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plugin:start [2019/02/01 05:05]
plugin:start [2019/04/12 11:13] (current)
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 +====== 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:​confined_displacement_algorithm_determines_true_and_random_colocalization_:​start|Confined Displacement Algorithm Determines True and Random Colocalization (CDA)]]
 +  * [[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:​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:​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]]