plugin interface and example source codes
  • Vaa3D-Neuron 2.0: 3D neuron paint and tracing
  • Vaa3D-Neuron 1.0: 3D neuron tracing, editing, transforming, and comparison
  • 3D cell segmentation
  • 3D deformable and also affine registration
  • 3D neuron structure comparison
  • 100+ Vaa3D image analysis plugins!
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