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Introduction

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!