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BAR plugins

While macros and scripts form the bulk of BAR, some BAR commands are pre-compiled java plugins bundled in a single JAR file. This directory contains the source code (a Maven project) for the bar package implementing such plugins. The project also includes plugins.config that organizes the BAR menu hierarchy.

List of Java plugins

  1. BAR Commander, a keyboard-based file browser
  2. BAR Utils, class providing convenience methods to script BAR
  3. Shen-Castan Edge Detector, described in Segmentation
  4. Snippet Creator, described in Snippets and lib

BAR-menu

The top-level BAR Menu is organized in the following manner (version 1.0.5):

BAR
├── Annotation
│   ├── Move Menu (Context<>Main)
│   ├── Combine Orthogonal Views
│   └── ROI Color Coder
├── Data Analysis
│   ├── Move Menu (Context<>Main)
│   ├── Clipboard to Results
│   ├── Distribution Plotter
│   ├── Find Peaks
│   ├── Fit Polynomial
│   ├── Multichannel Plot Profile
│   └── Plot Results
├── Morphometry
│   ├── Move Menu (Context<>Main)
│   └── Strahler Analysis
├── Segmentation
│   ├── Move Menu (Context<>Main)
│   ├── Shen-Castan Edge Detector
│   ├── Apply Threshold To ROI
│   ├── Clear Thresholded Pixels
│   ├── Remove Isolated Pixels
│   ├── Threshold From Background
│   └── Wipe Background
├── Snippets
│   ├── List Snippets
│   ├── Reveal Snippets
│   └── [...]
├── Tool Installers
│   ├── Install Calibration Menu
│   ├── Install List Folder Menu
│   ├── Install Segment Profile
│   ├── Install Shortcuts Menu
│   ├── ROI Manager Tools
│   └── Toolset Creator...
└── About BAR...

The relevant files get stored in the following locations (version 1.0.5):

Fiji.app
├── macros
│   ├── tools
│   │   ├── Calibration_Menu.ijm
│   │   ├── List_Folder_Menu.ijm
│   │   ├── Segment_Profile.ijm
│   │   └── Shortcuts_Menu.ijm
│   └── toolsets
│       ├── ROI Manager Tools.ijm
│       └── Toolset Creator.ijm
└── plugins
    ├── BAR_-1.0.5.jar
    └── Scripts
        └── BAR
            ├── Annotation
            │   ├── Combine_Orthogonal_Views.ijm
            │   └── ROI_Color_Coder.ijm
            ├── Data_Analysis
            │   ├── Clipboard_to_Results.py
            │   ├── Distribution_Plotter.ijm
            │   ├── Find_Peaks.bsh
            │   ├── Fit_Polynomial.bsh
            │   ├── Multichannel_Plot_Profile.bsh
            │   └── Plot_Results.bsh
            ├── Morphometry
            │   └── Strahler_Analysis.bsh
            ├── Segmentation
            │   ├── Apply_Threshold_To_ROI.ijm
            │   ├── Clear_Thresholded_Pixels.ijm
            │   ├── Remove_Isolated_Pixels.bsh
            │   ├── Threshold_From_Background.ijm
            │   └── Wipe_Background.ijm
            └── Snippets
                ├── Median_Filter.py
                ├── NN_Distances.py
                ├── Process_Folder_IJM.ijm
                ├── Process_Folder_PY.py
                └── Search_Snippets.bsh

###Notes

  • You can place BAR> submenus in the image's context menu (the menu that pops up when right-clicking on the image canvas) by using the Move Menu (Context<>Main). This facilitates accessibility of commonly-used commands. The transfer is bi-directional: once in the context menu, choosing Move Menu will replace the submenu in the main Menu bar.
  • While all files could be bundled in a single jar file (arguably a tidier approach), spreading files across folders has the main advantage of being compatible with the Shift-trick, while maintaining an organized menu hierarchy
  • Files are placed in the proper locations through a shell script (which is only useful for uploading files to the BAR update site)
  • The recursive lists above were created with tree
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