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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 biologyDictyosteliumdiffusionDNA damagedragonfly neurondrosophilaDrosophila melanogasterdrosophila wingE. coliEB1embryoendoplasmic reticulumendosomesendosomes (4656eosinEpidermisepitheliaevolutionExocytosisexosomesfiberfibronectinfilamentfilopodiaflowfluidFluoreceFocal Adhesionfocifruit fly neuronfungigangliongel analysisgene focigene lociglandglioblastomaGolgi apparatusgrayscale imagegrowthH&E stainingheartHela cellshematoxylinHippocampal NeuronshistopathologyHL60 cellshuman induced pluripotent stem cellimmune systeminterdigitation measurementsinvaginationinvasive breast carcinoma cellsinvasive cell migrationKi67kidney tubuleskinetochorelamellipodialarvaLeafleaf infectionligand-receptorlipid dropletslocalization of anatomical structures lunglung airwaysLymphatic Vessel DensitylysosomemacrophageMammary Epithelialmedakamembranemembrane dynamicsmiMicroArraymicrobeMicrogliamicrotubulesmineralsmitochondriamitosismoleculemorphological 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 cellsretinaRNAirod-shapedrootsingle moleculeskeletonskinSpatial 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
ZEN and APEER Machine Learning Platform	Software		arivis Vision4D, ZEN Blue, APEER	Collection, Component, Workflow	Automated, Manual, Semi-automated	Commercial, Free and open source	Image segmentation, Cell segmentation, Model-based segmentation, Pixel classification, Object classification, Image annotation	Digital histology, High content screening, Electron microscopy, Light microscopy, Fluorescence microscopy, Machine learning, Supervised learning
Zebrafish Embryo Tool	Software		ImageJ	Workflow	Semi-automated	Free and open source	Alignment construction	Fluorescence microscopy
Wound Healing Tool	Software		ImageJ	Workflow	Automated	Free and open source
Wound healing assay: analysis in ImageJ	Software		ImageJ	Workflow	Automated	Free and open source	Image segmentation, Wound-healing analysis
Wound healing assay: analysis in CellProfiler	Software		CellProfiler	Workflow	Automated	Free and open source	Image segmentation, Wound-healing analysis
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
VascuSynth	Software		ITK, CMake	Workflow	Automated	Free and open source	Image generation
Using ImageJ to Analyze the Size, Shape, and Directionality of Networks of Coupled Astrocytes	Software		Fiji	Workflow	Manual	Free but not open source	Object feature extraction	Bioimage informatics, Confocal microscopy
Uneven illumination correction	Software		CellProfiler, ImageJ	Workflow	Automated	I do not know	Illumination correction
Tracking of focal adhesions in 2D time lapse movies	Software		MATLAB	Workflow	Semi-automated	I do not know	Image segmentation, Object tracking	Fluorescence microscopy
Track cell intensity	Software			Workflow	Automated	Free and open source	Active contours, Cell tracking
Tracing data using PALMsiever	Software		PALMsiever	Workflow	Automated	I do not know
Tissue analysis from histological sections	Software		Fiji, Trainable Weka Segmentation	Workflow	Automated	Free and open source	Pixel classification	Digital histology, Machine learning
The NEMO dots assembly: Single-particle tracking and analysis	Software			Workflow		Commercial, Free and open source
TEM ExosomeAnalyzer	Software			Workflow		Free but not open source	Image segmentation, Image visualisation	Electron microscopy
SynActJ	Software		Fiji	Workflow	Automated	Free and open source	Neuron image analysis	Live sample imaging
SpotDetectionIJ	Software		ImageJ, FeatureJ Laplacian, Find Maxima	Workflow	Automated, Semi-automated	Free and open source	Spot detection	Microscopy
Spot Detection Dmap (ImageJ)	Software		ImageJ, FeatureJ Laplacian, ImageJ Built-in Macro Functions	Workflow	Automated	Free and open source	Spot detection, Distance transform
spot detection and codistribution analysis	Software		ImageJ, MATLAB	Workflow	Automated, Semi-automated	Free and open source	Colocalisation analysis, Object-based colocalisation, Spot detection, Object detection
Spot Detection 3D Hessian (ImageJ)	Software		ImageJ, FeatureJ Laplacian, ImageJ Built-in Macro Functions, FeatureJ Hessian	Workflow	Automated	Free and open source	Spot detection, Feature enhancement	Bioimage informatics