├── .gitignore ├── .travis.yml ├── .travis └── build.sh ├── BAR ├── .gitignore ├── EXTERNAL_OPS.md ├── LICENSE.txt ├── README.md ├── pom.xml └── src │ └── main │ ├── java │ └── bar │ │ ├── BAR.java │ │ ├── BARService.java │ │ ├── DefaultGCD.java │ │ ├── FileDrop.java │ │ ├── Installer.java │ │ ├── PlotUtils.java │ │ ├── Runner.java │ │ ├── Utils.java │ │ ├── gui │ │ └── GuiUtils.java │ │ └── plugin │ │ ├── Commander.java │ │ ├── Help.java │ │ ├── InteractivePlotter.java │ │ ├── MDReader.java │ │ ├── ShenCastan.java │ │ ├── SnippetCreator.java │ │ └── Tutorials.java │ ├── javadoc │ └── overview.html │ └── resources │ ├── boilerplate │ ├── README.md │ ├── beanshell.bsh │ ├── groovy.groovy │ ├── ijmlanguage.ijm │ ├── javascript.js │ ├── python.py │ └── ruby.rb │ ├── lib │ ├── BARlib.bsh │ ├── BARlib.clj │ ├── BARlib.groovy │ ├── BARlib.ijm │ ├── BARlib.js │ ├── BARlib.py │ ├── BARlib.rb │ └── README.md │ ├── plugins.config │ ├── script_templates │ └── BAR │ │ ├── Batch_Processors │ │ ├── Process_Folder_IJM.ijm │ │ └── Process_Folder_PY.py │ │ ├── External_Ops │ │ └── GCD.py │ │ └── Tracking_Analysis │ │ ├── Extract_Bouts_From_Tracks.py │ │ └── Tag_and_Onset_MtrackJ_paths.py │ ├── scripts │ └── BAR │ │ ├── Analysis │ │ ├── LoG-DoG_Spot_Counter.py │ │ ├── Multichannel_Plot_Profile.bsh │ │ ├── Multichannel_ZT-axis_Profile.bsh │ │ ├── README.md │ │ ├── Smoothed_Plot_Profile.bsh │ │ └── Time_Series │ │ │ ├── Multi_ROI_Profiler.groovy │ │ │ ├── Normalize_Against_F0.groovy │ │ │ ├── README.md │ │ │ └── Register_Against_Average.groovy │ │ ├── Annotation │ │ ├── Combine_Orthogonal_Views.ijm │ │ ├── Cumulative_Z-Project.bsh │ │ ├── README.md │ │ ├── ROI_Color_Coder.ijm │ │ └── ROI_Magnifier_Tool.js │ │ ├── Data_Analysis │ │ ├── Create_Boxplot.bsh │ │ ├── Create_Polar_Plot.bsh │ │ ├── Distribution_Plotter.ijm │ │ ├── Find_Peaks.bsh │ │ ├── Fit_Polynomial.bsh │ │ ├── NN_Distances.py │ │ └── README.md │ │ ├── Help │ │ └── Verify_BAR_Installation.groovy │ │ ├── My_Routines │ │ ├── Management │ │ │ ├── Browse..._.groovy │ │ │ ├── List..._.groovy │ │ │ ├── README.md │ │ │ ├── Reveal_Directory....groovy │ │ │ └── Search_Routines....bsh │ │ └── README.md │ │ ├── Segmentation │ │ ├── Apply_Threshold_To_ROI.ijm │ │ ├── Clear_Thresholded_Pixels.ijm │ │ ├── README.md │ │ ├── Remove_Isolated_Pixels.bsh │ │ ├── Segment_Profile_Tool.clj │ │ ├── Threshold_From_Background.ijm │ │ └── Wipe_Background.ijm │ │ └── Utilities │ │ ├── Create_Toolset....clj │ │ ├── Productivity_Menus....groovy │ │ ├── README.md │ │ └── ROI_Manager_Tools.clj │ ├── shared │ ├── README.md │ └── Utils.groovy │ ├── tools │ ├── CalibrationMenu.ijm │ ├── InsertMagnifiedROI.ijm │ ├── ListFolderMenu.ijm │ ├── README.md │ ├── ROIManagerTools.ijm │ ├── SegmentProfile.ijm │ ├── ShortcutsMenu.ijm │ └── ToolsetCreator.ijm │ └── tutorials │ ├── BeanShell01.bsh │ ├── BeanShell02.bsh │ ├── BeanShell03.bsh │ ├── BeanShell04.bsh │ ├── BeanShell05-1.bsh │ ├── BeanShell05-2.bsh │ ├── BeanShell05-3.bsh │ ├── BeanShell05-4.bsh │ ├── BeanShell06.bsh │ ├── Python01.py │ ├── Python02.py │ ├── Python03.py │ ├── Python04.py │ ├── Python05-1.py │ ├── Python05-2.py │ ├── Python05-3.py │ ├── Python05-4.py │ ├── Python06.py │ └── README.md ├── LICENSE.txt ├── README.md ├── ROI Manager Tools.txt ├── boneyard ├── CaptureWindow.ijm ├── Clipboard_to_Results.py ├── README.md ├── run-updater.ijm └── start-upload.sh ├── images ├── animated-poly-fit.gif ├── box-plot-demo.png ├── combine-orthogonal-views.png ├── commander-overview.png ├── distribution-plotter-demo.png ├── find-peaks-demo.png ├── multichannel-profiler-demo.gif ├── plotbuilder-demo.png ├── polar-plot-demo.png ├── roi-color-coder-demo.png ├── roi-color-coder-prompt.png ├── smoothed-plot-profile.png └── snippet-creator.png └── pom.xml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tferr/Scripts/HEAD/.gitignore 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