Free open source software for analysis and visualization of multidimensional biomedical images



  • Free and open source
  • All features support 3D time series (4D) data
  • Command pipelines and batch processing without programming
  • On-screen feature descriptions and color coding assist in use
  • Leverages VTK and ITK

File type support

  • Carl Zeiss LSM
  • Olympus OIF
  • Leica TXT & LIF
  • BioRad PIC
  • MRC
  • Interfile
  • TIFF, PNG, JPEG, BMP (read & write)
  • OME-TIFF (read & write)
  • VTK XML (write)
  • BioImageXD internal formats (read & write)

Image viewing modes

  • Slices
  • Gallery
  • Orthogonal sections
  • Maximum and average intensity projection
  • 3D rendering (interactive and full quality, several modules can be displayed at the same time)

3D modules

  • Volume rendering (software ray casting and OpenGL texture mapping)
  • Surface rendering
  • Ortogonal slices
  • Visualization of motion tracks
  • Clipping with plane and box
  • Warping
  • Visualization of Protein Data Bank (PDB) files
  • Axes, angle and distance measurements


  • Creates videos of any scene rendered in 3D mode
  • Supports two combinable techniques: virtual camera flight path and keyframes
  • Track-based user interface

Quantitative analysis

  • Colocalization analysis (voxel and object)
  • 3D segmentation methods
  • Object separation
  • Object analysis
  • Motion tracking
  • Internalization analysis
  • Region of interest (ROI) analysis
  • Fluorescence Recovery After Photobleaching (FRAP) analysis

Image processing

  • Color, brightness, contrast and gamma adjustment
  • Merging data channels into color images
  • Noise filtering and background subtraction methods
  • Morphological, logical and arithmetic operations
  • Fourier transforms
  • Feature detection methods
  • Registration methods
  • Deconvolution
  • Fluorescence bleach correction
  • Graphical color and intensity transfer function adjustments

Batch processor

  • Supports multiple parallel processing pipelines
  • Supports almost any operation in BioImageXD
  • Produces result images and aggregates selected result statistics into spreadsheets for further processing


  • Image resizing and resampling
  • Palette (color look-up-table) editing
  • Simulated data generation for method validation
You are here: Home Features