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General
- Matlab based scripts or compiled stand-alone package (Windows 64bit)
- Free and open source
- Support 2D-4D datasets (x,y,c,z,t)
- Up to 8 simultaneously opened datasets
- Bounding box for each dataset
- Extendible via plugins
- Log of performed actions
- Customizable undo system
- Customizable keyboard shortcuts
- Colorblind friendly color schemes
- Regions of interests
- Direct import/export with Matlab , Fiji , Imaris and system clipboard
- Direct import from Omero server and URL links
- Load and save to TIF (Tagged Image File Format), Amira Mesh, JPG (Joint Photographic Experts Group), Fiji BigDataViewer, HDF5 (Hierarchical Data Format),
MRC (Medical Research Council), NRRD (Nearly Raw Raster Data), PNG (Portable Network Graphics) formats
- Load up to 100 different image and video formats
- Microsoft Excel (export) for quantification
Quantification and Statistics
- Objects: Area (2D/3D)
- Objects: ConvexArea (2D)
- Objects: Curve Length (2D, pixels and image units)
- Objects: Eccentricity (2D)
- Objects: Equatorial Eccentricity (3D)
- Objects: Equiv Diameter (2D)
- Objects: Euler number (2D)
- Objects: Extent (2D)
- Objects: Filled area (2D/3D)
- Objects: Holes area (2D/3D)
- Objects: Length between end points (2D/3D)
- Objects: Major axis length (2D/3D)
- Objects: Meridional Eccentricity (3D)
- Objects: Orientation (2D)
- Objects: Perimeter (2D)
- Objects: Second axis length (2D/3D)
- Objects: Solidity (2D)
- Objects: Third axis length (3D)
- Intensity: Correlation (2D/3D)
- Intensity: Maximal (2D/3D)
- Intensity: Mean (2D/3D)
- Intensity: Minimal (2D/3D)
- Intensity: Standard deviation (2D/3D)
- Intensity: Sum (2D/3D)
Measurements
- Angles
- Caliper
- Circle, radius
- Freehand distance and intensity profile
- Linear distance and intensity profile
- Polyline distance and intensity profile
- Stereology
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Segmentation tools
- 3D ball (3D)
- Text annotations
- Brush tool (2D)
- Brush tool for 2D superpixels (SLIC , Watershed )
- Black and White Thresholding tool (global, local, adaptive; 2D/3D)
- Dilate (2D/3D, difference)
- Erode (2D/3D, difference)
- Fill holes (2D/3D)
- Frangi tubular filter (2D/3D)
- Graphcut based semi-automatic segmentation(2D/3D)
- Lasso tool (2D/3D)
- Magic Wand tool (2D/3D)
- Membrane Click Tracker tool (2D/3D)
- Morphological operations (branch points, diagonal fill, end points, skeleton, spur, thin, ultimate erosion)
- Object Picker (2D/3D)
- Quantification Filtering (2D/3D)
- Random Forest Classifier (2D/3D)
- Shape and Line Interpolation (3D)
- Smooth (2D/3D)
- Watershed for automatic image segmentation and object separation (2D/3D)
- Spot tool (2D/3D)
Image Processing
- Alignment
- Brightness, Contrast, Gamma adjustments
- Contrast-limited adaptive histogram equalization
- Color mode change (depth, color type)
- Color channel operations (add, copy, delete, invert, rotate, swap)
- Crop , Resize , Flip , Rotate , Transpose
- Chop and rechop large dataset to smaller volumes
- Invert
- Morphological operations (bottom-hat filter, clear border, morphological closing, dilate,
erode, fill regions, H-maxima transform, H-minima transform, morphological opening, top-hat filter)
- Image filters (Gaussian (2D/3D), Perona-Malik anisotropic diffusion, Average, Disk, Gradient (2D/3D), Frangi tubular filter (2D/3D), Laplacian, Log, Motion, Unsharp, Median, Weiner, Edge-engancing coherence filter)
- Intensity normalization in Z/T (complete slice, masked areas, background shift)
- Intensity replacement within selected areas
- Crop 2D/3D objects to files
Visualization
- Orthoslices (XY, ZX, ZY planes)
- Volume Rendering for small datasets
- Models with Matlab isosurfaces
- Models and volumes with Fiji 3D viewer
- Models and volumes with Imaris
- Export models to IMOD
- Export models to Amira
- Export models to 3D Slicer
- Export models in STL format
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