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Name Category Image requires Type interaction level License/Openness has function has topic
3D cell tracking using Gaussian Mixture Model (TGMM) Software need a thumbnail Workflow Free and open source Cell tracking Bioimage informatics, Live sample imaging, Light-sheet microscopy
3D confocal noise simulator Software Component Commercial
3D estimation of synaptic vesicle distribution in serial section TEM (ssTEM) Software need a thumbnail Workflow Automated I do not know
3D Fill holes (mcib3d) Software need a thumbnail mcib3d library, ImageJ Component Automated Free and open source Morphological operation
3D Generalized Riesz-Wavelet Toolbox for Matlab Software need a thumbnail MATLAB Component Semi-automated Free and open source Image feature detection Bioimage informatics
3D ImageJ Suite Software need a thumbnail ImageJ, ImageScience.jar Collection Automated, Manual, Semi-automated Free and open source Colocalisation analysis, Image segmentation, Object feature extraction, Morphological operation, Visualisation Bioimage informatics
3D intensity profile Software Fiji Component Automated Free and open source
3D Nuclei Clustering Tool Software ImageJ Workflow Automated, Semi-automated Free and open source Clustering Fluorescence microscopy
3D object based colocalisation Training Material
3D object based colocalization using KNIME Software KNIME Image Processing and Analysis Workflow Automated I do not know Object-based colocalisation, Colocalisation analysis
3D Objects Counter Software need a thumbnail Fiji, ImageJ Component Automated Free and open source Object feature extraction, Shape features, Object counting Fluorescence microscopy
3D OrthoViewer (Icy) Software need a thumbnail Component Semi-automated Free and open source Image visualisation Bioimage informatics
3D PSF estimator Software ImageJ, Fiji, MosaicSuite Component Automated Free and open source Image feature detection Fluorescence microscopy
3D Segmentation & visualization of nanoparticles attached to the surface of red blood cells Software image from the paper here:https://pubs.rsc.org/en/content/articlelanding/2019/nr/c8nr09960j ImageJ Workflow Automated Free and open source Object feature extraction Fluorescence microscopy
3D segmentation (reconstruction) and modeling using Free-D Software need a thumbnail Workflow Automated, Manual, Semi-automated Free but not open source Image registration, Analysis, Image segmentation
3D Slicer Software 3D slicer 3D Viewer, ITK Collection Automated Free and open source
3D Surface Plot Software ImageJ Component Manual Free and open source Visualisation Bioimage informatics
3D vessel segmentation of synchrotron phase contrast tomography Software Fiji, ilastik Workflow Semi-automated Free but not open source Image analysis, Interactive segmentation Bioimage informatics, Tomography, Machine learning
3D Viewer Software ImageJ, 3D Viewer Component Manual, Semi-automated Free and open source Visualisation Bioimage informatics
3D-DAOSTORM Software need a thumbnail Component Semi-automated Free and open source Single molecule localisation Super-resolution microscopy, Single molecule localization microscopy