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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
Cell segmentation and measurements	Software		CellProfiler, Segmentation of Clustered Cells in MATLAB	Workflow	Automated	I do not know
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 by EBImage, R	Software		Graylevel Watershed for ImageJ, Segmentation of Clustered Cells in MATLAB	Workflow	Automated	I do not know
CellProfiler Comet assay/DNA damage assay	Software		CellProfiler	Workflow	Automated	Free and open source, I do not know
CellProfiler Examples - Colocalization	Software		CellProfiler	Workflow	Semi-automated	Free and open source	Colocalisation analysis, Object-based colocalisation
Cells tracking in tissue	Software		ImageJ, MATLAB, Graylevel Watershed for ImageJ	Workflow	Automated	I do not know
Centromere Recognition and Quantification	Software		ImageJ, Spot Detection (KNIME)	Workflow	Semi-automated	Free and open source	Spot detection	Fluorescence microscopy
classification of hemp fibers based on morphological features	Software		ImageJ, MATLAB, MorphoLibJ	Workflow	Semi-automated	I do not know	Watershed segmentation, Object classification, Image feature detection, Object feature extraction, Morphological operation	Microscopy
Colony Blob Count Tool	Software		ImageJ	Workflow	Semi-automated	Free and open source	Object counting	Bright field microscopy
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
Creating an ImageJ plugin / command	Software		ImageJ, Fiji, IntelliJ IDEA, Fiji	Workflow	Automated, Manual, Semi-automated	Free and open source	Image processing	Bioimage informatics
CytooChip Analysis	Software		ImageJ	Workflow	Automated	Free and open source
Data-analysis strategies for image-based cell profiling	Software			Workflow	Automated, Semi-automated	Free but not open source	Analysis, Image segmentation, Object feature extraction, Shape features, Image correction	High content screening, Statistics
DBSCAN clustering using PALMsiever	Software		PALMsiever	Workflow	Automated	I do not know	Cell segmentation	Single molecule localization microscopy
DeepCLEM	Software		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
DNA MicroArray Image Processing Case Study	Software		MATLAB, Matlab Image Processing Toolbox, MATLAB Signal Processing Toolbox	Workflow	Semi-automated	Free and open source	Image segmentation, Spot detection
Drift correction using PALMsiever	Software		PALMsiever	Workflow	Automated	I do not know	Drift correction	Super-resolution microscopy
Effective image visualization for publications – a workflow using open access tools and concepts	Software			Workflow		Free and open source
Feature Calculation (KNIME)	Software		KNIME Image Processing and Analysis	Workflow	I do not know	Free and open source	Image feature detection, Image segmentation, Object feature extraction	Bioimage informatics