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Name Category Image requires Type interaction level License/Openness has function has topic
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
pyTFM Software https://pytfm.readthedocs.io/en/latest/_images/mask_force_measures.png Python Collection Semi-automated Free and open source Collective object tracking Bioimage informatics
napari-pyclesperanto-assistant Software Collection, Component Free and open source Image analysis Bioimage informatics
AnnotatorJ Software annotatorJ Fiji Component Manual, Semi-automated Free and open source Image annotation Machine learning
NDPI Export Regions Tool Software imagej toolset to export regions from ndpi and ndpa-files ImageJ Workflow Automated Free and open source Data handling Digital histology
APEER Software Collection, Component Commercial, Free and open source Analysis, Image segmentation, Cell segmentation, Model-based segmentation, Pixel classification, Annotation, Data handling, Image denoising Imaging, Microscopy, Machine learning
Phindr3D Software MATLAB Workflow Semi-automated Free and open source Analysis, Image analysis, Image classification, Image feature detection, Neuron image analysis, Classification, Clustering, Image processing, Pattern recognition, Visualisation Bioimage informatics, High content screening, Machine learning, Statistics
DeepCLEM Software F1000R Figure 1 DeepCLEM Fiji, Register Virtual Stack Slices (Fiji), CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Fiji Component, Workflow Automated Free and open source Image registration, Affine transformation Correlative Light and Electron Microscopy, Multimodal imaging
Analyze Spheroid Cell Invasion In 3D Matrix Software need a thumbnail MorphoLibJ Workflow Semi-automated Free and open source Cell segmentation, Object counting Live sample imaging, Widefield microscopy, Fluorescence microscopy
Analyze Complex Roots Tool Software Concentric circles on the mask of a root, created by the Analyze Complex Roots Tool Fiji Workflow Automated, Semi-automated Free and open source Image analysis, Image segmentation Bioimage informatics
Local Z Projector Software ImgLib2, ImageJ 2.x Component Automated Free and open source Image processing Live sample imaging, Confocal fluorescence microscopy
Effective image visualization for publications – a workflow using open access tools and concepts Software Workflow Free and open source
webKnossos: 3D image annotation, visualization and sharing Software Collection Manual, Semi-automated Free and open source Image segmentation, Interactive segmentation, Neuron image analysis, Image annotation, Data handling, Skeletonisation, Image visualisation, Overlay, Slice rendering, Volume rendering Data sharing, Magnetic resonance imaging, Electron microscopy, Fluorescence microscopy, Tomography
Viv Software Rendering a pyramidal, multiplexed immunofluorescence OME-TIFF image of a human kidney using additive blending to render four image channels into a single RGB image in the client. Component Manual Free and open source Visualisation, Image visualisation, Overlay, Slice rendering Data sharing, Imaging, Microscopy
BTrackMate Software Component, Workflow Free and open source
A simple MSER based segmentation tool for spot detection in 2/3/4D. Software Component Automated Free and open source