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Welcome to the IJ BAR: A collection of Broadly Applicable Routines for ImageJ, the de facto standard in scientific image processing in the life sciences.

To install BAR you just need to subscribe to the BAR update site. To know more about BAR, have a look at its Wiki Page. Below is a lis of some of the BAR routines:


Routines that complement built-in commands in the ImageJ Analyze> menu.

  1. (py) LoG-DoG Spot Counter
  2. (bsh) Multichannel Plot Profile
  3. (bsh) Multichannel ZT-axis Profile
  4. (bsh) Smoothed Plot Profile
  5. (groovy) Multi ROI Profiler
  6. (groovy) Normalize Against F0
  7. (groovy) Register Against Average

Data Analysis

Operations related to statistics, profiles, histograms and curve fitting.

  1. (bsh) Create Boxplot
  2. (bsh) Create Polar Plot
  3. (ijm) Distribution Plotter
  4. (bsh) Find Peaks
  5. (bsh) Fit Polynomial
  6. (java) Interactive Plotting
  7. (py) NN Distances

Image Annotation

Aiders for the annotation of scientific images.

  1. (ijm) Combine Orthogonal Views
  2. (bsh) Cumulative Z-Project
  3. (ijm) ROI Color Coder
  4. (ijm) ROI Magnifier Tool

Image Segmentation

Routines for partitioning images into analyzable parts.

  1. (ijm) Apply Threshold To ROI
  2. (ijm) Clear Thresholded Pixels
  3. (bsh) Remove Isolated Pixels
  4. (ijm) Segment Profile Tool
  5. (java) Shen-Castan Edge Detector
  6. (ijm) Threshold From Background
  7. (ijm) Wipe Background


Productivity tools.

  1. (java) Commander
  2. (ijm) Calibration Menu
  3. (ijm) List Folder Menu
  4. (java) New Snippet
  5. (ijm) Shortcuts Menu
  6. (ijm) ROI Manager Tools
  7. (ijm) Toolset Creator

My Routines

An infrastructure to help users tinkering with ImageJ.

  1. Multi-language libs: User-defined libraries (BeanShell, Clojure, Groovy, IJ Macro, JavaScript, Python, Ruby)
  2. Boilerplate Scripts, multi-language skeletons for new scripts that load lib files.
  3. Script Templates, multi-language snippets

Java Classes

Maven project implementing the backbone of BAR, including several IJ1 plugins and IJ2 commands, External Ops, and the BAR API.


  1. Introduction to Scripting: 101 of (IJ1) scripting using BeanShell and Python (Jython)

  2. External Ops: Advanced tutorial exemplifying how to provide ImageJ Ops





This program is free software: you can redistribute them and/or modify them under the terms of the GNU General Public License as published bythe Free Software Foundation, either version 3 of the License, or (at your option) any later version.


BAR was created and is maintained by Tiago Ferreira with contributions from Maxime Pinchon, Johannes Schindelin, Wayne Rasband, Mark Hiner, Jerome Mutterer, Kota Miura, Nicolas Vanderesse, Peter J. Lee, Jan Eglinger and others. BAR uses public domain code from Robert Harder and Nathan Blomquist. This project would not have been possible without the support of the outstanding ImageJ community.

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