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General
- Matlab based scripts or compiled stand-alone package (Windows, MacOS, Linux)
- Free and open source
- Support 2D-4D datasets (x,y,c,z,t)
- Up to 9 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
- Virtual stacking mode for working with datasets that are larger than available memory
- Batch processing mode
- 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
- Rename and shuffle tool for unbiased classification and segmentation
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
- Wound healing assay
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Segmentation tools
- 3D ball (3D)
- 3D lines (3D)
- Annotations with values
- Brush tool (2D)
- Brush tool for 2D superpixels (SLIC , Watershed )
- Black and White Thresholding tool (global, local, adaptive; 2D/3D)
- Deep convolutional neural networks for train and prediction
- Dilate (2D/3D, difference)
- Drag & Drop
- Erode (2D/3D, difference)
- Fill holes (2D/3D)
- Frame selection tool
- 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)
- Spot tool (2D/3D)
- Watershed for automatic image segmentation and object separation (2D/3D)
Image Processing
- Add frame around the dataset
- Alignment
- Brightness, Contrast, Gamma adjustments
- Chop and re-chop large dataset to smaller volumes
- Content-aware fill
- Contrast-limited adaptive histogram equalization
- Color mode change (depth, color type)
- Color channel operations (add, copy, delete, invert, rotate, shift, swap)
- Crop , Resize , Flip , Rotate , Transpose
- Crop 2D/3D objects to files
- Debris removal
- Image arithmetics
- Image filters (<30 ) including
external BMxD (2D/3D) and DNN denoising
- Intensity normalization in Z/T (complete slice, masked areas, background shift)
- Intensity replacement within selected areas
- Invert
- Manipulations with slices: insert, copy, delete
- Intensity projections
and focus stacking
- Morphological operations (bottom-hat filter, clear border, morphological closing, dilate,
erode, fill regions, H-maxima transform, H-minima transform, morphological opening, top-hat filter)
Visualization
- Orthoslices (XY, ZX, ZY planes)
- Volume Rendering (hardware)
- Volume Rendering (software)
- 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 and volumes to Matlab Volume Viewer
- Export models in STL format
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