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Name Category Image requires Type interaction level License/Openness has function has topic
eC-CLEM Software logo ec-clem Component Manual, Semi-automated Free and open source Alignment construction, Image registration, Affine registration, Rigid registration, Deformable registration Correlative Light and Electron Microscopy, Multimodal imaging
ec-clem autofinder Software logo autofinder Component Semi-automated Free and open source Image registration, Affine registration, Rigid registration Correlative Light and Electron Microscopy
Icy Protocols Software need a thumbnail JavaDoc Parser, Icy Protocols SDK Component Manual Free and open source Data handling Bioimage informatics
ImageJFX Software ImageJFX screen Capture Fiji Collection Manual, Semi-automated Free and open source Image analysis, Data handling Bioimage informatics
CellTrack Software GUI image (from http://sacan.biomed.drexel.edu/celltrack) Collection Semi-automated Free and open source Object detection, Object feature extraction, Cell tracking, Trajectory analysis Bioimage informatics
Advanced Cell Classifier Software Advanced Cell Classifier Matlab Image Processing Toolbox, Matlab compiler runtime Collection Automated, Manual, Semi-automated Free and open source Image analysis, Image classification, Image annotation, Image visualisation Bioimage informatics, Machine learning
BioImageXD Software Screen capture of BioImageXD Collection Manual, Semi-automated Free and open source Image analysis, Image processing, Image visualisation
ADAPT Software ADAPT logo ImageJ Component Automated Free and open source Analysis, Object detection Fluorescence microscopy
CellProfiler Software Collection Automated, Semi-automated Free and open source
Spotsizer Software screenshot of the spotsizer gui Collection I do not know Free but not open source Bioimage informatics
Super-Resolution Radial Fluctuations (SRRF) Software Comparison TIRF - SRRF ImageJ Component Semi-automated Free and open source Image deconvolution, Image denoising Live sample imaging, Widefield microscopy, Super-resolution microscopy, Confocal microscopy
ImageJ Software logo ImageJ Collection Semi-automated, Manual, Automated Free and open source
JACoP Software example of partial colocalisation from reference publication ImageJ Component Automated, Semi-automated Free and open source Object-based colocalisation, Object-based colocalisation, Pixel-based colocalisation, Colocalisation analysis, Colocalisation analysis Fluorescence microscopy
Spot Detector (Icy) Software logo spot detector Component Semi-automated Free and open source Spot detection, Image segmentation, Cell segmentation Electron microscopy, Light microscopy, Bright field microscopy
performing automatic registration for CLEM Software Workflow results Workflow Automated, Semi-automated Free and open source Alignment construction, Image registration, Affine registration, Rigid registration, Spot detection Correlative Light and Electron Microscopy
SOAX Software snapshot microtubules soax Active Contours Collection Semi-automated Free and open source Image analysis, Filament tracing, Active contours, Skeletonisation Fluorescence microscopy, Confocal fluorescence microscopy
Angiogenesis / Sprout Analyzer (ImageJ) Software graphical abstract ImageJ Component Semi-automated Free and open source Filament tracing, Neuron image analysis Bioimage informatics, Fluorescence microscopy
Scipion Software http://scipion.cnb.csic.es/m/home/ Collection Semi-automated Free and open source Alignment construction, Image reconstruction, Tomographic reconstruction Electron microscopy
QuimP Software Screenshot Collection Automated, Manual, Semi-automated Free and open source Cell segmentation, Interactive segmentation, Shape features, Object tracking, Cell tracking Fluorescence microscopy
Vaa3D Software Vaa3D_logo Vaa3D, ITK, ICY Annotation, 3D Viewer Collection Automated, Manual, Semi-automated Free and open source Image registration, Cell segmentation, Annotation, Data handling, Visualisation Bioimage informatics, Statistics