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Name Category Image requires Type interaction level License/Openness has function has topic
2-D Colocalisation in Cells Software CellProfiler, CellProfiler Workflow Automated Free and open source Colocalisation analysis, Object-based colocalisation
2D and 3D mitochondrial shape analysis and network properties Software ImagePro Workflow Automated Commercial Analysis, Image segmentation Confocal fluorescence microscopy
2D and 3D tracking based on global cost function optimization Software ImageJ, MTrackJ, ImageScience.jar, Jama, Tracking2.0 Workflow Automated Free and open source Object tracking, Particle tracking, Trajectory analysis Bioimage informatics, Machine learning
2D brain slice region annotation: SliceMap Software Example: SliceMaps brain region segmentation Workflow Semi-automated Free and open source Image registration, Image segmentation Widefield microscopy, Fluorescence microscopy
2D cell tracking and analysis of morphological dynamics Software ImageJ, QuimP Workflow Semi-automated I do not know Cell segmentation, Active contours, Cell tracking
2D Gaussian fitting macro (Fiji/ImageJ) for multiple signals. Software ImageJ, Fiji Workflow Semi-automated Free and open source Image analysis, Single molecule localisation Bioimage informatics, Single molecule localization microscopy
2D spots counting using KNIME Software KNIME Image Processing and Analysis Workflow Automated Free and open source Spot detection
2D tracking using KNIME and Fiji Software KNIME Image Processing and Analysis, Fiji Workflow Semi-automated Free and open source Object tracking
3-D Density Kernel Estimation Software Jupyter notebook, Python, VIGRA, scikit-learn (sklearn), scikit-image Workflow Manual Free and open source Pixel classification, Prediction and recognition, Object counting Confocal microscopy, Machine learning
3D cell tracking and quantification of shape changes Software need a thumbnail MATLAB Workflow Automated I do not know Cell tracking
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 estimation of synaptic vesicle distribution in serial section TEM (ssTEM) Software need a thumbnail Workflow Automated I do not know
3D Nuclei Clustering Tool Software ImageJ Workflow Automated, Semi-automated Free and open source Clustering Fluorescence microscopy
3D object based colocalization using KNIME Software KNIME Image Processing and Analysis Workflow Automated I do not know Object-based colocalisation, Colocalisation analysis
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 segmentation of cells based on 2D Cellpose and CellStitch Software example of usage Workflow Automated Free and open source Cell segmentation Fluorescence microscopy
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
Adipocyte quantification ImageJ by Baecker Software ImageJ Workflow Automated Free and open source Cell segmentation Digital histology
Adipocyte quantification MATLAB Software MATLAB Workflow Semi-automated Free but not open source Cell segmentation Digital histology