====== Plugins ====== Descriptions and downloads for ImageJ plugins stored here. There are many more plugins in the ImageJ website. ===== Acquisition ===== * [[plugin:acquisition:imagejvi:start|ImageJVI]] ===== Aligning ===== * [[plugin:aligning:align_4:start|Align_4]] * [[plugin:aligning:align_rgb_planes:start|Align_RGB_planes]] * [[plugin:aligning:align_slice:start|Align_Slice]] * [[plugin:aligning:bunwarpj:consistent_and_elastic_2d_image_registration:start|bUnwarpJ: consistent and elastic registration]] * [[plugin:aligning:image_stabilizer:start|Image Stabilizer]] ===== Analysis ===== * [[plugin:analysis:aatap:start|]] * [[plugin:analysis:analyzeskeleton:start|Analyze Skeleton (2D/3D)]] * [[plugin:analysis:autodetection_of_neuronal_labeling_in_histological_image_series:start|Automatic detection of neuronal labeling in histological image series]] * [[plugin:analysis:asa:start|Bitmap Sholl Analysis]] * [[plugin:analysis:geodesic_distances:start|Chamfer Distances and Geodesic Diameters]] * [[plugin:analysis:clonaltools:start|ClonalTools (analysis of mosaic images)]] * [[plugin:analysis:colocalizationfinder:start|Colocalization Finder]] * [[plugin:analysis:confined_displacement_algorithm_determines_true_and_random_colocalization_:start|Confined Displacement Algorithm Determines True and Random Colocalization (CDA)]] * [[plugin:analysis:distance_analysis_diana_2d_3d:start|Distance Analysis (DiAna)]] * [[plugin:analysis:feature_finder:start|Feature Finder (Template matching)]] * [[plugin:analysis:frap_normalization:start|Frap_Norm (FRAP measurement and normalization)]] * [[plugin:analysis:frap_analysis:start|FRAP Analysis (analysis of FRAP experiments)]] * [[plugin:analysis:fourier_shape_analysis:start|Fourier Shape Analysis]] * [[plugin:analysis:colocalization_analysis_macro_for_red_and_green_puncta:start|Green and Red Puncta Colocalization]] * [[plugin:analysis:heatmap_histogram:start|HeatMap Histogram]] * [[plugin:analysis:ivim_and_adc_analysis_tool:start|Intravoxel Incoherent Motion (IVIM) Analysis and ADC analysis]] * [[plugin:analysis:jacop_2.0:just_another_colocalization_plugin:start|JACoP (Just Another Co-localization Plugin)]] * [[plugin:analysis:droplet_counter:start|Lipid Droplet (or any other spots) Counter]] * [[plugin:analysis:lemos_asymetry_analysis:start|Lemos Asymmetry Analysis (asymmetry measurements from dental panoramic radiograph images)]] * [[plugin:analysis:poissonnmf:start|PoissonNMF: Linear unmixing without reference spectra]] * [[plugin:analysis:shapelogic:start|ShapeLogic categorizer: Machine learning or rule based]] * [[plugin:analysis:micropatterned_single_cell_sorting_mscs_:start|MSCS (Micropatterned Single Cell Sorting)]] * [[plugin:analysis:3d_object_counter:start|3D Object Counter]] * [[plugin:stacks:3d_roi_manager:start|3D Roi Manager]] * [[plugin:analysis:3d_analysis:start|3D Analysis]] * [[plugin:analysis:3d_mereotopology:start|3D Mereotopology]] * [[plugin:analysis:spatial_statistics_2d_3d:start|2D/3D Spatial statistics]] * [[plugin:analysis:metroloj:start|MetroloJ]] * [[plugin:analysis:openmims:start|OpenMIMS (open, process and analyze images captured with NanoSIMS 50 & 50L secondary ion mass spectrometers)]] * [[plugin:analysis:radial_thickness_measure:start|Radial thickness measure]] * [[plugin:analysis:SarConfoCal:start|SarConfoCal (Simultaneous Fluorescence and Sarcomere Length Measurements from LSCM Images)]] * [[plugin:analysis::SarcOptiM:start|SarcOptiM (High Frequency Online Sarcomere Length Measurement)]] * [[plugin:analysis:Time gated phasor:start|Time gated phasor]] * [[plugin:analysis:three-way_pca:start|Three-way PCA]] * [[plugin:analysis::ttorg_transverse_tubular_system_regularity_analysis_:start|TTorg (Transverse tubular system regularity analysis)]] * [[plugin:analysis:wand_tracker:start|Wand Tracker (track objects by selecting them with the magic wand)]] * [[plugin:analysis:microscope_image_correlation_spectroscopy:start|]] * [[plugin:analysis:neurite-j:start|Neurite-J, Sholl analysis for organotypic cultures]] * [[plugin:analysis:Find_min_max:start]] * [[plugin:analysis:fleye:start|FLEYE, ommatidia analysis]] * [[plugin:3d:tissue_organization_toolbox:start|3D tissue organisation]] ===== Collections ==== * [[plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start|MiToBo - a microscope image analysis toolbox (basic image processing tools, active contours, cell/nuclei/neurite segmentation, scratch assay analysis, ...)]] ===== Color ===== * [[plugin:color:Chart_White_Balance:start|Chart White Balance]] * [[plugin:color:colour_deconvolution:start|Colour Deconvolution]] * [[plugin:color:Color_Pixel_Counter:start|Color Pixel Counter]] * [[plugin:color:lut_panel:start|Lut Panel]] * [[plugin:color:threshold_colour:start|Threshold Colour]] * [[plugin:color:colour_deconvolution:optimizing_selection_of_unitary_optical_density_vectors:start|Color Deconvolution: Optimizing handling of 3D unitary optical density vectors with polar coordinates]] * [[plugin:color:channel_merger_:start]] * [[plugin:color:conversions_between_rgb_color_space_and_lab_color_space:start]] * [[plugin:color:set_min_and_max_values_for_lut:start]] ===== Filters ===== * [[plugin:filter:digital_darkfield_decomposition:start|Digital Darkfield Decomposition]] * [[plugin:filter:edge_detection:start|Edge Detection]] * [[plugin:filter:expression:start|Expression]] * [[plugin:filter:fast_filters:start|Fast Filters]] * [[plugin:filter:fit_polynomial:start|Fit_Polynomial]] * [[plugin:filter:highpass_filter:start|Highpass filter]] * [[plugin:filter:hill_shade:start|Hill Shade]] * [[plugin:filter:mri_processor:start]] * [[plugin:filter:nonuniform_background_removal:start|Nonuniform Background Removal]] * [[plugin:filter:periodic_boundary_blur:start|Periodic_Boundary_Blur]] * [[plugin:filter:surface_blur:start|Surface Blur]] * [[plugin:filter:thresholded_blur:start|Thresholded Blur]] * [[plugin:filter:3d_filters:start|]] * [[plugin:filter:3d_filters_with_jni:start|]] * [[plugin:filter:differential_contrast_enhancement:start | Differential contrast enhancement]] * [[plugin:filter:line_lab_selective_median_filtering:start]] * [[plugin:filter:lab_nonlocal_mean_with_same_pixel_luminance_neighborhood:start]] ===== Input / Output ===== * [[plugin:inputoutput:apng:start|Animated PNG Writer]] * [[plugin:inputoutput:bio_formats:start|Bio-Formats]] * [[plugin:inputoutput:jcbf:start|CBF Reader]] * [[plugin:inputoutput:dicom_open:start|]] * [[plugin:inputoutput:hpgl:start|HPGL_Reader]] * [[plugin:inputoutput:lsm_reader:start|LSM_Reader]] * [[plugin:inputoutput:lsmtoolbox:start|LSMToolbox]] * [[plugin:inputoutput:nd_stacks_builder:start|Metamorph nd & ROI files importer (nd stack builder)]] * [[plugin:inputoutput:okolab_data_import:start|Okolab Data Import]] * [[plugin:stacks:perkin_elmer_reader:start|Perkin Elmer Reader]] * [[plugin:inputoutput:pgm_16_bit_export:start|PGM 16 bit exporter]] * [[plugin:inputoutput:sims_toolbox:start|SIMS_Toolbox]] * [[plugin:inputoutput:tomoj:start|TomoJ]] * [[plugin:inputoutput:the_tudor_dicom_toolkit:start|The Tudor DICOM Toolkit]] * [[plugin:inputoutput:picoquant_.pt3_image_reader:start| Pt3Reader, a Picoquant .pt3 files importer]] ===== Morphology ===== * [[plugin:morphology:morphological_operators_for_imagej:start|Morphological Operators for ImageJ]] * [[plugin:morphology:graymorphology:start|Non binary Morphological Operators for ImageJ]] * [[plugin:morphology:fast_morphological_filters:start|Fast Morphological Filters]] * [[plugin:morphology:mitochondrial_morphology_macro_plug-in:start|Mitochondrial Morphology]] * [[plugin:morphology:skeletonize3d:start| 2D/3D Skeletonization]] * [[plugin:morphology:3d_mathematical_morphology_:start|]] * [[plugin:morphology:euclidean_minimum_spanning_tree:start|]] * [[plugin:morphology:apoptosis_and_cell_count_macro:start|Apoptosis Macro]] ===== Segmentation ===== * [[plugin:segmentation:active_mask_segmentation_of_fluorescence_microscope_cell_images_:start|Active Mask Segmentation (2D)]] * [[plugin:segmentation:active_contour:start|Active contour (Snake)]] * [[plugin:segmentation:adjustable_watershed:start|Adjustable Watershed]] * [[plugin:segmentation:hysteresis_thresholding:start|Hysteresis thresholding]] * [[plugin:segmentation:livewire_plugin:start|LiveWire Plugin]] * [[plugin:segmentation:morphological_segmentation:start|Morphological Segmentation (2D/3D)]] * [[plugin:segmentation:simple_image_pixel_editor:start|Simple Image Pixel Editor]] * [[plugin:segmentation:spectral_phasor:start|Spectral Phasor]] * [[plugin:segmentation:thresholding_by_connection:start|Thresholding by connection]] * [[plugin:segmentation:threshold_colour:start|Threshold_Colour]] * [[plugin:segmentation:versatile_wand:start|Versatile Wand]] * [[plugin:segmentation:yawi_2d:start|Yawi 2D (Wand)]] * [[plugin:segmentation:3d_spots_segmentation:start|3D Segmentation]] * [[plugin:segmentation:chow_and_kaneko_binarization:start|Chow and Kaneko binarization]] * [[plugin:segmentation:jSLIC:start|jSLIC superpixels]] ===== Stacks ===== * [[plugin:stacks:attenuation_correction:start|Attenuation Correction]] * [[plugin:stacks:frame_projector:start|Frame Projector]] * [[plugin:stacks:heatmap_from_stack:start|HeatMap From Stack]] * [[plugin:stacks:hypervolume_browser:start|HyperVolume_Browser]] * [[plugin:stacks:image5d:start|Image5D]] * [[plugin:aligning:image_stabilizer:start|Image Stabilizer]] * [[plugin:stacks:image_stack_merger_plus_background_remover_:start|Image Stack Merger Plus]] * [[plugin:stacks:microscobioj:start|MicroSCoBioJ]] * [[plugin:stacks:multi_image_stack_operator:start|]] * [[plugin:stacks:nonuniform_background_removal:start|Nonuniform Background Removal]] * [[plugin:stacks:normal_map_computing_using_ptm:start|]] * [[plugin:stacks:nuclear_analysis_plugin:start|NucleusJ]] * [[plugin:stacks:perkin_elmer_reader:start|Perkin Elmer Reader]] * [[plugin:stacks:plot_stack_points:start|]] * [[plugin:stack:stack_fitter:start]] * [[plugin:filter:3d_filters:start|]] * [[plugin:stacks:3d_tools:start|3D Tools]] * [[plugin:stacks:3d_ij_suite:start|]] ===== 3D Modelling ===== * [[plugin:3d:3d_mandelbrot_fractals:start|Fractal3D]] * [[plugin:3d:trakem2:start|TrakEM2]] * [[plugin:3d:phantomaj:start|PhantomaJ]] ===== Utilities ===== * [[plugin:utilities:action_bar:start|Action Bar]] * [[plugin:utilities:alpha_channel:start|Alpha Channel]] * [[plugin:utilities:annotation_roi_3d:start|Annotation ROI 3D]] * [[plugin:utilities:bezier_curve_roi:start|Bezier Curve ROI]] * [[plugin:utilities:cairm_image_splitter:start|Cairn Image Splitter]] * [[plugin:utilities:contmensili:start|ContMensili (update 05 mar 2011)]] * [[plugin:utilities:dicom_explode:start|]] * [[plugin:utilities:droplet:start|Droplet: a Drag and Drop image processor]] * [[plugin:utilities:figurej:start|FigureJ: easy article figures]] * [[plugin:utilities:ij_ed:start|IJ Ed (jEdit for ImageJ)]] * [[plugin:utilities:imageflow:start|Imageflow]] * [[plugin:utilities:ijupdate:start|IJUpdate]] * [[plugin:utilities:ijproxy:start|IJProxy]] * [[plugin:utilities:livemacro:start|Live Macro (experiment with a webcam and macro language)]] * [[plugin:inputoutput:lsmtoolbox:start|LSM Toolbox]] * [[plugin:utilities:midij_-_midi_plugin_for_imagej:start|MidiJ - Midi Plugin for ImageJ]] * [[plugin:utilities:mri_cell_image_analyzer:start|MRI Cell Image Analyzer]] * [[plugin:utilities:mvfg_-_multi-format_video_frame_grabber_imagej_plugin:start|MVFG - Multi-format Video Frame Grabber]] * [[plugin:utilities:multi_undo:start|Multi Undo]] * [[plugin:utilities:neuronpersistentj:start|NeuronPersistentJ]] * [[plugin:utilities:pdf_macro_extension:start|PDF macro extension]] * [[plugin:utilities:pixel_inspector:start|Pixel_Inspector]] * [[plugin:utilities:python_dm3_reader:start|Python DM3 Reader]] * [[plugin:utilities:quadratic_curve ROI:start|Quadratic Curve ROI]] * [[plugin:utilities:save_all:start|Save All]] * [[plugin:utilities:seam_carving:start|Seam Carving]] * [[plugin:utilities:serial_macro_extensions:start|Serial Macro extensions]] * [[plugin:utilities:synapsescountj:start|SynapCountJ]] * [[plugin:utilities:tapas_:integrated_framework_for_automated_processing_and_analysis:start|TAPAS]] * [[plugin:utilities:wait_for_user:start|Wait_For_User]]