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- Any -DatasetSoftwareTraining Material

For which operation? Operation-Alignment construction--Image registration---Affine registration----Rigid registration---Deformable registration---Feature-based registration-Analysis--Frequency analysis--Image analysis---Colocalisation analysis----Object-based colocalisation----Pixel-based colocalisation---Filament tracing---Image classification---Image feature detection----Edge detection----Spot detection---Image segmentation----Adaptative thresholding----Cell segmentation----Image thresholding----Interactive segmentation----Local thresholding----Model-based segmentation-----Active contours----Pixel classification----Region growing----Watershed segmentation---Neuron image analysis---Object classification---Object counting---Object detection----Single molecule localisation---Object feature extraction----Homogeneity----Shape features----Texture extraction---Object tracking----Collective object tracking----Isolated object tracking-----Cell tracking-----Particle tracking----Trajectory analysis----Wound-healing analysis---Optical flow analysis-Annotation--Image annotation---Landmark assignment-Classification--Image classification--Object classification--Pixel classification-Clustering-Data handling--Conversion--Editing-Generation--Image generation---Image reconstruction----Image deconvolution----Image denoising----Image projection----Image stitching----Selective plane illumination microscopy reconstruction----Single molecule localisation----Structured illumination reconstruction----Tomographic reconstruction---Synthetic image generation-Image processing--Frequency analysis--Geometrical transformation---Affine transformation----Linear transformation----Rotation---Warping--Image convolution--Image correction---Chromatic aberration correction---Detector bias correction---Detector gain correction---Drift correction---Geometric distortion correction---Illumination correction---Spectral unmixing--Image crop--Image enhancement---Contrast enhancement---Feature enhancement---Image denoising---Smoothing--Image reconstruction---Image deconvolution---Image denoising---Image projection---Image stitching---Selective plane illumination microscopy reconstruction---Single molecule localisation---Structured illumination reconstruction---Tomographic reconstruction--Image registration---Affine registration----Rigid registration---Deformable registration---Feature-based registration--Image segmentation---Adaptative thresholding---Cell segmentation---Image thresholding---Interactive segmentation---Local thresholding---Model-based segmentation----Active contours---Pixel classification---Region growing---Watershed segmentation--Morphological operation---Closing---Dilation---Distance transform---Erosion---Opening---Skeletonisation---Top-hat transform-Optimisation or refinement--Parameter optimisation-Prediction and recognition--Pattern recognition-Validation--Image validation-Visualisation--Image visualisation---Anaglyph---Montage---Overlay---Slice rendering---Surface rendering---Volume rendering--Plotting

for which topic? Topic-Bioimage informatics-Data sharing-Digital histology-High content screening-Imaging--Bioluminescence imaging--Fixed sample imaging--Live sample imaging---Ex-vivo imaging---In-vitro imaging---In-vivo imaging--Magnetic resonance imaging--Microscopy---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-----Electron tomography------Cryo electron tomography-----Scanning transmission electron microscopy---Light microscopy----Area-capturing microscopy-----Light-sheet microscopy-----Widefield microscopy----Fluorescence microscopy-----Confocal fluorescence microscopy-----Fluctuation based microscopy-----Fluorescence correlative spectroscopy-----Fluorescence lifetime imaging microscopy-----Fluorescence recovery after photobleaching-----Förster resonance energy transfer-----Image correlation spectroscopy-----Super-resolution microscopy------Single molecule localization microscopy------Stimulated Emission Depletion microscopy------Structured illumination microscopy----Point-scanning microscopy-----Confocal microscopy------Confocal fluorescence microscopy-----Light-sheet microscopy-----Multi-photon microscopy----Transmission light microscopy-----Bright field microscopy-----Dark field microscopy-----DIC microscopy-----Phase contrast microscopy-----Polarized light microscopy----Widefield microscopy--Multimodal imaging--Spectroscopy---Fluorescence correlative spectroscopy---Nuclear magnetic resonance spectroscopy--Tomography---Computerized tomography---Photoacoustic tomography---Positron emission tomography---Single-photon emission computed tomography--Ultrasonography-In-silico reconstruction-Machine learning--Reinforcement learning--Supervised learning--Unsupervised learning-Sample-Sample preparation--Critical-point drying--Cryo fixation---High-pressure freezing---Plunge freezing--Freeze fracturing-Statistics

Supported image dimension 2D3Dmulti-channeltime-series

Type

- Any -CollectionComponentI do not knowWorkflow

Interaction level AutomatedI do not knowManualSemi-automated

License/Openness CommercialFree and open sourceFree but not open sourceI do not know

Programming language CC#C++CellProfiler PipelineClojureCUDAGNU BashIcy ProtocolsImageJ MacrosJavaJavascriptJythonKNIME WorkflowMatlabPerlPythonQtR

specific biological term 2D Gaussian FittingActinactomyosinadenocarcinomaadipocyteadipose tissue cellularityAlzheimer's diseaseamoeboid cellsangiogenesisantsArabidopsis ovulesArabidopsis thalianaArabidopsis thaliana seedlingsArtemiaarteriolesAstrocytesaxonbacteriabacterial coloniesbeadblood cellsblood vesselsbonesbrainbranchingbreast cancerbrownian motionc. elegansC.elegans embryo developmentCa2+Caenorhabditis eleganscalcium signallingcalcium sparkscancerCapillariescardiomyocytescell areacell biologycell membranecell migrationcell motilitycell organellescell protrusioncell retractioncell trackingcell volumecellscentral nervous systemcentriolecentromerechromatinclathrinclustered cellscollagenconnectomicsCOVIDcytoocytoplasmcytoskeletondendritesDendritic Spinedevelopmental biologyDictyosteliumdiffusiondivisionDNA damagedragonfly neurondrosophilaDrosophila melanogasterdrosophila wingE-CadherinE. coliEB1embryoendoplasmic reticulumendosomesendosomes (4656eosinEpidermisepitheliaevolutionExocytosisexosomesextrusionfiberfibronectinfilamentfilopodiaflowfluidFluoreceFocal Adhesionfocifruit fly neuronfungigangliongel analysisgene focigene lociglandglioblastomaGolgi apparatusgrayscale imagegrowthH&E stainingheartHela cellshematoxylinHippocampal NeuronshistopathologyHL60 cellshuman induced pluripotent stem cellhuman oocyteimmune systeminterdigitation measurementsinvaginationinvasive breast carcinoma cellsinvasive cell migrationKi67kidney tubuleskinetochoreLabel freelamellipodialarvaLeafleaf infectionligand-receptorlipid dropletslocalization of anatomical structures lunglung airwaysLymphatic Vessel DensitylysosomemacrophageMammary EpithelialMaturationmedakaMeiosismembranemembrane dynamicsmiMiceMicroArraymicrobeMicrogliamicrotubulesmineralsmitochondriamitosismoleculemorphological phenotypemosaicmousemouse brainmRNAMusclemuscle fiber orientationMuscle Stem Cellsmyelinmyofibresmyosinnanoparticlesndpineocortical axonsnetworkneurite arborneurite areaneurite attachment pointsneurite endpointsneurite lengthneurite outgrowth measurementneuritesneuroanatomyneuroblastomaneuromuscular axonsneuronneuronal arborsneuronsNIH-3T3NucelusNuclear pores nucleinucleusolfactory axonsolfactory fibreolfactory projection fibresoligodendrocyteOligodendrocytesOligodendrocytes, Oligodendrocytes differentiation, Morphological Analysis Oocyteorganoidovarian cancerparticlespathologyPhagocytosisPhysiologyplantplant virursplant virus, leaf infectionplate numberPressure myographyprogesterone receptorproteinspulmonary airwaysREF-52 cellsretinaRNAFishRNAirod-shapedrootsea urchin oocytesensory organ precusorsingle moleculeskeletonskinsmFishSpatial omicsSpatial transcriptomicsspheroidspindle elongationspotsstationary noisestem cellsstereo logysubcellular compartmentssubcellular interactionssubcellular structuresynapsetextilesthickness measurementstiled imagestilestissuetissue engineeringtissuestoxicologyTrabeculaeTrack Editingtraffickingtranscriptstransfectedtubular networktubular structuretubulintumorvesiclevesiclesVimentinviral particlesViruswell numberwormwound closureyeastyeast Schizosaccharomyces pombezebrafishzyxin

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listing content

Name	Category	Image	requires	Type	interaction level	License/Openness	has function	has topic
2D cell tracking and analysis of morphological dynamics	Software		ImageJ, QuimP	Workflow	Semi-automated	I do not know	Cell segmentation, Active contours, Cell tracking
3D Active Meshes (Icy)	Software		Spot detection utilities, Icy HK-Means, EzPlug SDK, Icy Protocols SDK	Component	Automated	Free and open source	Cell segmentation, Cell tracking	Bioimage informatics
3D cell tracking and quantification of shape changes	Software		MATLAB	Workflow	Automated	I do not know	Cell tracking
3D cell tracking using Gaussian Mixture Model (TGMM)	Software			Workflow		Free and open source	Cell tracking	Bioimage informatics, Live sample imaging, Light-sheet microscopy
3DeeCellTracker	Software		Tensorflow, Jupyter notebook	Workflow	Semi-automated	Free and open source	Cell segmentation, Cell tracking	Bioimage informatics
Aivia - Aivia Cloud - Aivia Web	Software			Collection, Workflow	Automated, Manual, Semi-automated	Commercial	Analysis, Frequency analysis, Image analysis, Colocalisation 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, Image deconvolution, Visualisation, Image visualisation, Volume rendering, Plotting	Machine learning
Bayesian Tracker (btrack)	Software		Python	Collection	Manual, Semi-automated	Free and open source	Analysis, Cell segmentation, Cell tracking	Live sample imaging, Fluorescence microscopy, Machine learning
bleb dynamics	Software		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
Cell segmentation and quantification with CellX	Software		Matlab Image Processing Toolbox, MATLAB	Workflow	Automated	Free and open source	Image segmentation, Cell tracking	Bright field microscopy, Phase contrast microscopy
Cell segmentation in phase contrast images	Software		MATLAB	Component	Semi-automated	Free and open source	Cell segmentation, Active contours, Object tracking, Cell tracking	Phase contrast microscopy
CellStitch	Software		Python	Component	Automated	Free and open source	Cell segmentation, Cell tracking, Image reconstruction	Microscopy, Electron microscopy, Fluorescence microscopy
CellTrack	Software			Collection	Semi-automated	Free and open source	Object detection, Object feature extraction, Cell tracking, Trajectory analysis	Bioimage informatics
CellTracker	Software			Component	Automated	Free but not open source	Object tracking, Cell tracking	Live sample imaging, Fluorescence microscopy
Cicardian Gene Expression	Software		ImageJ	Component	Semi-automated	Free and open source	Cell tracking
DeepCell	Software		Tensorflow, Keras	Component	Automated, Semi-automated	Free and open source	Cell segmentation, Cell tracking, Morphological operation	Fluorescence microscopy, Phase contrast microscopy
ELEPHANT	Software			Collection	Semi-automated	Free and open source	Object detection, Cell tracking, Trajectory analysis, Visualisation	Bioimage informatics, Live sample imaging, Light-sheet microscopy, Confocal fluorescence microscopy, Machine learning
ImageJ Plugin LineageTracker	Software		ImageJ	Component	Automated	Free and open source	Cell tracking	Bioimage informatics, Fluorescence microscopy
ISBI Tracking Challenge Batch Scoring	Software		Icy	Component	Automated	Free and open source	Analysis, Cell tracking	Bioimage informatics, Statistics
MaMuT	Software		Fiji, BigDataViewer, TrackMate	Collection	Manual, Semi-automated	Free and open source	Image feature detection, Object tracking, Cell tracking, Image visualisation, Overlay, Plotting, Image annotation	Live sample imaging, Light-sheet microscopy
Measure cell volume over time	Software		ImageJ, Imaris	Workflow	Semi-automated	Free and open source	Cell tracking