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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

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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
ImageJ2 Ops Scripting	Training Material
Interactive Data Visualization 101 with Fiji & Friends	Training Material
Introduction to 3D Analysis with 3D ImageJ Suite	Training Material
Introduction to Bio Image analysis	Training Material
Introduction to Image Segmentation	Training Material
Introduction to ImageJ basic operations	Training Material
Introduction to ImageJ macro language	Training Material
Introduction to ImageJ macros: Quantify the enrichment of NPC proteins at the nuclear envelope, relative to its cytoplasmic localisation	Training Material
Introduction to ImageJ: basic operations	Training Material
Introduction to ImarisXT using MATLAB	Training Material
Introduction to Matlab	Training Material
Introduction to R for bioimage analysis	Training Material
KNIME Workflow	Training Material
Kota Miura (ed) "Bioimage Data Analysis", Textbook, Wiley	Training Material
Lecture Applied Bio-image Analysis at Biotechnology Center, TU Dresden, 2020	Training Material
Lecture Bio-image analysis, biostatistics, programming and machine learning for computational biology at the Biotechnology Center, TU Dresden, 2021	Training Material
Macro Programming in ImageJ	Training Material
Mathematical morphology with morphoLibJ	Training Material
Metric Reloaded: how to select and use your metrics	Training Material
Microscopie image analysis on Bio Image Archive	Training Material