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General
- 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)
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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
Animator
- 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
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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
Other
- Image resizing and resampling
- Palette (color look-up-table) editing
- Simulated data generation for method validation
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Features