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Name Category Image requires Type interaction level License/Openness has function has topic
MosaicExplorerJ Software ImageJ Component Manual, Semi-automated Free and open source Data handling, Image stitching Light-sheet microscopy
Incucyte Base Analysis Software Software need a thumbnail Collection Semi-automated Commercial Analysis, Cell segmentation, Image visualisation Live sample imaging, Fluorescence microscopy, Phase contrast microscopy, Machine learning
ImageJ Threshold Software need a thumbnail ImageJ Component Manual, Semi-automated Free and open source Image thresholding Bioimage informatics
Semi-automated quantification of three stages of phagocytosi using ImageJ Software ImageJ Workflow Semi-automated Free and open source Cell segmentation, Interactive segmentation, Object classification Fluorescence microscopy, Bright field microscopy
FluoGAN Software FluoGan Python, PyTorch Component Semi-automated Free and open source Image reconstruction, Image deconvolution Widefield microscopy, Confocal fluorescence microscopy
Relate Software Relate analysis workflow example Collection Manual Commercial Image registration, Image analysis, Image segmentation, Particle tracking, Image deconvolution, Image denoising, Visualisation, Overlay, Slice rendering, Surface rendering, Plotting Correlative Light and Electron Microscopy, Electron microscopy, Scanning electron microscopy, Cryo scanning electron microscopy, Focused ion beam scanning electron microscopy, Serial block-face scanning electron microscopy, Transmission electron microscopy, Scanning transmission electron microscopy, Light microscopy, Point-scanning microscopy, Multimodal imaging, Spectroscopy, Statistics
Junction Mapper Software junction mapper Workflow Semi-automated Analysis, Filament tracing, Object feature extraction, Shape features Fluorescence microscopy, Confocal fluorescence microscopy
SynActJ Software SynActJ workflow Fiji Workflow Automated Free and open source Neuron image analysis Live sample imaging
Point Cloud Analyst (PoCA) Software Visualization, segmentation and exploration of 3D SMLM data Collection Manual, Semi-automated Free and open source Analysis, Colocalisation analysis, Object-based colocalisation, Cell segmentation, Interactive segmentation, Visualisation Super-resolution microscopy, Single molecule localization microscopy
Orthanc Software orthanc Component Free and open source Data handling, Image visualisation Magnetic resonance imaging, Multimodal imaging, Positron emission tomography, Ultrasonography
Correlia Software Correlia ImageJ Component Automated, Manual, Semi-automated Free and open source Image registration, Affine registration, Deformable registration, Visualisation Correlative Light and Electron Microscopy, Multimodal imaging
empanada-napari Software Empanada-napari Napari image viewer Component Automated, Semi-automated Free and open source Image segmentation, Cell segmentation Electron microscopy, Machine learning
MIA Software Fiji, MorphoLibJ Collection Automated, Manual, Semi-automated Free and open source Image registration, Image analysis, Image segmentation, Object counting, Object detection, Object tracking, Morphological operation, Image visualisation High content screening
ASTEC Software Astec embryon Collection, Workflow Automated, Semi-automated Free and open source Cell segmentation, Drift correction Light-sheet microscopy
ClearMap Software ClearMap SCreenshot OpenCV, scikit-image Collection Automated, Semi-automated Free and open source Alignment construction, Image registration, Image analysis, Filament tracing, Cell segmentation, Neuron image analysis, Data handling, Image stitching, Visualisation Light-sheet microscopy
BaSiC Software A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images Fiji Collection I do not know Free and open source Image correction Light microscopy, Fluorescence microscopy
Voxelytics-Align Software webKnossos: 3D image annotation, visualization and sharing Workflow I do not know Commercial Alignment construction, Image reconstruction, Image stitching Electron microscopy, Serial block-face scanning electron microscopy
hot-knife Software Collection Free and open source Alignment construction, Data handling, Image stitching, Geometric distortion correction Electron microscopy, Focused ion beam scanning electron microscopy
Render Software ImgLib2 Collection Automated Free and open source Alignment construction, Feature-based registration, Object feature extraction, Data handling, Image stitching, Visualisation, Image visualisation, Montage Data sharing, Electron microscopy, Scanning electron microscopy
EVER-ImageJ-Plugin Software ImageJ Component Automated, Semi-automated Free and open source Image processing Single molecule localization microscopy