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BBBC002v1 Software need a thumbnail I do not know Automated I do not know
EBImage Software EBImage Bioconductor Collection I do not know Free and open source Cell segmentation, Morphological operation Bioimage informatics, High content screening
(Z,T) Hyperstack Stitcher Software need a thumbnail ImageJ Component Automated I do not know
(Z,T,C) Stitcher Software need a thumbnail ImageJ Component Automated I do not know
2-D Colocalisation in Cells Software need a thumbnail CellProfiler, CellProfiler Workflow Automated Free and open source Object-based colocalisation, Colocalisation analysis
2-D Colocalisation in Cells Software need a thumbnail CellProfiler, CellProfiler Workflow Automated Free and open source Object-based colocalisation, Colocalisation analysis
2D and 3D mitochondrial shape analysis and network properties Software need a thumbnail ImagePro Workflow Automated I do not know
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
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
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
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
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
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
2D bright field yeast cell images with ground truth annotations Dataset 2D bright field yeast cell images
2D cell tracking and analysis of morphological dynamics Software need a thumbnail ImageJ, QuimP Workflow Semi-automated I do not know Active contours, Cell segmentation, Cell tracking
2D cell tracking and analysis of morphological dynamics Software need a thumbnail ImageJ, QuimP Workflow Semi-automated I do not know Active contours, Cell segmentation, 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 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
2D tracking using KNIME and Fiji Software KNIME Image Processing and Analysis, Fiji Workflow Semi-automated Free and open source Object tracking
2D-3D distributed parallel region competition segmentation Software need a thumbnail Component Automated I do not know
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
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
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
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
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 Active Meshes Software need a thumbnail Active Contours, Level Sets Component Automated I do not know
3D Active Meshes Software need a thumbnail Active Contours, Level Sets Component Automated I do not know
3D Active Meshes Software need a thumbnail Active Contours, Level Sets Component Automated I do not know
3D affine transformation based on paired points Software Fiji Component Automated Free and open source Affine transformation, Linear transformation
3D Area Software need a thumbnail Processing Component Automated I do not know
3D Area Software need a thumbnail Processing Component Automated I do not know
3D cell tracking and quantification of shape changes Software need a thumbnail MATLAB Workflow Automated I do not know Cell tracking
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 Generalized Riesz-Wavelet Toolbox for Matlab Software need a thumbnail MATLAB, ImageJ Component Automated I do not know
3D Generalized Riesz-Wavelet Toolbox for Matlab Software need a thumbnail MATLAB, ImageJ Component Automated I do not know
3D intensity profile Software Fiji Component Automated Free and open source
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 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 Software need a thumbnail 3D Viewer Component Automated I do not know Image visualisation
3D OrthoViewer Software need a thumbnail 3D Viewer Component Automated I do not know Image visualisation
3D segmentation (reconstruction) and modeling using Free-D Software need a thumbnail Workflow Automated I do not know
3D Slicer Software 3D slicer 3D Viewer, ITK Collection Automated Free and open source
3D Slicer Software 3D slicer 3D Viewer, ITK Collection Automated Free and open source
3D Surface Plot Software need a thumbnail ImageJ Component Automated I do not know
3D Surface Plot Software need a thumbnail ImageJ Component Automated I do not know
3D Viewer Software need a thumbnail ImageJ, 3D Viewer, display, Orthogonal Views Component Automated I do not know
3D Viewer Software need a thumbnail ImageJ, 3D Viewer, display, Orthogonal Views Component Automated I do not know
3D Viewer Software need a thumbnail ImageJ, 3D Viewer, display, Orthogonal Views Component Automated I do not know
3D Viewer Software need a thumbnail ImageJ, 3D Viewer, display, Orthogonal Views Component Automated I do not know
3D Viewer Software need a thumbnail ImageJ, 3D Viewer, display, Orthogonal Views Component Automated I do not know
3D-DAOSTORM Software need a thumbnail Component Semi-automated Free and open source Single molecule localisation Single molecule localization microscopy
3View import list Software ImageJ, TrakEM2 Component Automated Free and open source
3View import list Software ImageJ, TrakEM2 Component Automated Free and open source
@msdanalyzer Software Examples of tracks to perform MSD analysis. MATLAB Curve Fitting Toolbox, MATLAB Component Automated, Semi-automated Free and open source Trajectory analysis Live sample imaging, Statistics
@msdanalyzer Software Examples of tracks to perform MSD analysis. MATLAB Curve Fitting Toolbox, MATLAB Component Automated, Semi-automated Free and open source Trajectory analysis Live sample imaging, Statistics
A Unifying Parametric Framework for 2D Steerable Wavelet Transforms Software need a thumbnail MATLAB, ImageJ Component Automated I do not know
A Unifying Parametric Framework for 2D Steerable Wavelet Transforms Software need a thumbnail MATLAB, ImageJ Component Automated I do not know
A Unifying Parametric Framework for 2D Steerable Wavelet Transforms Software need a thumbnail MATLAB, ImageJ Component Automated I do not know
About BISE Basic page
ABSnake Software need a thumbnail Segmentation of Clustered Cells in MATLAB, ImageJ Component Automated I do not know
ABSnake Software need a thumbnail Segmentation of Clustered Cells in MATLAB, ImageJ Component Automated I do not know
acquiarium Software Acquiarium functionalities diagram Collection I do not know Free and open source Spot detection, Chromatic aberration correction, Geometric distortion correction, Illumination correction High content screening, Fluorescence microscopy, Confocal fluorescence microscopy
ActionBar Software ActionBar screenshot ImageJ Component Automated I do not know
Active Cells Software need a thumbnail Active Contours, Segmentation of Clustered Cells in MATLAB, Level Sets Component Automated I do not know
Active Cells Software need a thumbnail Active Contours, Segmentation of Clustered Cells in MATLAB, Level Sets Component Automated I do not know
Active Cells Software need a thumbnail Active Contours, Segmentation of Clustered Cells in MATLAB, Level Sets Component Automated I do not know
Active Cells Software need a thumbnail Active Contours, Segmentation of Clustered Cells in MATLAB, Level Sets Component Automated I do not know
Active Cells 3D Software need a thumbnail Active Contours Component Automated I do not know Cell segmentation, Active contours
Active Cells 3D Software need a thumbnail Active Contours Component Automated I do not know Cell segmentation, Active contours
Active Cells 3D Software need a thumbnail Component Automated I do not know
Active Cells Tracker Software need a thumbnail Active Contours Component Automated I do not know
Active Cells Tracker Software need a thumbnail Active Contours Component Automated I do not know
Active Contours Software need a thumbnail Active Contours, Segmentation of Clustered Cells in MATLAB Component Automated I do not know
Active Contours Software need a thumbnail Active Contours, Segmentation of Clustered Cells in MATLAB Component Automated I do not know
Active Contours Software need a thumbnail Active Contours, Segmentation of Clustered Cells in MATLAB Component Automated I do not know
ADAPT Software ADAPT logo Component I do not know
Adaptive histogram equalization Software need a thumbnail Histogram, Histogram Equalization, CLAHE Component Automated I do not know
Adaptive histogram equalization Software need a thumbnail Histogram, Histogram Equalization, CLAHE Component Automated I do not know
Adaptive histogram equalization Software need a thumbnail Histogram, Histogram Equalization, CLAHE Component Automated I do not know
Adaptive histogram equalization Software need a thumbnail Histogram, Histogram Equalization, CLAHE Component Automated I do not know
Adaptive Thresholding (EBImage) Software Component Automated Free and open source Adaptative thresholding, Cell segmentation
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
Adiposoft Software ImageJ Workflow Automated Free and open source Cell segmentation, Image thresholding, Watershed segmentation Digital histology
Advanced Cell Classifier Software Advanced Cell Classifier Collection Free and open source
affine Software need a thumbnail Component Automated I do not know
Affine transformation software Software Component Automated Free and open source Affine transformation, Image processing
AIR tools Software need a thumbnail Collection Automated I do not know
Aivia Software Collection, Workflow Commercial Analysis, Frequency analysis, Image analysis, Object-based colocalisation, Pixel-based colocalisation, Filament tracing, Image feature detection, Image segmentation, Cell segmentation, Pixel classification, Neuron image analysis, Object classification, Object counting, Texture extraction, Object tracking, Cell tracking, Particle tracking, Annotation, Classification, Editing, Visualisation, Image visualisation, Volume rendering, Plotting, Colocalisation analysis, Colocalisation analysis Machine learning
Align Image by line ROI Software need a thumbnail ImageJ, rotate, CellProfiler Align Component Automated I do not know
Align Image by line ROI Software need a thumbnail ImageJ, rotate, CellProfiler Align Component Automated I do not know
Align Image by line ROI Software need a thumbnail ImageJ, rotate, CellProfiler Align Component Automated I do not know
Align Image by line ROI Software need a thumbnail ImageJ, rotate, CellProfiler Align Component Automated I do not know
Align slices in stack Software ImageJ Component Automated Free and open source Image registration
Alignment of FIBSEM or SBFSEM images Software need a thumbnail Fiji, Open Virtual stack in Fiji, TrakEM2, Create new TrakEM project in Fiji, import images into TrakEM, Linear Stack Alignment with SIFT Component Semi-automated
Alignment of FIBSEM or SBFSEM images Software need a thumbnail Fiji, Open Virtual stack in Fiji, TrakEM2, Create new TrakEM project in Fiji, import images into TrakEM, Linear Stack Alignment with SIFT Component Semi-automated
Alignment of FIBSEM or SBFSEM images Software need a thumbnail Fiji, Open Virtual stack in Fiji, TrakEM2, Create new TrakEM project in Fiji, import images into TrakEM, Linear Stack Alignment with SIFT Component Semi-automated
Alignment of FIBSEM or SBFSEM images Software need a thumbnail Fiji, Open Virtual stack in Fiji, TrakEM2, Create new TrakEM project in Fiji, import images into TrakEM, Linear Stack Alignment with SIFT Component Semi-automated
Alignment of FIBSEM or SBFSEM images Software need a thumbnail Fiji, Open Virtual stack in Fiji, TrakEM2, Create new TrakEM project in Fiji, import images into TrakEM, Linear Stack Alignment with SIFT Component Semi-automated
Alignment of FIBSEM or SBFSEM images Software need a thumbnail Fiji, Open Virtual stack in Fiji, TrakEM2, Create new TrakEM project in Fiji, import images into TrakEM, Linear Stack Alignment with SIFT Component Semi-automated
Amira Software Amira's interface MATLAB Collection Automated Commercial
Anaglyph for Red Cyan glasses Software need a thumbnail ImageJ Component Automated I do not know
Anaglyph for Red Cyan glasses Software need a thumbnail ImageJ Component Automated I do not know
Analyze 12.0 Software Collection Semi-automated Commercial, I do not know
Analyze Particles Software need a thumbnail ImageJ, Fiji Component Automated I do not know Image feature detection Microscopy
Analyze Particles Software need a thumbnail ImageJ, Fiji Component Automated I do not know Image feature detection Microscopy
Analyze Skeleton 2D time series Software need a thumbnail ImageJ, AnalyzeSkeleton Component Automated I do not know
Analyze Skeleton 2D time series Software need a thumbnail ImageJ, AnalyzeSkeleton Component Automated I do not know
Analyze Skeleton 2D time series Software need a thumbnail ImageJ, AnalyzeSkeleton Component Automated I do not know
AnalyzeSkeleton Software ImageJ, Analyze 12.0 Component Automated, Semi-automated Filament tracing, Object detection, Pixel classification
AnalyzeSkeleton Software ImageJ, Analyze 12.0 Component Automated, Semi-automated Filament tracing, Object detection, Pixel classification
Analyzing gels and western blots with ImageJ Software ImageJ Workflow Manual Free and open source
AnaMorf Software AnaMorph ImageJ Component Automated Free and open source Filament tracing
AnaMorf Software AnaMorph ImageJ Component Automated Free and open source Filament tracing
Angiogenesis / Sprout Analyzer Software graphical abstract ImageJ Component Semi-automated Free and open source Filament tracing, Neuron image analysis Bioimage informatics, Fluorescence microscopy
Angiogenesis / Sprout Analyzer Software graphical abstract ImageJ Component Semi-automated Free and open source Filament tracing, Neuron image analysis Bioimage informatics, Fluorescence microscopy
Angiogenesis Analyzer for ImageJ Software ImageJ Workflow Automated I do not know Image analysis Imaging
Angle Helper Software need a thumbnail display Component Automated I do not know
Angle Helper Software need a thumbnail display Component Automated I do not know
Animated overlay tutorial Software need a thumbnail Component Automated I do not know
Animation 3D Software need a thumbnail Component Automated I do not know
Anisotropic Diffusion 2D Software need a thumbnail ImageJ, KNIME Anisotropic Diffusion Component Automated I do not know
Anisotropic Diffusion 2D Software need a thumbnail ImageJ, KNIME Anisotropic Diffusion Component Automated I do not know
Anisotropic Diffusion 2D Software need a thumbnail ImageJ, KNIME Anisotropic Diffusion Component Automated I do not know
Anisotropic Filter Software need a thumbnail KNIME Anisotropic Diffusion Component Automated I do not know
Anisotropic Filter Software need a thumbnail KNIME Anisotropic Diffusion Component Automated I do not know
Annotated two-photon images of dendritic spines Software need a thumbnail I do not know Automated I do not know
ANTs: Advanced Normalization Tools Software Advanced Normalization Tools ITK Collection Automated Free and open source Image registration, Affine registration, Rigid registration, Deformable registration, Image segmentation, Pixel classification, Illumination correction Bioimage informatics
Any volonteer to tag the Nature Methods Challenge paper Forum topic
Aphelion Software need a thumbnail Collection Automated Commercial
APP (All-path pruning) Software APP_Vaa3D_example_results Vaa3D Component Automated Free and open source Filament tracing, Image thresholding, Neuron image analysis Confocal microscopy
APP2 Software APP2_Vaa3D_example_Result Vaa3D Component Automated, Semi-automated Free and open source Filament tracing, Neuron image analysis, Distance transform Confocal microscopy
Aquarium Software need a thumbnail Component Automated I do not know
Aquiarium Software need a thumbnail Collection Automated Free and open source
Arabidopsis plants (high resolution) Dataset arabidopsis plant (high resolution)
Arabidopsis plants (low resolution) Dataset arabidopsis plant (low resolution)
Arabidopsis Seedlings Tool Software ImageJ toolbar of the arabidopsis seedlings tool ImageJ Workflow Automated Free and open source Image thresholding Bioimage informatics
Arabidopsis Seedlings Tool Software ImageJ toolbar of the arabidopsis seedlings tool ImageJ Workflow Automated Free and open source Image thresholding Bioimage informatics
Arabidopsis thaliana seedlings Dataset thumbnail of Arabidopsis thaliana seedlings
Arrow Software need a thumbnail ImageJ, ICY Annotation, Arrow Component Automated I do not know Annotation
Arrow Software need a thumbnail ImageJ, ICY Annotation, Arrow Component Automated I do not know Annotation
Arrow Software need a thumbnail ImageJ, ICY Annotation, Arrow Component Automated I do not know Annotation
Artemia color analysis Software Artemia color analysis toolset ImageJ Workflow Semi-automated Free and open source Object feature extraction Bioimage informatics
Artemia color images Dataset artemia color image
ASAP Software need a thumbnail Collection Automated Free and open source
ATLAS Vesicle segmentation method Software Component Automated Free but not open source Object detection, Spot detection
Auto Local Threshold Software need a thumbnail Local Thresholding Component Automated I do not know
Auto Threshold Software need a thumbnail ImageJ, Histogram Component Automated I do not know
Auto Threshold Software need a thumbnail ImageJ, Histogram Component Automated I do not know
Auto Threshold Software need a thumbnail ImageJ, Histogram Component Automated I do not know
Auto-Bayes Software need a thumbnail Collection Automated Free and open source
Autofocus Software need a thumbnail ImageJ, Autofocus Component Automated I do not know
Autofocus Software need a thumbnail ImageJ, Autofocus Component Automated I do not know
Automated velocity mapping of migrating cell populations (AVeMap) Software need a thumbnail MATLAB Workflow Automated I do not know
Automatic 2D/3D Tracking using ilastik Software need a thumbnail VIGRA, ilastik, ilastik Workflow Automated I do not know Image segmentation, Object tracking Bioimage informatics, Machine learning
Automatic 2D/3D Tracking using ilastik Software need a thumbnail VIGRA, ilastik, ilastik Workflow Automated I do not know Image segmentation, Object tracking Bioimage informatics, Machine learning
Automatic 2D/3D Tracking using ilastik Software need a thumbnail VIGRA, ilastik, ilastik Workflow Automated I do not know Image segmentation, Object tracking Bioimage informatics, Machine learning
AutoQuant Software Image restoration with AutoQuant Collection Automated I do not know Image deconvolution Fluorescence microscopy
AVEMAP Software AveMAP Matlab blocks Component Automated Free and open source Image analysis, Optical flow analysis Topic, Imaging, Fluorescence microscopy
Avizo Software need a thumbnail Collection Automated Commercial
Background Subtractor Software need a thumbnail Component Automated I do not know
Balanced SOFI Software need a thumbnail MATLAB Collection Automated Free and open source
Batch spot detection with custom output Software need a thumbnail Workflow Automated Free and open source Spot detection
BBBC003v1 MOUSE EMBRYOS Software need a thumbnail I do not know Automated I do not know
BEEPS (Bi-Exponential Edge-Preserving Smoother) Software ImageJ Component Automated Free and open source Smoothing, Image processing, Image processing
Best Threshold Software need a thumbnail Component Automated I do not know Image segmentation
bftools Software need a thumbnail
BiDiFuse Software need a thumbnail Component Automated I do not know
BigDataViewer Software ImgLib2 Component Manual Free and open source Image registration, Affine registration, Rigid registration, Visualisation, Image visualisation Imaging, Light-sheet microscopy
BigStitcher Software ImageJ, ImgLib2, BigDataViewer Collection Automated, Manual, Semi-automated Free and open source Image registration, Affine registration, Rigid registration, Data handling, Affine transformation, Image deconvolution, Image stitching, Selective plane illumination microscopy reconstruction, Visualisation
BigStitcher Software ImageJ, ImgLib2, BigDataViewer Collection Automated, Manual, Semi-automated Free and open source Image registration, Affine registration, Rigid registration, Data handling, Affine transformation, Image deconvolution, Image stitching, Selective plane illumination microscopy reconstruction, Visualisation
BigStitcher Software ImageJ, ImgLib2, BigDataViewer Collection Automated, Manual, Semi-automated Free and open source Image registration, Affine registration, Rigid registration, Data handling, Affine transformation, Image deconvolution, Image stitching, Selective plane illumination microscopy reconstruction, Visualisation
Bigwarp Software need a thumbnail Component Manual Free and open source Image registration, Deformable registration, Warping Correlative Light and Electron Microscopy, Electron microscopy
Bilateral Filter Software need a thumbnail Component Automated I do not know
Binary Image Operations Software need a thumbnail Component Automated I do not know
Bio-Formats Software need a thumbnail ImageJ Component Automated I do not know
Bio-Formats Software need a thumbnail ImageJ Component Automated I do not know
Bio-Formats Software need a thumbnail ImageJ Component Automated I do not know
Bio7 Software need a thumbnail ImageJ Collection Automated I do not know
BioCat Software need a thumbnail Java 8 Collection Semi-automated Free and open source Image classification Machine learning
Bioconductor Software Collection I do not know Free and open source Analysis Bioimage informatics, High content screening
BioImageXD Software Screen capture of BioImageXD Collection Manual, Semi-automated Free and open source
BioImageXD Software need a thumbnail Collection Automated Free and open source
BisQue Software bisque screenshot Collection Automated, Manual, Semi-automated Free and open source Image analysis, Data handling Data sharing
blackTopHatGreyScale Software need a thumbnail closing, Morphological Operations Component Automated I do not know
blackTopHatGreyScale Software need a thumbnail closing, Morphological Operations Component Automated I do not know
blackTopHatGreyScale Software need a thumbnail closing, Morphological Operations Component Automated I do not know
Bleach Correction Software need a thumbnail Bleach Correction Component Automated I do not know Image correction Fluorescence microscopy
bleb dynamics Software need a thumbnail Gaussian blur in ImageJ, Otsu Thresholding, radial reslice, kymograph generation Workflow Semi-automated Free and open source Shape features, Cell tracking Fluorescence microscopy, Confocal fluorescence microscopy
bleb dynamics Software need a thumbnail Gaussian blur in ImageJ, Otsu Thresholding, radial reslice, kymograph generation Workflow Semi-automated Free and open source Shape features, Cell tracking Fluorescence microscopy, Confocal fluorescence microscopy
bleb dynamics Software need a thumbnail Gaussian blur in ImageJ, Otsu Thresholding, radial reslice, kymograph generation Workflow Semi-automated Free and open source Shape features, Cell tracking Fluorescence microscopy, Confocal fluorescence microscopy
bleb dynamics Software need a thumbnail Gaussian blur in ImageJ, Otsu Thresholding, radial reslice, kymograph generation Workflow Semi-automated Free and open source Shape features, Cell tracking Fluorescence microscopy, Confocal fluorescence microscopy
Blend two images Software need a thumbnail ImageJ Component Automated I do not know
Blend two images Software need a thumbnail ImageJ Component Automated I do not know
Blender Software need a thumbnail Collection
Blob Detector Software need a thumbnail Component Automated I do not know
Blob segmentation Software need a thumbnail Fiji, MorphoLibJ Component Automated Free and open source Image segmentation
Blob segmentation Software need a thumbnail Fiji, MorphoLibJ Component Automated Free and open source Image segmentation
Blood vessel segmentation and network analysis Software Fiji Workflow Automated Free and open source Image segmentation
BM3D denoising Software Component
Boost C++ Software need a thumbnail
Bounding Box 3D Software need a thumbnail CellProfiler Crop Component Automated I do not know
Bounding Box 3D Software need a thumbnail CellProfiler Crop Component Automated I do not know
BSIF (Binarized Statistical Image Features) Software need a thumbnail Component Automated I do not know
BUnwarpJ Software need a thumbnail ImageJ Component Automated I do not know
BUnwarpJ Software need a thumbnail ImageJ Component Automated I do not know
bwlabel Software need a thumbnail Component Automated I do not know
CalculateImageOverlap Software need a thumbnail CellProfiler Component Automated I do not know
CalculateMath Software need a thumbnail CellProfiler Component Automated I do not know
CalculateStatistics Software need a thumbnail CellProfiler Component Automated I do not know
Cancer Imaging Phenomics Toolkit (CaPTk) Software CaPTk Collection Automated, Semi-automated Free and open source
CATMAID Software CATMAID ImageJ, ICY Annotation Collection Automated I do not know
CATMAID Software CATMAID ImageJ, ICY Annotation Collection Automated I do not know
CATMAID Software CATMAID ImageJ, ICY Annotation Collection Automated I do not know
CBIRetrieval Software need a thumbnail Component Automated I do not know
Cell Counter ImageJ Software ImageJ Component Manual Free and open source Object counting
Cell or particle Counting and scoring stained objects using CellProfiler Software jupyter Cell or particle counting and scoring the percentage of stained objects, idr-py Workflow Automated Free and open source Object classification, Analysis Bioimage informatics, Fluorescence microscopy
Cell or particle Counting and scoring stained objects using CellProfiler Software jupyter Cell or particle counting and scoring the percentage of stained objects, idr-py Workflow Automated Free and open source Object classification, Analysis Bioimage informatics, Fluorescence microscopy
Cell or particle counting and scoring the percentage of stained objects Software Positivepercentcell CellProfiler Workflow Automated Free and open source Cell segmentation, Object classification Fluorescence microscopy
Cell segmentation and measurements Software need a thumbnail CellProfiler, Segmentation of Clustered Cells in MATLAB Workflow Automated I do not know
Cell segmentation and measurements Software need a thumbnail CellProfiler, Segmentation of Clustered Cells in MATLAB Workflow Automated I do not know
Cell segmentation and quantification with CellX Software MATLAB, Matlab Image Processing Toolbox Workflow Automated Free and open source Image segmentation, Cell tracking Bright field microscopy, Phase contrast microscopy
Cell segmentation and quantification with CellX Software MATLAB, Matlab Image Processing Toolbox Workflow Automated Free and open source Image segmentation, Cell tracking Bright field microscopy, Phase contrast microscopy
Cell segmentation by EBImage, R Software need a thumbnail Watershed, watershed, Segmentation of Clustered Cells in MATLAB Workflow Automated I do not know
Cell segmentation by EBImage, R Software need a thumbnail Watershed, watershed, Segmentation of Clustered Cells in MATLAB Workflow Automated I do not know
Cell segmentation by EBImage, R Software need a thumbnail Watershed, watershed, Segmentation of Clustered Cells in MATLAB Workflow Automated I do not know
Cell segmentation by EBImage, R Software need a thumbnail Watershed, watershed, Segmentation of Clustered Cells in MATLAB Workflow Automated I do not know
Cell segmentation by EBImage, R Software need a thumbnail Watershed, watershed, Segmentation of Clustered Cells in MATLAB Workflow Automated I do not know
Cell segmentation in phase contrast images Software initialisation MATLAB Component Automated I do not know Active contours, Cell segmentation, Object tracking, Cell tracking Phase contrast microscopy
CellCognition Software Cell Cognition logo Segmentation of Clustered Cells in MATLAB, ICY Annotation Collection Automated Free and open source
CellCognition Software Cell Cognition logo Segmentation of Clustered Cells in MATLAB, ICY Annotation Collection Automated Free and open source
CellProfiler Software CellProfiler logo Collection Automated, Semi-automated Free and open source
CellProfiler Align Software CellProfiler Component Automated Free and open source Rigid registration
CellProfiler Comet assay/DNA damage assay Software CellProfiler Workflow Automated Free and open source, I do not know
CellProfiler Crop Software need a thumbnail CellProfiler Component Automated Free and open source
CellProfiler Examples - Colocalization Software CellProfiler Workflow Semi-automated Free and open source Object-based colocalisation, Colocalisation analysis
CellProfiler Examples - Speckle Counting Software CellProfiler Component Automated Free and open source Image segmentation, Spot detection
CellProfiler Threshold Software need a thumbnail CellProfiler Component Automated I do not know
Cellquant Software need a thumbnail Component Automated I do not know
Cells tracking in tissue Software need a thumbnail ImageJ, MATLAB, Watershed, watershed Workflow Automated I do not know
Cells tracking in tissue Software need a thumbnail ImageJ, MATLAB, Watershed, watershed Workflow Automated I do not know
Cells tracking in tissue Software need a thumbnail ImageJ, MATLAB, Watershed, watershed Workflow Automated I do not know
Cells tracking in tissue Software need a thumbnail ImageJ, MATLAB, Watershed, watershed Workflow Automated I do not know
Cells tracking in tissue Software need a thumbnail ImageJ, MATLAB, Watershed, watershed Workflow Automated I do not know
CellSegm Software need a thumbnail Collection Automated Free and open source
CellTrack Software need a thumbnail Collection Free and open source
CellTrack Software need a thumbnail Collection Automated Free and open source
CellTracker Software need a thumbnail Component Automated I do not know
Celsius to fahrenheit Software need a thumbnail Component Automated I do not know
CEM Software Myelin ImageJ Collection Semi-automated Free and open source Neuron image analysis, Dilation, Pixel-based colocalisation, Image feature detection, Colocalisation analysis High content screening
Centromere Recognition and Quantification Software ImageJ, Spot Detection Workflow Semi-automated I do not know Spot detection Fluorescence microscopy
Centromere Recognition and Quantification Software ImageJ, Spot Detection Workflow Semi-automated I do not know Spot detection Fluorescence microscopy
Chainer Software Python Collection Free and open source
channel Software need a thumbnail rgbImage Component Automated I do not know
channel Software need a thumbnail rgbImage Component Automated I do not know
Channel Montage Software need a thumbnail channel Component Automated I do not know
Channel Montage Software need a thumbnail channel Component Automated I do not know
Chart tutorial 1 Software need a thumbnail Component Automated I do not know
Chart tutorial 2 Software need a thumbnail Component Automated I do not know
Chart1DCanvas Software need a thumbnail Component Automated I do not know
Chess Software need a thumbnail ImageJ, Chess Component Automated I do not know
Chess Software need a thumbnail ImageJ, Chess Component Automated I do not know
Chess Software need a thumbnail ImageJ, Chess Component Automated I do not know
Chronometer Software need a thumbnail Chronometer Component Automated I do not know
Chronometer Software need a thumbnail Chronometer Component Automated I do not know
Cicardian Gene Expression Software need a thumbnail ImageJ Component Automated I do not know
Cicardian Gene Expression Software need a thumbnail ImageJ Component Automated I do not know
CIDRE Software Illumination correction method MATLAB, ImageJ Collection Automated Free and open source Illumination correction High content screening, Light microscopy
CIDRE Software Illumination correction method MATLAB, ImageJ Collection Automated Free and open source Illumination correction High content screening, Light microscopy
CLAHE Software need a thumbnail Histogram Equalization Component Automated I do not know
classification of hemp fibers based on morphological features Software hemp analysis ImageJ, MATLAB, MorphoLibJ Workflow Semi-automated I do not know Watershed segmentation, Object classification, Image feature detection, Object feature extraction, Morphological operation Microscopy
classification of hemp fibers based on morphological features Software hemp analysis ImageJ, MATLAB, MorphoLibJ Workflow Semi-automated I do not know Watershed segmentation, Object classification, Image feature detection, Object feature extraction, Morphological operation Microscopy
classification of hemp fibers based on morphological features Software hemp analysis ImageJ, MATLAB, MorphoLibJ Workflow Semi-automated I do not know Watershed segmentation, Object classification, Image feature detection, Object feature extraction, Morphological operation Microscopy
ClassifyObjects Software need a thumbnail ilastik, CellProfiler Component Automated I do not know
ClassifyObjects Software need a thumbnail ilastik, CellProfiler Component Automated I do not know
ClassifyPixels Software need a thumbnail ilastik, CellProfiler Component Automated I do not know
ClassifyPixels Software need a thumbnail ilastik, CellProfiler Component Automated I do not know
ClearCL Software Java 8, OpenCL Component Manual Free and open source Image processing Bioimage informatics
ClearCL Software Java 8, OpenCL Component Manual Free and open source Image processing Bioimage informatics
ClearGL Software Java 8 Component Manual Free and open source Visualisation Bioimage informatics
ClearVolume Software Java 8, ClearCL, ClearGL Component Manual Free and open source Volume rendering Microscopy, Light microscopy, Light-sheet microscopy
ClearVolume Software Java 8, ClearCL, ClearGL Component Manual Free and open source Volume rendering Microscopy, Light microscopy, Light-sheet microscopy
ClearVolume Software Java 8, ClearCL, ClearGL Component Manual Free and open source Volume rendering Microscopy, Light microscopy, Light-sheet microscopy
Clojure Software need a thumbnail Clojure Component Automated I do not know
Clojure Software need a thumbnail Clojure Component Automated I do not know
closing Software need a thumbnail Morphological Operations Component Automated I do not know
closing Software need a thumbnail Morphological Operations Component Automated I do not know
closingGreyScale Software need a thumbnail Morphological Operations Component Automated I do not know
closingGreyScale Software need a thumbnail Morphological Operations Component Automated I do not know
Clus-Doc Software need a thumbnail Collection Automated I do not know
Clustered cell nuclei Software need a thumbnail I do not know Automated I do not know Object detection
CMTK Software need a thumbnail Component Automated Free and open source Image registration, Affine registration, Deformable registration, Image analysis, Image classification, Image processing Bioimage informatics, Statistics
CMYK exporter Software need a thumbnail Component Automated I do not know
Colocalization Analysis Software need a thumbnail ImageJ, Auto Threshold Component Automated I do not know
Colocalization Analysis Software need a thumbnail ImageJ, Auto Threshold Component Automated I do not know
Colocalization Analysis Software need a thumbnail ImageJ, Auto Threshold Component Automated I do not know
Colocalization Scatter Plot Software need a thumbnail Component Automated I do not know
Colocalization Test Software need a thumbnail ImageJ Component Automated I do not know
Colocalization Test Software need a thumbnail ImageJ Component Automated I do not know
Colocalization Threshold Software need a thumbnail ImageJ, Auto Threshold Component Automated I do not know
Colocalization Threshold Software need a thumbnail ImageJ, Auto Threshold Component Automated I do not know
Colocalization Threshold Software need a thumbnail ImageJ, Auto Threshold Component Automated I do not know
Colocalizer Software need a thumbnail Component Automated I do not know Colocalisation analysis Fluorescence microscopy
Colony Blob Count Tool Software ImageJ Workflow Semi-automated Free and open source Object counting Bright field microscopy
Color Inspector 3D Software need a thumbnail ImageJ Component Automated I do not know
Color Inspector 3D Software need a thumbnail ImageJ Component Automated I do not know
Color normalization of H&E stains Software MATLAB Component Semi-automated I do not know Image deconvolution Digital histology
Color Picker Threshold Software need a thumbnail Component Automated I do not know
ColorLab Software need a thumbnail Component Automated I do not know
Colormine Software need a thumbnail Collection Automated I do not know
ColorToGray Software need a thumbnail CellProfiler, channel Component Automated I do not know
ColorToGray Software need a thumbnail CellProfiler, channel Component Automated I do not know
Colour Deconvolution Software Fiji Component Semi-automated Free and open source Spectral unmixing Digital histology, Bright field microscopy
Colour merge Software need a thumbnail ImageJ Component Automated I do not know
Colour merge Software need a thumbnail ImageJ Component Automated I do not know
Colour Mode Conversion Software need a thumbnail rgbImage, channel Component Automated I do not know
Colour Mode Conversion Software need a thumbnail rgbImage, channel Component Automated I do not know
Colour Mode Conversion Software need a thumbnail rgbImage, channel Component Automated I do not know
Columbus Image Data Storage and Analysis System Software Columbus screenshot Collection Automated Commercial
combine Software need a thumbnail Component Automated I do not know
Compaction Profiler Software need a thumbnail Convex Hull Component Automated I do not know
Compaction Profiler Software need a thumbnail Convex Hull Component Automated I do not know
Complex toolbox Software need a thumbnail Component Automated I do not know
CompuCell3D Software Collection Manual Free and open source Synthetic image generation, Plotting In-silico reconstruction
computeFeatures Software need a thumbnail Feature Extraction Component Automated I do not know
computeFeatures Software need a thumbnail Feature Extraction Component Automated I do not know
Connected Component Analysis Software need a thumbnail Component Automated I do not know
Connected Component Painter Software need a thumbnail Component Automated I do not know
Connected Components Software need a thumbnail Component Automated I do not know
Connected components XLS export Block Software need a thumbnail Component Automated I do not know
Context Menu Software need a thumbnail Component Automated I do not know
Continuous-Time ARMA Identification Software need a thumbnail MATLAB Component Automated I do not know
Contour Curvature Software need a thumbnail Component Automated I do not know
Contour Plot Software need a thumbnail display Component Automated I do not know
Contour Plot Software need a thumbnail display Component Automated I do not know
ConvertObjectsToImage Software need a thumbnail CellProfiler Component Automated I do not know
Convex Hull Software need a thumbnail Convex Hull Component Automated I do not know
Convolve with 2D Bessel function Software need a thumbnail Component Automated I do not know
Convolver Software need a thumbnail Fast Fourier Transform Component Automated I do not know
Copy Pixel Size Software need a thumbnail ImageJ Component Automated I do not know
Copy Pixel Size Software need a thumbnail ImageJ Component Automated I do not know
Correct 3D drift Software need a thumbnail Component Automated I do not know
CorrectIlluminationApply Software need a thumbnail CellProfiler Component Automated I do not know
CorrectIlluminationCalculate Software need a thumbnail CellProfiler Component Automated I do not know
CorrelationCalculator Software need a thumbnail
Count Chromosomes Software need a thumbnail Count Chromosomes Component Automated I do not know
Counting Clumped Cells Software ImageJ Workflow Semi-automated Free and open source Cell segmentation, Object counting
Counting foci in ImageJ Software ImageJ Workflow Manual Free and open source
Cover Maker Software need a thumbnail ImageJ Component Automated I do not know
Cover Maker Software need a thumbnail ImageJ Component Automated I do not know
Create new TrakEM project in Fiji Software need a thumbnail Component Manual
CreateBatchFiles Software need a thumbnail CellProfiler Component Automated I do not know
Creating an ImageJ plugin / command Software ImageJ, Fiji, IntelliJ, Fiji Workflow Automated, Manual, Semi-automated Free and open source Image processing Bioimage informatics
Creating an ImageJ plugin / command Software ImageJ, Fiji, IntelliJ, Fiji Workflow Automated, Manual, Semi-automated Free and open source Image processing Bioimage informatics
Creating an ImageJ plugin / command Software ImageJ, Fiji, IntelliJ, Fiji Workflow Automated, Manual, Semi-automated Free and open source Image processing Bioimage informatics
Creating an ImageJ plugin / command Software ImageJ, Fiji, IntelliJ, Fiji Workflow Automated, Manual, Semi-automated Free and open source Image processing Bioimage informatics
CreaTools Software need a thumbnail ITK Component Automated I do not know
CREMI challenge Dataset cremi samples A and B
Crop 5D Software need a thumbnail CellProfiler Crop Component Automated I do not know
Crop 5D Software need a thumbnail CellProfiler Crop Component Automated I do not know
CSBDeep, a toolbox for Content-aware Image Restoration (CARE) in Fiji Software CARE Fiji Component Semi-automated I do not know Image denoising, Image reconstruction, Image deconvolution, Image projection, Selective plane illumination microscopy reconstruction Light microscopy, Light-sheet microscopy
CSBDeep, a toolbox for Content-aware Image Restoration (CARE) in Knime Software KNIME Collection, Component Semi-automated Image denoising, Image deconvolution Light microscopy, Light-sheet microscopy
Ctrax - Caltech Multiple Fly Tracker Software need a thumbnail Collection Automated I do not know
cvMatch_Template Software ImageJ, OpenCV Component Semi-automated Free and open source Image segmentation, Pattern recognition Electron microscopy
cvMatch_Template Software ImageJ, OpenCV Component Semi-automated Free and open source Image segmentation, Pattern recognition Electron microscopy
cython Software need a thumbnail
Cytomine Software cytomine logo Collection Automated, Manual, Semi-automated Free and open source Data handling, Image annotation Data sharing, Digital histology
CytooChip Analysis Software need a thumbnail ImageJ Workflow Automated Free and open source
CytoPacq Software need a thumbnail Component Automated I do not know
Data-analysis strategies for image-based cell profiling Software need a thumbnail Workflow Automated, Semi-automated High content screening
DBSCAN clustering using PALMsiever Software need a thumbnail PALMsiever Workflow Automated I do not know Cell segmentation Single molecule localization microscopy
Debleach Software need a thumbnail Component Automated I do not know Image correction Fluorescence microscopy
DeconvolutionLab Software need a thumbnail ImageJ Component Automated I do not know
DeconvolutionLab Software need a thumbnail ImageJ Component Automated I do not know
DeconvolutionLab2 Software need a thumbnail Component Automated I do not know
DEFCoN-ImageJ Software Fiji Component Free and open source Object counting, Spot detection Machine learning
DefineGrid Software need a thumbnail CellProfiler Component Automated I do not know
Definiens Developer Software need a thumbnail Collection Automated Commercial
Delaunay Voronoi Software need a thumbnail ImageJ, Grid, Distance Map Component Automated I do not know
Delaunay Voronoi Software need a thumbnail ImageJ, Grid, Distance Map Component Automated I do not know
Delaunay Voronoi Software need a thumbnail ImageJ, Grid, Distance Map Component Automated I do not know
Delaunay Voronoi Software need a thumbnail ImageJ, Grid, Distance Map Component Automated I do not know
Delayed Snapshot Software need a thumbnail ImageJ Component Automated I do not know
Delayed Snapshot