ImageJ

Analyze

• Color Histogram - file ColorHistogram_ -- java jar file
• Color Inspector 3D - file Color_Inspector_3D -- java jar file
• Directionality - file fiji.analyze.directionality.Directionality_ -- java jar file
• Helmholtz Analysis - file Helmholtz_Analysis -- java jar file
• 3D Surface Plot - file Interactive_3D_Surface_Plot -- java jar file
• Shape Index Map - file fiji.geom.Shape_Index_Map -- java jar file
• 3D OC Options - file _3D_OC_Options -- java jar file
• 3D Objects Counter - file _3D_objects_counter -- java jar file

Analyze > Classification

• IsoData Classifier - file IsoData_Classifier -- java jar file

Analyze > Colocalization

• Coloc 2 - file Coloc_2 -- java jar file
• Colocalization Test - file Colocalisation_Test -- java jar file
• Colocalization Threshold - file Colocalisation_Threshold -- java jar file

Analyze > Local Thickness

• Local Thickness to Cleaned-Up Local Thickness - file Clean_Up_Local_Thickness("run") -- java jar file
• Distance Map to Distance Ridge - file Distance_Ridge("run") -- java jar file
• Geometry to Distance Map - file EDT_S1D("run") -- java jar file
• Local Thickness (complete process) - file Local_Thickness_Driver("run") -- java jar file
• Distance Ridge to Local Thickness - file Local_Thickness_Parallel("run") -- java jar file

Analyze > Optic Flow

• FlowJ - file FlowJ_ -- java jar file
• PIV analysis - file PIV_analyser -- java jar file

Analyze > QuickPALM

• Analyse Particles - file QuickPALM.Analyse_Particles -- java jar file
• Correct Particles Drift (based on ROI) - file QuickPALM.Correct_Drift2 -- java jar file
• Create 3D calibration (requires astigmatism) - file QuickPALM.Create_3D_calibration -- java jar file
• Load Particles (.tif file - fast) - file QuickPALM.Load_particles_tableFromImg -- java jar file
• Reconstruct Dataset - file QuickPALM.Reconstruct_Dataset -- java jar file
• Save Particles (.tif file - fast) - file QuickPALM.Save_particles_table2img -- java jar file
• Stop Analyse Particles (kills the threads) - file QuickPALM.Stop_processing -- java jar file
• About... - file QuickPALM.Run_MyMacro("About_.txt") -- java jar file
• Fast VirtualStack Opener - file QuickPALM.Run_MyMacro("Fast_VirtualStack_Opener.txt") -- java jar file
• Sort Particles by frame (in a .tif particle table file) - file QuickPALM.Run_MyMacro("Sort_particles.txt") -- java jar file
• Update QuickPALM - file QuickPALM.Run_MyMacro("Update_.txt") -- java jar file

Analyze > Tools

• PointPicker - file PointPicker_ -- java jar file
• Sync Measure 3D - file Sync_Measure_3D("") -- java jar file
• Sync Windows - file Sync_Windows("") -- java jar file

Analyze > TopoJ

• Compute Topography - file Compute_Topography -- java jar file
• Remove Slope - file Remove_Slope -- java jar file

Edit

Edit > Selection

• Points from Mask - file fiji.selection.Binary_to_Point_Selection -- java jar file
• Fit Circle to Image - file fiji.util.Circle_Fitter -- java jar file
• Fill ROI holes - file Fill_holes -- java jar file
• Select Bounding Box - file fiji.selection.Select_Bounding_Box -- java jar file
• Select Bounding Box (guess background color) - file fiji.selection.Select_Bounding_Box("autoselect") -- java jar file

File

File > Import

• Amira... - file AmiraMeshReader_ -- java jar file
• Show Amira Surface - file isosurface.AmiraSurface -- java jar file
• Analyze... - file Analyze_Reader -- java jar file
• Animated Gif... - file io.Animated_Gif_Reader -- java jar file
• Biorad... - file Biorad_Reader -- java jar file
• DM3 Reader... - file io.DM3_Reader -- java jar file
• Extract Images From PDF... - file io.Extract_Images_From_PDF -- java jar file
• FIB-SEM ... - file io.FIBSEM_Reader -- java jar file
• ICO... - file io.ICO_Reader -- java jar file
• IPLab Reader... - file io.IPLab_Reader -- java jar file
• Icns... - file io.Icns_Reader -- java jar file
• Open with preview ... - file net.sf.ij.plugin.ImageIOOpenPlugin("preview") -- java jar file
• [[Open [Image IO]]] - file net.sf.ij.plugin.ImageIOOpenPlugin("simple") -- java jar file
• LSM... - file LSM_Reader -- java jar file
• Show LSMToolbox - file LSM_Toolbox("") -- java jar file
• LSS16... - file io.LSS16_Reader -- java jar file
• Leica SP... - file leica.Leica_SP_Reader -- java jar file
• Bio-Formats (Remote) - file loci.plugins.LociImporter("location=[Internet]") -- java jar file
• Bio-Formats - file loci.plugins.LociImporter("location=[Local machine] windowless=false ") -- java jar file
• Bio-Formats (Windowless) - file loci.plugins.LociImporter("location=[Local machine] windowless=true ") -- java jar file
• Amira as TrakEM2... - file ini.trakem2.New_Project("amira") -- java jar file
• Nrrd ... - file io.Nrrd_Reader -- java jar file
• DAT EMMENU ... - file io.Open_DAT_EMMENU -- java jar file
• DF3... - file io.Open_DF3 -- java jar file
• MRC Leginon ... - file io.Open_MRC_Leginon -- java jar file
• TrakEM2 XML... - file ini.trakem2.Open_Project -- java jar file
• PDF ... - file io.PDF_Viewer -- java jar file
• Reconstruct Project... - file reconstructreader.reconstruct.Reconstruct_Reader -- java jar file
• SPIM - file spimopener.SPIM_Opener -- java jar file
• SVG... - file io.SVG_Reader -- java jar file
• TorstenRaw GZ Reader... - file io.TorstenRaw_GZ_Reader -- java jar file

File > Import > QuickPALM

• Load Particles (.tif file - fast) - file QuickPALM.Load_particles_tableFromImg -- java jar file
• Save Particles (.tif file - fast) - file QuickPALM.Save_particles_table2img -- java jar file
• Open VirtualStack - file QuickPALM.Run_MyMacro("Fast_VirtualStack_Opener.txt") -- java jar file

File > New

• TrakEM2 (from template) - file ini.trakem2.New_Project -- java jar file
• TrakEM2 (blank) - file ini.trakem2.New_Project("blank") -- java jar file
• Script - file fiji.scripting.Script_Editor -- java jar file

File > Open Samples

• Shepp-Logan Phantom (Plugin) - file SheppLogan_ -- java jar file
• The New Lenna (95K) - file ij.plugin.URLOpener("") -- java jar file
• Malaria Sporozoites (9.2MB) - file ij.plugin.URLOpener("https://fiji.sc/samples/_malaria_parasites.tif") -- java jar file
• First-instar brain (6.3MB) - file ij.plugin.URLOpener("https://fiji.sc/samples/first-instar-brain.zip") -- java jar file
• Sintered Alumina (2.6MB) - file ij.plugin.URLOpener("https://fiji.sc/samples/Sintered_Alumina.tif.zip") -- java jar file

File > Open_Samples

• Adelsons Squares - file Adelsons_Squares.ijm -- macro
• Spirals - file Spirals_.ijm -- macro

File > Save As

• AmiraMesh ... - file AmiraMeshWriter_ -- java jar file
• AmiraTable ... - file AmiraTableWriter_ -- java jar file
• Analyze... - file Analyze_Writer -- java jar file
• Biorad ... - file Biorad_Writer -- java jar file
• Wavefront .OBJ ... - file marchingcubes.ExportMesh_ -- java jar file
• EPS ... - file io.Export_EPS -- java jar file
• Animated Gif ... - file io.Gif_Stack_Writer -- java jar file
• ICO ... - file io.ICO_Writer -- java jar file
• Icns ... - file io.Icns_Writer -- java jar file
• PNG ... - file net.sf.ij.plugin.ImageIOSaveAsPlugin("PNG") -- java jar file
• PNM ... - file net.sf.ij.plugin.ImageIOSaveAsPlugin("PNM") -- java jar file
• Compressed TIFF ... - file net.sf.ij.plugin.ImageIOSaveAsPlugin("TIFF") -- java jar file
• LSS16 ... - file io.LSS16_Writer -- java jar file
• Leica SP ... - file leica.Leica_SP_Writer -- java jar file
• Nrrd ... - file io.Nrrd_Writer -- java jar file
• PDF ... - file io.PDF_Writer -- java jar file
• DF3 ... - file io.Save_DF3 -- java jar file
• XPM ... - file io.XPM_Writer -- java jar file

Help

• Report a Bug - file Bug_Submitter.Bug_Submitter -- java jar file
• Help on Menu Item - file fiji.help.Context_Help -- java jar file
• Upload Sample Image - file fiji.util.Fiji_Uploader -- java jar file
• Update Fiji - file fiji.updater.Updater("update") -- java jar file
• Licenses - file ij.plugin.BrowserLauncher("https://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=blob_plain;f=LICENSES;hb=HEAD") -- java jar file
• Fiji Wiki - file ij.plugin.BrowserLauncher("https://fiji.sc/") -- java jar file

Help > About Plugins

• LOCI Plugins... - file loci.plugins.About("") -- java jar file
• Image IO ... - file net.sf.ij.plugin.AboutImageIO("") -- java jar file
• Robust Automatic Threshold Selection - file About_RATS -- java jar file
• Color Histogram... - file ColorHistogram_("about") -- java jar file
• About bUnwarpJ... - file bunwarpj.Credits -- java jar file
• FeatureJ... - file FJ_Website -- java jar file
• Gray Morphology... - file GrayMorphology_("about") -- java jar file
• Image5D... - file I5D_about("about") -- java jar file
• LSMReader... - file LSM_Reader("about") -- java jar file
• LSMToolbox... - file LSM_Toolbox("about") -- java jar file
• RandomJ... - file RJ_Website -- java jar file
• Sync Measure 3D... - file Sync_Measure_3D("about") -- java jar file
• Sync Windows... - file Sync_Windows("about") -- java jar file
• TransformJ... - file TJ_Website -- java jar file
• About TrakEM2... - file ini.trakem2.utils.Utils -- java jar file

Image

Image > Adjust

• Auto Local Threshold - file fiji.threshold.Auto_Local_Threshold -- java jar file
• Auto Threshold - file fiji.threshold.Auto_Threshold -- java jar file
• Bleach Correction - file emblcmci.BleachCorrection -- java jar file
• Scale to DPI - file Scale_to_DPI.js -- javascript script
• Auto Crop (guess background color) - file fiji.selection.Select_Bounding_Box("autoautocrop") -- java jar file
• Auto Crop - file fiji.selection.Select_Bounding_Box("autocrop") -- java jar file
• Threshold Colour - file Threshold_Colour -- java jar file

Image > Annotate

• Arrow - file fiji.util.ArrowTool -- java jar file

Image > Color

• Average Color - file Average_Color -- java jar file
• Colour Deconvolution - file Colour_Deconvolution -- java jar file
• Replace Red with Magenta - file fiji.color.Convert_Red_To_Magenta -- java jar file
• Replace Red with Magenta (system clipboard) - file fiji.color.Convert_Red_To_Magenta_Clipboard -- java jar file
• Dichromacy - file Dichromacy_ -- java jar file
• Simulate Color Blindness - file Dichromacy_ -- java jar file
• RGB to CIELAB - file RGB_to_CIELAB -- java jar file
• RGB to Luminance - file util.RGB_to_Luminance -- java jar file
• RGBtoLab - file RGBtoLab_ -- java jar file
• RGBtoYUV - file RGBtoYUV_ -- java jar file
• Retinex - file Retinex_ -- java jar file
• Set Color By Wavelength - file Set_Color_By_Wavelength.ijm -- macro

Image > Drawing

• Linear Gradient - file fiji.drawing.Linear_Gradient -- java jar file
• Radial Gradient - file fiji.drawing.Radial_Gradient -- java jar file

Image > Hyperstacks

• Re-order Hyperstack ... - file fiji.stacks.Hyperstack_rearranger -- java jar file
• Temporal-Color Code - file Temporal-Color_Code.ijm -- macro

Image > Selection

• Make rectangular selection rounded - file fiji.selection.Rounded_Rectangle -- java jar file

Image > Stacks

• Dynamic Reslice - file fiji.stacks.Dynamic_Reslice -- java jar file
• Kalman Stack Filter - file Kalman_Filter -- java jar file
• Radial Reslice - file fiji.stacks.Radial_Reslice -- java jar file
• Reslice Z - file Reslice_Z -- java jar file
• Series Labeler - file Series_Labeler -- java jar file
• Time Stamper - file Time_Stamper -- java jar file

Image > Stacks > Tools_

• Deinterleave - file DeInterleave_ -- java jar file
• Slice Keeper - file Slice_Keeper -- java jar file
• Slice Remover - file Slice_Remover -- java jar file
• Interleave - file Stack_Interleaver -- java jar file
• Stack Sorter - file Stack_Sorter -- java jar file
• Stack Splitter - file Stack_Splitter -- java jar file

Image > Stacks > View5D

• start viewer - file view5d.View5D_("") -- java jar file

Image > Video Editing

• Add Empty Frame - file video2.Add_Empty_Frame -- java jar file
• Delete Frame - file video2.Delete_Frame -- java jar file
• Draw Roi - file video2.Draw_Roi -- java jar file
• Duplicate Frame - file video2.Duplicate_Frame -- java jar file
• Insert Stack - file video2.Insert_Stack -- java jar file
• Make Transition - file video2.Make_Transition -- java jar file
• Move Roi - file video2.Move_Roi -- java jar file
• New Video - file video2.New_Video -- java jar file
• Open Video - file video2.Open_Video -- java jar file

Plugins

• 3D Viewer - file ImageJ_3D_Viewer -- java jar file
• Volume Viewer - file Volume_Viewer -- java jar file

Plugins > Analyze

• Compute Curvatures - file Compute_Curvatures -- java jar file
• Delaunay Voronoi - file Delaunay_Voronoi -- java jar file
• Dynamic ROI Profiler - file Dynamic_ROI_Profiler.clj -- clojure script
• Find differences - file FindIt_ -- java jar file
• 2D Histogram - file util.Histogram_2D -- java jar file
• Measure RGB - file Measure_RGB.txt -- macro
• Surfaceness - file features.Surfaceness_ -- java jar file
• Tubeness - file features.Tubeness_ -- java jar file
• VIB Protocol - file VIB_Protocol -- java jar file
• View5D - file view5d.View5D_ -- java jar file
• Visual grep - file Visual_Grep -- java jar file

Plugins > Examples

• Add Popup Split Channels - file Add_Popup_Split_Channels.bsh -- beanshell script
• Anaglyph for Red Cyan glasses - file Anaglyph_for_Red_Cyan_glasses.rb -- jruby script
• Blobs Demo in Ruby - file Blobs_Demo_in_Ruby.rb -- jruby script
• Delayed Snapshot - file Delayed_Snapshot.py -- jython script
• Delayed Snapshot Window - file Delayed_Snapshot_Window.bsh -- beanshell script
• Edit LUT As Text - file Edit_LUT_As_Text.py -- jython script
• Extended Profile Plot - file Extended_Profile_Plot.bsh -- beanshell script
• Fiji Cube - file Fiji_Cube.ijm -- macro
• Fiji Logo 3D - file Fiji_Logo_3D.js -- javascript script
• Find Dimension of Raw Image - file Find_Dimension_of_Raw_Image.py -- jython script
• Image To Tool Icon - file Image_To_Tool_Icon.bsh -- beanshell script
• Spheres and Tubes in 3D - file customnode.Mesh_Maker -- java jar file
• Multithreaded Image Processing - file Multithreaded_Image_Processing.clj -- clojure script
• Multithreaded Image Processing in Javascript - file Multithreaded_Image_Processing_in_Javascript.js -- javascript script
• Plasma Cloud - file Plasma_Cloud.rb -- jruby script
• Same Slice in Multiple Images - file Same_Slice_in_Multiple_Images.rb -- jruby script
• Single Voxel in 3D - file tracing.Test_Single_Voxel -- java jar file
• The Hue Game - file The_Hue_Game.bsh -- beanshell script
• blend two images - file blend_two_images.clj -- clojure script
• celsius to fahrenheit - file celsius_to_fahrenheit.clj -- clojure script
• chess - file chess_.py -- jython script
• downsample - file downsample_.js -- javascript script
• list all threads - file list_all_threads.py -- jython script
• random noise example - file random_noise_example.clj -- clojure script

Plugins > Examples > Command_Launchers

• Command Launcher BeanShell - file Command_Launcher_BeanShell.bsh -- beanshell script
• Command Launcher Clojure - file Command_Launcher_Clojure.clj -- clojure script
• Command Launcher Javascript - file Command_Launcher_Javascript.js -- javascript script
• Command Launcher Python - file Command_Launcher_Python.py -- jython script
• Command Launcher Ruby - file Command_Launcher_Ruby.rb -- jruby script

Plugins > Examples > CoverMaker

• Cover Maker - file Cover_Maker.py -- jython script
• Prepare Cover Maker Database - file Prepare_Cover_Maker_Database.py -- jython script

Plugins > Examples > TrakEM2_Example_Scripts

• Homogenize Ball Radius - file Homogenize_Ball_Radius.py -- jython script
• Measure AreaLists - file Measure_AreaLists.py -- jython script
• T2 Select All - file T2_Select_All.py -- jython script
• T2 set all transforms to identity - file T2_set_all_transforms_to_identity.py -- jython script
• extract stack under arealist - file extract_stack_under_arealist.py -- jython script

Plugins > Feature Extraction

• Extract Block Matching Correspondences - file mpicbg.ij.plugin.BlockMatching_ExtractPoinRoi -- java jar file
• Extract MOPS Correspondences - file MOPS_ExtractPointRoi -- java jar file
• Extract SIFT Correspondences - file SIFT_ExtractPointRoi -- java jar file

Plugins > Feature Extraction > FeatureJ

• FeatureJ Derivatives - file FJ_Derivatives -- java jar file
• FeatureJ Edges - file FJ_Edges -- java jar file
• FeatureJ Hessian - file FJ_Hessian -- java jar file
• FeatureJ Laplacian - file FJ_Laplacian -- java jar file
• FeatureJ Options - file FJ_Options -- java jar file
• FeatureJ Panel - file FJ_Panel -- java jar file
• FeatureJ Statistics - file FJ_Statistics -- java jar file
• FeatureJ Structure - file FJ_Structure -- java jar file

Plugins > Image5D

• Duplicate - file Duplicate_Image5D("") -- java jar file
• Hypervolume Opener - file Hypervolume_Opener("") -- java jar file
• Image5D Extensions - file Image5D_Extensions("") -- java jar file
• Image5D Stack to RGB - file Image5D_Stack_to_RGB("") -- java jar file
• Image5D to Stack - file Image5D_to_Stack("") -- java jar file
• Make Montage - file Make_Montage("") -- java jar file
• New Image5D - file New_Image5D("") -- java jar file
• Open Image5D - file Open_Image5D("") -- java jar file
• Open Series As Image5D - file Open_Series_As_Image5D("") -- java jar file
• RGB to Image5D - file RGB_to_Image5D("") -- java jar file
• Save Image5D - file Save_Image5D("") -- java jar file
• Set Channel Display - file Set_Channel_Display("") -- java jar file
• Set Channel Labels - file Set_Channel_Labels("") -- java jar file
• Set Position - file Set_Position("") -- java jar file
• Stack to Image5D - file Stack_to_Image5D("") -- java jar file
• Transfer Channel Settings - file Transfer_Channel_Settings("") -- java jar file
• Virtual Image5D Opener - file Virtual_Image5D_Opener("") -- java jar file
• Z Project - file Z_Project("") -- java jar file

Plugins > Integral Image Filters

• Mean - file mpicbg.ij.plugin.Mean -- java jar file
• Normalize Local Contrast - file mpicbg.ij.plugin.NormalizeLocalContrast -- java jar file
• Remove Outliers - file mpicbg.ij.plugin.RemoveOutliers -- java jar file
• Sample Variance - file mpicbg.ij.plugin.SampleVariance -- java jar file
• Standard Deviation - file mpicbg.ij.plugin.StandardDeviation -- java jar file

Plugins > LOCI

• LOCI Plugins Configuration - file loci.plugins.config.LociConfig("") -- java jar file
• Bio-Formats Exporter - file loci.plugins.LociExporter("") -- java jar file
• Bio-Formats Macro Extensions - file loci.plugins.macro.LociFunctions("") -- java jar file
• Bio-Formats Remote Importer - file loci.plugins.LociImporter("location=[Internet]") -- java jar file
• Bio-Formats Importer - file loci.plugins.LociImporter("location=[Local machine] windowless=false ") -- java jar file
• Bio-Formats Windowless Importer - file loci.plugins.LociImporter("location=[Local machine] windowless=true ") -- java jar file
• LOCI Plugins Shortcut Window - file loci.plugins.shortcut.ShortcutPanel("") -- java jar file
• Stack Slicer - file loci.plugins.Slicer("") -- java jar file
• Update LOCI Plugins - file loci.plugins.Updater("") -- java jar file

Plugins > Landmarks

• Name Landmarks and Register - file landmarks.Name_Points -- java jar file

Plugins > Macros

• About Plugin Macros - file About_Plugin_Macros.txt -- macro
• Bulls Eye - file Bulls_Eye.txt -- macro
• Polygon - file Polygon_.txt -- macro
• RGB Histogram - file RGB_Histogram.txt -- macro
• batch convert any to tif - file batch_convert_any_to_tif.txt -- macro

Plugins > Optic Flow

• Integral Block MSE - file mpicbg.ij.plugin.MSEBlockFlow -- java jar file
• Gaussian Window MSE - file mpicbg.ij.plugin.MSEGaussianFlow -- java jar file
• Integral Block PMCC - file mpicbg.ij.plugin.PMCCBlockFlow -- java jar file

Plugins > Process

• ImgLib Algorithm Launcher - file AlgorithmLauncher("") -- java jar file
• Anisotropic Diffusion 2D - file anisotropic_diffusion.Anisotropic_Diffusion_2D -- java jar file
• Bilateral Filter - file Bilateral_Filter -- java jar file
• Convolve (3D) - file process3d.Convolve_3d -- java jar file
• Dilate (3D) - file process3d.Dilate_ -- java jar file
• Distance Transform 3D - file process3d.Distance_Transform_3D -- java jar file
• Extended Depth of Field (Easy mode)... - file EDF_Easy_ -- java jar file
• Extended Depth of Field (Expert mode)... - file EDF_Expert_ -- java jar file
• Exact Euclidean Distance Transform (3D) - file fiji.process3d.EDT -- java jar file
• Erode (3D) - file process3d.Erode_ -- java jar file
• Fast FFT (2D/3D) - file registration3d.Fast_FourierTransform -- java jar file
• Find Connected Regions - file util.Find_Connected_Regions -- java jar file
• Flood Fill(3D) - file process3d.Flood_Fill -- java jar file
• Frangi Vesselness (imglib, experimental) - file fiji.features.Frangi_("") -- java jar file
• Gradient (3D) - file process3d.Gradient_ -- java jar file
• IFT (3D) - file process3d.IFT_ -- java jar file
• Implicit Interpolate Binary - file Implicit_Interpolate_Binary -- java jar file
• Laplace (3D) - file process3d.Laplace_ -- java jar file
• Mask Of Nearby Points - file util.Mask_Of_Nearby_Points -- java jar file
• Max (3D) - file process3d.Maximum_ -- java jar file
• Maximum (3D) - file process3d.Maximum_ -- java jar file
• Median (3D) - file process3d.Median_ -- java jar file
• Minimum (3D) - file process3d.Minimum_ -- java jar file
• Particle Analyzer (3D) - file process3d.Particle_Analyzer_3D -- java jar file
• Quantile Based Normalization - file util.Quantile_Based_Normalization -- java jar file
• Rebin (3D) - file process3d.Rebin_ -- java jar file
• Replace value - file Replace_Value -- java jar file
• Resample - file vib.Resample_ -- java jar file
• Shape-Based Averaging (Experimental) - file util.RohlfingSBA -- java jar file
• Shape-based averaging - file Rohlfing_SBA -- java jar file
• Exact Signed Euclidean Distance Transform (3D) - file fiji.process3d.SEDT -- java jar file
• Seam remover - file Seam_Remover -- java jar file
• Show Color Surfaces - file isosurface.Show_Colour_Surfaces -- java jar file
• Show label centers - file Show_Label_Centers -- java jar file
• Smooth (3D) - file process3d.Smooth_ -- java jar file
• Triangle Algorithm - file Triangle_Algorithm -- java jar file

Plugins > Registration

• Align Image by line ROI - file Align_Image -- java jar file
• Correct 3D drift - file Correct_3D_drift.py -- jython script
• Descriptor-based registration (2d/3d) - file plugin.Descriptor_based_registration -- java jar file
• Descriptor-based series registration (2d/3d + t) - file plugin.Descriptor_based_series_registration -- java jar file
• Manual landmark selection (3d) - file plugin.Manual_Landmark_Selection -- java jar file
• Moving Least Squares - file Moving_Least_Squares -- java jar file
• Register Virtual Stack Slices - file register_virtual_stack.Register_Virtual_Stack_MT -- java jar file
• Rigid Registration - file vib.RigidRegistration_ -- java jar file
• Linear Stack Alignment with SIFT - file SIFT_Align -- java jar file
• StackReg - file StackReg_ -- java jar file
• TurboReg - file TurboReg_ -- java jar file
• UnwarpJ - file UnwarpJ_ -- java jar file
• bUnwarpJ - file bunwarpj.bUnwarpJ_ -- java jar file

Plugins > Registration > Elastic

• Test Block Matching Parameters - file mpicbg.ij.plugin.BlockMatching_TestParameters -- java jar file
• Elastic Stack Alignment - file mpicbg.ij.plugin.ElasticAlign -- java jar file
• Elastic Montaging - file mpicbg.ij.plugin.ElasticMontage -- java jar file

Plugins > SPIM Registration

• Bead-based registration - file fiji.plugin.Bead_Registration -- java jar file
• Multi-view fusion - file fiji.plugin.Multi_View_Fusion -- java jar file

Plugins > SPIM Registration > Utilities

• Apply external transformation - file fiji.plugin.Apply_External_Transformation -- java jar file

Plugins > SPIM Registration > deprecated

• MultiChannel Registration - file MultiChannel_SPIM_Registration -- java jar file
• Registration - file SPIM_Registration -- java jar file
• Advanced Registration - file SPIM_Registration_File -- java jar file

Plugins > Scripting

• BeanShell Interpreter - file BSH.BSH_Interpreter -- java jar file
• Macro Interpreter - file CLI.CLI_ -- java jar file
• Clojure Interpreter - file Clojure.Clojure_Interpreter -- java jar file
• JRuby Interpreter - file JRuby.JRuby_Interpreter -- java jar file
• Javascript Interpreter - file Javascript.Javascript_Interpreter -- java jar file
• Jython Interpreter - file Jython.Jython_Interpreter -- java jar file
• Open Source for Menu Item - file fiji.scripting.OpenSourceForMenuItem -- java jar file
• Refresh BSH Scripts - file BSH.Refresh_BSH_Scripts -- java jar file
• Refresh Clojure Scripts - file Clojure.Refresh_Clojure_Scripts -- java jar file
• Refresh JRuby Scripts - file JRuby.Refresh_JRuby_Scripts -- java jar file
• Refresh Javas - file fiji.scripting.java.Refresh_Javas -- java jar file
• Refresh Javascript Scripts - file Javascript.Refresh_Javascript_Scripts -- java jar file
• Refresh Jython Scripts - file Jython.Refresh_Jython_Scripts -- java jar file
• Refresh Macros - file CLI.Refresh_Macros -- java jar file
• Script Editor - file fiji.scripting.Script_Editor -- java jar file

Plugins > Segmentation

• Balloon - file BalloonSegmentation_ -- java jar file
• Segment blob in 3D Viewer - file ij3d.segmentation.Blob_Segmentation_in_3D -- java jar file
• Graph Cut - file graphcut.Graph_Cut -- java jar file
• Blow/Lasso Tool - file plugin.Lasso_ -- java jar file
• Level Sets - file levelsets.ij.LevelSet -- java jar file
• Apply saved SIOX segmentator - file siox.Load_Segmentation -- java jar file
• Robust Automatic Threshold Selection - file RATS_ -- java jar file
• Statistical Region Merging - file SRM_ -- java jar file
• Segmentation Editor - file Segmentation_Editor -- java jar file
• Simple Neurite Tracer - file tracing.Simple_Neurite_Tracer -- java jar file
• SIOX: Simple Interactive Object Extraction - file siox.Siox_Segmentation -- java jar file
• Snakuscule - file Snakuscule_ -- java jar file
• Trainable Segmentation - file trainableSegmentation.Trainable_Segmentation -- java jar file
• Advanced Weka Segmentation - file trainableSegmentation.Weka_Segmentation -- java jar file

Plugins > Skeleton

• Analyze Skeleton (2D/3D) - file skeleton_analysis.AnalyzeSkeleton_ -- java jar file
• Skeletonize (2D/3D) - file Skeletonize3D_.Skeletonize3D_ -- java jar file

Plugins > Stacks

• Average Images - file vib.Average_Images -- java jar file
• Crop (3D) - file stacks.Three_Pane_Crop -- java jar file

Plugins > Stitching

• MosaicJ - file MosaicJ_ -- java jar file
• Grid/Collection stitching - file plugin.Stitching_Grid -- java jar file
• Pairwise stitching - file plugin.Stitching_Pairwise -- java jar file

Plugins > Stitching > deprecated

• Stitch Collection of Images - file Stitch_Image_Collection -- java jar file
• Stitch Directory with Images (unknown configuration) - file Stitch_Image_Directory -- java jar file
• Stitch Grid of Images - file Stitch_Image_Grid -- java jar file
• Stitch Sequence of Grids of Images - file Stitch_Image_Grid_Sequence -- java jar file
• Stitch Multiple Series or Tile Scan File - file Stitch_Multiple_Series_File -- java jar file
• 2D Stitching - file Stitching_2D -- java jar file
• 3D Stitching - file Stitching_3D -- java jar file

Plugins > Tracking

• MTrack2 - file MTrack2_ -- java jar file
• Manual Tracking - file Manual_Tracking -- java jar file
• ToAST - file ToAST25_ -- java jar file
• TrackMate - file fiji.plugin.trackmate.TrackMate_ -- java jar file

Plugins > Transform

• Distortion Correction - file lenscorrection.Distortion_Correction -- java jar file
• Panorama equirectangular view - file mpicbg.panorama.Panorama_View -- java jar file
• Spline Deformation Generator - file SplineDeformationGenerator.SplineDeformationGenerator_ -- java jar file
• Interactive Stack Rotation - file Stack_Rotate -- java jar file
• Interactive Affine - file Transform_Affine -- java jar file
• Interactive Moving Least Squares - file Transform_MovingLeastSquaresMesh -- java jar file
• Interactive Perspective - file Transform_Perspective -- java jar file
• Interactive Rigid - file Transform_Rigid -- java jar file
• Landmark Correspondences - file Transform_Roi -- java jar file
• Interactive Similarity - file Transform_Similarity -- java jar file
• Transform Virtual Stack Slices - file register_virtual_stack.Transform_Virtual_Stack_MT -- java jar file

Plugins > Transform > TransformJ

• TransformJ Affine - file TJ_Affine -- java jar file
• TransformJ Crop - file TJ_Crop -- java jar file
• TransformJ Embed - file TJ_Embed -- java jar file
• TransformJ Matrix - file TJ_Matrix -- java jar file
• TransformJ Mirror - file TJ_Mirror -- java jar file
• TransformJ Options - file TJ_Options -- java jar file
• TransformJ Panel - file TJ_Panel -- java jar file
• TransformJ Rotate - file TJ_Rotate -- java jar file
• TransformJ Scale - file TJ_Scale -- java jar file
• TransformJ Translate - file TJ_Translate -- java jar file
• TransformJ Turn - file TJ_Turn -- java jar file

Plugins > Utilities

• CPU Meter - file CPU_Meter -- java jar file
• Close All Without Saving - file Close_All_Without_Saving.txt -- macro
• Collect Garbage - file CollectGarbage_ -- java jar file
• IJ Robot - file IJ_Robot -- java jar file
• Make Fiji Package - file fiji.packaging.Package_Maker -- java jar file
• Repeat a Recent Command - file fiji.util.Recent_Commands -- java jar file
• Thread killer - file Thread_Killer -- java jar file
• Record Desktop - file Jython.Refresh_Jython_Scripts("../scripts/Record_Desktop.py") -- java jar file
• Record Window - file Jython.Refresh_Jython_Scripts("../scripts/Record_Window.py") -- java jar file

Plugins > Utilities > Debugging

• Test Marching Cubes - file MC_Test -- java jar file
• Test Java3D - file Test_Java3D -- java jar file

Plugins > Utilities > Fiji

• Inspect Java Objects - file fiji.debugging.Object_Inspector -- java jar file
• Upload Image to Fiji Wiki - file fiji.Upload_Image_To_Wiki -- java jar file
• New Fiji News - file fiji.Wiki_Editor("news") -- java jar file
• New Fiji Wiki Screenshot - file fiji.Wiki_Editor("screenshot") -- java jar file
• New Fiji Tutorial - file fiji.Wiki_Editor("tutorial-maker") -- java jar file

Process

• Calculator Plus - file Calculator_Plus -- java jar file
• Image Expression Parser - file fiji.process.Image_Expression_Parser -- java jar file
• Multiple Image Processor - file MultipleImageProcessor -- java jar file
• Enhance Local Contrast (CLAHE) - file mpicbg.ij.clahe.PlugIn -- java jar file

Process > Filters

• Differentials - file Differentials_ -- java jar file
• Linear Kuwahara - file Kuwahara_LinearStructure_Filter_v3 -- java jar file

Process > Morphology

• Gray Morphology - file GrayMorphology_ -- java jar file

Process > Noise

• ROF Denoise - file fiji.denoise.ROF_Denoise -- java jar file

Process > Noise > RandomJ

• RandomJ Binomial - file RJ_Binomial -- java jar file
• RandomJ Exponential - file RJ_Exponential -- java jar file
• RandomJ Gamma - file RJ_Gamma -- java jar file
• RandomJ Gaussian - file RJ_Gaussian -- java jar file
• RandomJ Options - file RJ_Options -- java jar file
• RandomJ Panel - file RJ_Panel -- java jar file
• RandomJ Poisson - file RJ_Poisson -- java jar file
• RandomJ Uniform - file RJ_Uniform -- java jar file