Software/Image/NIH ImageJ/Fiji/Plugins_Menu

---

Fiji's Menu

The hierarchy of the Fiji's Menu is shown here, with a few words of explanation for each menu entry and links to more documentation where available. If you know about a menu entry that is in this list, but which doesn't yet have a description, please add it.

This list is generated automatically from a script that can be found in the development folder.

Plugins †

---

• Volume Viewer - file Volume_Viewer.jar -- java jar file
• 3D Viewer - file ImageJ_3D_Viewer in package VIB_ -- java jar file

Plugins > Macros †

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

Plugins > Utilities †

• Thread killer - file Thread_Killer in package VIB_ -- java jar file
• Record Window - file Jython.Refresh_Jython_Scripts("../scripts/Record_Window.py") in package Record_Screen -- java jar file
• Collect Garbage - file CollectGarbage_ in package VIB_ -- java jar file IJ Robot - file IJ_Robot in package IJ_Robot -- java jar file
• Record Desktop - file Jython.Refresh_Jython_Scripts("../scripts/Record_Desktop.py") in package Record_Screen -- java jar file
• Close All Without Saving - file Close_All_Without_Saving.txt -- macro

Plugins > Utilities > Debugging †

• Test Java3D - file Test_Java3D in package VIB_ -- java jar file
• Test Marching Cubes - file MC_Test in package VIB_ -- java jar file

Plugins > Examples †

• Edit LUT As Text - file Edit_LUT_As_Text.py -- jython script
• Single Voxel in 3D - file tracing.Test_Single_Voxel in package VIB_ -- java jar file
• random noise example - file random_noise_example.clj -- clojure script
• list all threads - file list_all_threads.py -- jython script
• downsample - file downsample_.js -- javascript file
• Plasma Cloud - file Plasma_Cloud.rb -- jruby script
• Delayed Snapshot - file Delayed_Snapshot.py -- jython script
• Find Dimension of Raw Image - file Find_Dimension_of_Raw_Image.py -- jython script
• Blobs Demo in Ruby - file Blobs_Demo_in_Ruby.rb -- jruby script
• Same Slice in Multiple Images - file Same_Slice_in_Multiple_Images.rb -- jruby script
• celsius to fahrenheit - file celsius_to_fahrenheit.clj -- clojure script
• blend two images - file blend_two_images.clj -- clojure script
• Anaglyph for Red Cyan glasses - file Anaglyph_for_Red_Cyan_glasses.rb -- jruby script
• Multithreaded Image Processing - file Multithreaded_Image_Processing.clj -- clojure script
• Fiji Logo 3D - file Fiji_Logo_3D.js -- javascript file
• Spheres and Tubes in 3D - file customnode.Mesh_Maker in package VIB_ -- java jar file
• Multithreaded Image Processing in Javascript - file Multithreaded_Image_Processing_in_Javascript.js -- javascript file
• chess - file chess_.py -- jython script

Plugins > Examples > Command_Launchers †

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

Plugins > Examples > TrakEM2_Example_Scripts †

• T2 set all transforms to identity - file T2_set_all_transforms_to_identity.py -- jython script
• T2 Select All - file T2_Select_All.py -- jython script
• Measure AreaLists? - file Measure_AreaLists?.py -- jython script

Plugins > Analyze †

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

Plugins > Feature Extraction †

• Extract SIFT Correspondences - file SIFT_ExtractPointRoi? in package mpicbg_ -- java jar file
• Extract MOPS Correspondences - file MOPS_ExtractPointRoi? in package mpicbg_ -- java jar file

Plugins > Transform †

• TJ Embed - file TJ_Embed in package TransformJ_ -- java jar file
• TJ Options - file TJ_Options in package TransformJ_ -- java jar file
• Interactive Moving Least Squares - file Transform_MovingLeastSquaresMesh? in package mpicbg_ -- java jar file
• TJ Mirror - file TJ_Mirror in package TransformJ_ -- java jar file
• Interactive Similarity - file Transform_Similarity in package mpicbg_ -- java jar file
• TJ Shift - file TJ_Shift in package TransformJ_ -- java jar file
• Spline Deformation Generator - file SplineDeformationGenerator?.SplineDeformationGenerator_ in package SplineDeformationGenerator_ -- java jar file
• Transform Virtual Stack Slices - file register_virtual_stack.Transform_Virtual_Stack_MT in package register_virtual_stack_slices -- java jar file
• TJ Scale - file TJ_Scale in package TransformJ_ -- java jar file
• Landmark Correspondences - file Transform_Roi in package mpicbg_ -- java jar file
• Interactive Rigid - file Transform_Rigid in package mpicbg_ -- java jar file
• Distortion Correction - file lenscorrection.Distortion_Correction in package TrakEM2_ -- java jar file
• TJ Turn - file TJ_Turn in package TransformJ_ -- java jar file
• TJ Panel - file TJ_Panel in package TransformJ_ -- java jar file
• TJ Affine - file TJ_Affine in package TransformJ_ -- java jar file
• Interactive Affine - file Transform_Affine in package mpicbg_ -- java jar file
• Interactive Stack Rotation - file Stack_Rotate in package mpicbg_ -- java jar file
• Interactive Perspective - file Transform_Perspective in package mpicbg_ -- java jar file
• TJ Rotate - file TJ_Rotate in package TransformJ_ -- java jar file
• TJ Crop - file TJ_Crop in package TransformJ_ -- java jar file

Plugins > Registration †

• Register Virtual Stack Slices - file register_virtual_stack.Register_Virtual_Stack_MT in package register_virtual_stack_slices -- java jar file
• Rigid Registration - file vib.RigidRegistration_ in package VIB_ -- java jar file
• TurboReg? - file TurboReg_ in package TurboReg_ -- java jar file
• Moving Least Squares - file Moving_Least_Squares in package VIB_ -- java jar file
• Align Image by line ROI - file Align_Image in package VIB_ -- java jar file
• bUnwarpJ - file bunwarpj.bUnwarpJ_ in package bUnwarpJ_ -- java jar file
• Linear Stack Alignment with SIFT - file SIFT_Align in package mpicbg_ -- java jar file

Plugins > Scripting †

• Refresh Javascript Scripts - file Javascript.Refresh_Javascript_Scripts in package Javascript_ -- java jar file
• Refresh Jython Scripts - file Jython.Refresh_Jython_Scripts in package Jython_Interpreter -- java jar file
• Refresh Javas - file fiji.scripting.java.Refresh_Javas in package Refresh_Javas -- java jar file
• BeanShell? Interpreter - file BSH.BSH_Interpreter in package BeanShell_Interpreter -- java jar file
• Clojure Interpreter - file Clojure.Clojure_Interpreter in package Clojure_Interpreter -- java jar file
• Refresh BSH Scripts - file BSH.Refresh_BSH_Scripts in package BeanShell_Interpreter -- java jar file
• Refresh JRuby Scripts - file JRuby.Refresh_JRuby_Scripts in package JRuby_Interpreter -- java jar file
• Jython Interpreter - file Jython.Jython_Interpreter in package Jython_Interpreter -- java jar file
• Javascript Interpreter - file Javascript.Javascript_Interpreter in package Javascript_ -- java jar file
• Script Editor - file fiji.scripting.Script_Editor in package Script_Editor -- java jar file
• Macro Interpreter - file CLI.CLI_ in package CLI_ -- java jar file
• Refresh Clojure Scripts - file Clojure.Refresh_Clojure_Scripts in package Clojure_Interpreter -- java jar file
• JRuby Interpreter - file JRuby.JRuby_Interpreter in package JRuby_Interpreter -- java jar file

Plugins > Segmentation †

• Statistical Region Merging - file SRM_ in package Statistical_Region_Merging -- java jar file
• Simple Neurite Tracer - file tracing.Simple_Neurite_Tracer in package VIB_ -- java jar file
• Level Sets - file levelsets.ij.LevelSet? in package level_sets -- java jar file
• Blow/Lasso Tool - file plugin.Lasso_ in package VIB_ -- java jar file
• Segmentation Editor - file Segmentation_Editor in package VIB_ -- java jar file

Plugins > Image5D †

• Virtual Image5D Opener - file Virtual_Image5D_Opener("") in package Image_5D -- java jar file
• New Image5D - file New_Image5D("") in package Image_5D -- java jar file
• Save Image5D - file Save_Image5D("") in package Image_5D -- java jar file
• Z Project - file Z_Project("") in package Image_5D -- java jar file
• Transfer Channel Settings - file Transfer_Channel_Settings("") in package Image_5D -- java jar file
• Open Image5D - file Open_Image5D("") in package Image_5D -- java jar file
• Open Series As Image5D - file Open_Series_As_Image5D("") in package Image_5D -- java jar file
• Set Channel Display - file Set_Channel_Display("") in package Image_5D -- java jar file
• Stack to Image5D - file Stack_to_Image5D("") in package Image_5D -- java jar file
• Image5D to Stack - file Image5D_to_Stack("") in package Image_5D -- java jar file
• Image5D Stack to RGB - file Image5D_Stack_to_RGB("") in package Image_5D -- java jar file
• Set Channel Labels - file Set_Channel_Labels("") in package Image_5D -- java jar file
• RGB to Image5D - file RGB_to_Image5D("") in package Image_5D -- java jar file
• Hypervolume Opener - file Hypervolume_Opener("") in package Image_5D -- java jar file
• Set Position - file Set_Position("") in package Image_5D -- java jar file
• Make Montage - file Make_Montage("") in package Image_5D -- java jar file

Plugins > Process †

• Shape-based averaging - file Rohlfing_SBA in package VIB_ -- java jar file
• Median (3D) - file process3d.Median_ in package VIB_ -- java jar file
• Reslice Z - file Reslice_Z in package VIB_ -- java jar file
• Flood Fill(3D) - file process3d.Flood_Fill in package VIB_ -- java jar file
• Seam remover - file Seam_Remover in package VIB_ -- java jar file
• Smooth (3D) - file process3d.Smooth_ in package VIB_ -- java jar file
• Laplace (3D) - file process3d.Laplace_ in package VIB_ -- java jar file
• Maximum (3D) - file process3d.Maximum_ in package VIB_ -- java jar file
• Max (3D) - file process3d.Maximum_ in package VIB_ -- java jar file
• Resample - file vib.Resample_ in package VIB_ -- java jar file
• Gradient (3D) - file process3d.Gradient_ in package VIB_ -- java jar file
• IFT (3D) - file process3d.IFT_ in package VIB_ -- java jar file
• Fast FFT (2D/3D) - file registration3d.Fast_FourierTransform? in package registration_3d -- java jar file
• Minimum (3D) - file process3d.Minimum_ in package VIB_ -- java jar file
• Show label centers - file Show_Label_Centers in package VIB_ -- java jar file
• Mask Of Nearby Points - file util.Mask_Of_Nearby_Points in package VIB_ -- java jar file
• Rebin (3D) - file process3d.Rebin_ in package VIB_ -- java jar file
• Erode (3D) - file process3d.Erode_ in package VIB_ -- java jar file
• Quantile Based Normalization - file util.Quantile_Based_Normalization in package VIB_ -- java jar file
• Show Color Surfaces - file isosurface.Show_Colour_Surfaces in package VIB_ -- java jar file
• Particle Analyzer (3D) - file process3d.Particle_Analyzer_3D in package VIB_ -- java jar file
• Bilateral Filter - file Bilateral_Filter in package VIB_ -- java jar file
• Shape-Based Averaging (Experimental) - file util.RohlfingSBA in package VIB_ -- java jar file
• Dilate (3D) - file process3d.Dilate_ in package VIB_ -- java jar file
• Distance Transform 3D - file process3d.Distance_Transform_3D in package VIB_ -- java jar file
• Implicit Interpolate Binary - file Implicit_Interpolate_Binary in package VIB_ -- java jar file
• Find Connected Regions - file util.Find_Connected_Regions in package VIB_ -- java jar file
• Replace value - file Replace_Value in package VIB_ -- java jar file
• Triangle Algorithm - file Triangle_Algorithm in package VIB_ -- java jar file
• Convolve (3D) - file process3d.Convolve_3d in package VIB_ -- java jar file

Plugins > Tracking †

• ToAST - file ToAST25_ in package ToAST_ -- java jar file
• Manual Tracking - file Manual_Tracking in package Manual_Tracking -- java jar file
• MTrack2 - file MTrack2_ in package MTrack2_ -- java jar file

Plugins > Stitching †

• 3D Stitching - file Stitching_3D in package Stitching_ -- java jar file
• Stitch Collection of Images - file Stitch_Image_Collection in package Stitching_ -- java jar file
• 2D Stitching - file Stitching_2D in package Stitching_ -- java jar file
• Stitch Grid of Images - file Stitch_Image_Grid in package Stitching_ -- java jar file
• Stitch Directory with Images (unknown configuration) - file Stitch_Image_Directory in package Stitching_ -- java jar file

Plugins > LOCI †

• Update LOCI Plugins - file loci.plugins.Updater("") in package loci_tools -- java jar file
• Bio-Formats Exporter - file loci.plugins.LociExporter?("") in package loci_tools -- java jar file
• Bio-Formats Importer - file loci.plugins.LociImporter?("location=[Local machine] windowless=false ") in package loci_tools -- java jar file
• Bio-Formats Remote Importer - file loci.plugins.LociImporter?("location=[Internet]") in package loci_tools -- java jar file
• Bio-Formats Macro Extensions - file loci.plugins.macro.LociFunctions?("") in package loci_tools -- java jar file
• Data Browser - file loci.plugins.LociImporter?("location=[Local machine] view=[Data Browser] stack_order=[XYCZT] group_files=true use_virtual_stack=true ") in package loci_tools -- java jar file
• Bio-Formats Windowless Importer - file loci.plugins.LociImporter?("location=[Local machine] windowless=true ") in package loci_tools -- java jar file
• LOCI Plugins Configuration - file loci.plugins.config.LociConfig?("") in package loci_tools -- java jar file
• Stack Slicer - file loci.plugins.Slicer("") in package loci_tools -- java jar file
• Stack Colorizer - file loci.plugins.Colorizer("") in package loci_tools -- java jar file
• LOCI Plugins Shortcut Window - file loci.plugins.shortcut.ShortcutPanel?("") in package loci_tools -- java jar file

Plugins > Stacks †

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

Plugins > Landmarks †

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

Plugins > Skeleton †

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

Analyze †

• 3D OC Options - file _3D_OC_Options in package 3D_Objects_Counter -- java jar file
• Color Histogram - file ColorHistogram_ in package Color_Histogram -- java jar file
• Color Inspector 3D - file Color_Inspector_3D in package Color_Inspector_3D -- java jar file
• 3D Surface Plot - file Interactive_3D_Surface_Plot in package Interactive_3D_Surface_Plot -- java jar file
• 3D Objects Counter - file _3D_objects_counter in package 3D_Objects_Counter -- java jar file

Analyze > Colocalization †

• Colocalization Threshold - file Colocalisation_Threshold in package Colocalisation_Analysis -- java jar file
• Colocalization Test - file Colocalisation_Test in package Colocalisation_Analysis -- java jar file

Analyze > Tools †

• Sync Measure 3D - file Sync_Measure_3D("") in package Sync_Win -- java jar file
• Sync Windows - file Sync_Windows("") in package Sync_Win -- java jar file

Analyze > Local Thickness †

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

Analyze > Optic Flow †

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

File †

File > New †

• TrakEM2 (from template) - file ini.trakem2.New_Project in package TrakEM2_ -- java jar file
• Fiji Tutorial - file fiji.Tutorial_Maker in package Tutorial_Maker -- java jar file
• TrakEM2 (blank) - file ini.trakem2.New_Project("blank") in package TrakEM2_ -- java jar file
• Script - file fiji.scripting.Script_Editor in package Script_Editor -- java jar file

File > Save As †

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

File > Import †

• [ [Open [Image IO] ] ] - file net.sf.ij.plugin.ImageIOOpenPlugin?("simple") in package ij-ImageIO_ -- java jar file
• Show LSMToolbox - file LSM_Toolbox("") in package LSM_Toolbox -- java jar file
• TorstenRaw? GZ Reader... - file io.TorstenRaw_GZ_Reader in package IO_ -- java jar file
• Amira as TrakEM2... - file ini.trakem2.New_Project("amira") in package TrakEM2_ -- java jar file
• DF3... - file io.Open_DF3 in package IO_ -- java jar file
• DM3 Reader... - file io.DM3_Reader in package IO_ -- java jar file
• Amira... - file AmiraMeshReader_ in package VIB_ -- java jar file
• Show Amira Surface - file isosurface.AmiraSurface? in package VIB_ -- java jar file
• Animated Gif... - file io.Animated_Gif_Reader in package IO_ -- java jar file
• MRC Leginon ... - file io.Open_MRC_Leginon in package IO_ -- java jar file
• LSM... - file LSM_Reader in package LSM_Reader -- java jar file
• Leica SP... - file leica.Leica_SP_Reader in package VIB_ -- java jar file
• Open with preview ... - file net.sf.ij.plugin.ImageIOOpenPlugin?("preview") in package ij-ImageIO_ -- java jar file
• IPLab Reader... - file io.IPLab_Reader in package IO_ -- java jar file
• Extract Images From PDF... - file io.Extract_Images_From_PDF in package IO_ -- java jar file
• Biorad... - file Biorad_Reader in package VIB_ -- java jar file
• Nrrd ... - file io.Nrrd_Reader in package IO_ -- java jar file
• SVG... - file io.SVG_Reader in package IO_ -- java jar file
• TrakEM2 XML... - file ini.trakem2.Open_Project in package TrakEM2_ -- java jar file
• Analyze... - file Analyze_Reader in package Analyze_Reader_Writer -- java jar file
• PDF ... - file io.PDF_Viewer in package IO_ -- java jar file
• Icns... - file io.Icns_Reader in package IO_ -- java jar file
• LSS16... - file io.LSS16_Reader in package IO_ -- java jar file
• ICO... - file io.ICO_Reader in package IO_ -- java jar file
• DAT EMMENU ... - file io.Open_DAT_EMMENU in package IO_ -- java jar file

File > Open Samples †

• Malaria Sporozoites (9.2MB) - file ij.plugin.URLOpener("http://pacific.mpi-cbg.de/samples/_malaria_parasites.tif") in package ToAST_ -- java jar file

Help †

• Update Fiji - file fiji.updater.Updater("update") in package Fiji_Updater -- java jar file
• Upload Sample Image - file fiji.util.Fiji_Uploader in package Fiji_Plugins -- java jar file
• Report a Bug - file Bug_Submitter.Bug_Submitter in package Bug_Submitter -- java jar file
• Fiji Wiki - file ij.plugin.BrowserLauncher?("http://pacific.mpi-cbg.de/") in package Fiji_Updater -- java jar file

Help > About Plugins †

• LSMReader... - file LSM_Reader("about") in package LSM_Reader -- java jar file
• Sync Windows... - file Sync_Windows("about") in package Sync_Win -- java jar file
• LOCI Plugins... - file loci.plugins.About("") in package loci_tools -- java jar file
• Color Histogram... - file ColorHistogram_("about") in package Color_Histogram -- java jar file
• About TrakEM2... - file ini.trakem2.utils.Utils in package TrakEM2_ -- java jar file
• Image5D... - file I5D_about("about") in package Image_5D -- java jar file
• Sync Measure 3D... - file Sync_Measure_3D("about") in package Sync_Win -- java jar file
• Image IO ... - file net.sf.ij.plugin.AboutImageIO("") in package ij-ImageIO_ -- java jar file
• LSMToolbox... - file LSM_Toolbox("about") in package LSM_Toolbox -- java jar file
• Gray Morphology... - file GrayMorphology_("about") in package Gray_Morphology -- java jar file
• About bUnwarpJ... - file bunwarpj.Credits in package bUnwarpJ_ -- java jar file

Image †

Image > Color †

• RGB to Luminance - file util.RGB_to_Luminance in package VIB_ -- java jar file
• RGB to CIELAB - file RGB_to_CIELAB in package VIB_ -- java jar file
• Average Color - file Average_Color in package VIB_ -- java jar file
• Simulate Color Blindness - file Simulate_Color_Blindness in package Daltonize_ -- java jar file

Image > Drawing †

• Radial Gradient - file fiji.drawing.Radial_Gradient in package Fiji_Plugins -- java jar file

Image > Selection †

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

Image > Stacks †

• Time Stamper - file Time_Stamper in package Time_Stamper -- java jar file
• Radial Reslice - file fiji.stacks.Radial_Reslice in package Fiji_Plugins -- java jar file
• Dynamic Reslice - file fiji.stacks.Dynamic_Reslice in package Fiji_Plugins -- java jar file

Image > Stacks > Manipulation †

• Concatenate - file Concatenate_ in package Stack_Manipulation -- java jar file
• Substack Maker - file Substack_Maker in package Stack_Manipulation -- java jar file
• Grouped ZProjector - file Grouped_ZProjector in package Stack_Manipulation -- java jar file
• Stack Inserter - file Stack_Inserter in package Stack_Manipulation -- java jar file
• Stack Spliter - file Stack_Splitter in package Stack_Manipulation -- java jar file
• Stack Sorter - file Stack_Sorter in package Stack_Manipulation -- java jar file
• Stack Combiner - file Stack_Combiner in package Stack_Manipulation -- java jar file
• Interleave - file Stack_Interleaver in package Stack_Manipulation -- java jar file
• Stack Reverser - file Stack_Reverser in package Stack_Manipulation -- java jar file
• Slice Keeper - file Slice_Keeper in package Stack_Manipulation -- java jar file
• Stack Maker - file Stack_Maker in package Stack_Manipulation -- java jar file
• Slice Remover - file Slice_Remover in package Stack_Manipulation -- java jar file
• Deinterleave - file DeInterleave_ in package Stack_Manipulation -- java jar file

Image > Stacks > View5D †

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

Image > Annotate †

• Arrow - file Arrow_ in package Arrow_ -- java jar file

Image > Video Editing †

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

Image > Adjust †

• Auto Local Threshold - file Auto_Local_Threshold in package Auto_Threshold -- java jar file
• Auto Threshold - file Auto_Threshold in package Auto_Threshold -- java jar file

Process †

• Calculator Plus - file Calculator_Plus in package Calculator_Plus -- java jar file
• Multiple Image Processor - file MultipleImageProcessor? in package M_I_P -- java jar file

Process > Morphology †

• Gray Morphology - file GrayMorphology_ in package Gray_Morphology -- java jar file

Edit †

Edit > Selection †

• Fill ROI holes - file Fill_holes in package VIB_ -- java jar file
• Fit Circle to Image - file fiji.util.Circle_Fitter in package Fiji_Plugins -- java jar file

Edit > Options †

• Configure Fiji Updater - file fiji.updater.UptodateCheck?("config") in package Fiji_Updater -- java jar file