General Data import/export Image Processing Segmentation tools

Deep Learning Quantification and Statistics Measurements Visualization

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

Data import/export (click here for complete list) Direct import/export with MATLAB , Fiji , Imaris and system clipboard Direct import from Omero server and URL links Load up to 100 different image and video formats Microsoft Excel (export) for quantification Rename and shuffle tool for unbiased classification and segmentation

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

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) White balance correction

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) Segment-anything (2D) Shape and Line Interpolation (3D) Smooth (2D/3D) Spot tool (2D/3D) Watershed for automatic image segmentation and object separation (2D/3D)

Deep Learning 2D Semantic segmentation 2.5D Semantic segmentation 3D Semantic segmentation 2D Patch-wise segmentation Activation explorer

Extraction of patches for training Augmentations: 17 for 2D and 18 for 3D Overlapping tiles for prediction Dynamic masking for prediction Evaluation of results

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

Kymographs Polyline distance and intensity profile Stereology Wound healing assay

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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