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.

The easiest way is to install these scripts is to use Fiji and subscribe to the BAR update site. Alternatively, you can navigate the collection using the sections below, and download individual routines as needed. For more details refer to the BAR documentation page.

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

1. (bsh) Multichannel Plot Profile
2. (bsh) Multichannel ZT-axis Profile
3. (bsh) Smoothed Plot Profile

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

1. (py) Clipboard to Results
2. (ijm) Distribution Plotter
3. (bsh) Find Peaks
4. (bsh) Fit Polynomial
5. (bsh) Plot Results

Aiders for the annotation of scientific images.

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

Routines for partitioning images into analyzable parts.

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

Scripts related to the quantification of neuronal arbors and other tree-like structures.

1. (bsh) Strahler Analysis

Additions to the ImageJ toolbar.

1. (ijm) Calibration Menu
2. (ijm) List Folder Menu
3. (ijm) Segment Profile Tool
4. (ijm) Shortcuts Menu
5. (ijm) ROI Manager Tools
6. (ijm) Toolset Creator

Example scripts (in several languages) to be used as scripting templates, including:

1. (py) Median Filter
2. (py) NN Distances
3. Batch Processors 1. (ijm) Process Folder IJM 2. (py) Process Folder PY
4. (bsh) Search BAR

User-defined libraries (scripting additions) in a centralized repository. These are methods and functions that can be conveniently shared across files.

1. BeanShell library
2. Clojure library
3. Groovy library
4. IJ Macro library
5. JavaScript library
6. Python library
7. Ruby library

Productivity software.

1. BAR Commander, a keyboard-based file browser that produces filtered lists of directory contents. Features include: drag-and-drop support, interaction with native file manager, regex filtering, and built-in console for common operations. (Documentation page)

Maven project implementing the backbone of BAR, including several Java plugins, the structure of the BAR menu and the BAR API. While BAR is mainly a suite of ImageJ1 add-ons, some of the BAR plugins have started to explore some of the scripting capabilities of ImageJ2.

• List of Java plugins

• Want to Contribute to BAR?
  • Thanks! Please, please do! See here and here for details on how to fork BAR or here on how to initiate a pull request
  • Documentation updates are also welcome, so go ahead and improve the BAR documentation page
• Having problems? Found a bug? Need to ask a question?
  • See the BAR FAQs, Fiji FAQs and Bug reporting best practices. Then, you can either:
    • Open an issue on this repository
    • Report it on the ImageJ mailing list

BAR scripts have contributed to the following publications:

1. Ferreira et al. Neuronal morphometry directly from bitmap images. Nature Methods (2014), 11(10):982–984. PMID 25264773
2. Pope and Voigt. Peripheral glia have a pivotal role in the initial response to axon degeneration of peripheral sensory neurons in zebrafish. PLoS ONE (2014), 9(7):e103283. PMID 25058656
3. Medda et al. Investigation of early cell-surface interactions of human mesenchymal stem cells on nanopatterned β-type titanium-niobium alloy surfaces. Interface Focus (2014), 4(1):20130046. PMID 24501674
4. Ferreira et al. Dendrite architecture is organized by transcriptional control of F-actin nucleation. Development (2014), 141(3):650–60. PMID 24449841
5. Dobens and Dobens. FijiWings: an open source toolkit for semiautomated morphometric analysis of insect wings. G3 (Bethesda) (2013), 3(8):1443-9. PMID 23797110
6. van der Meer et al. Three-dimensional co-cultures of human endothelial cells and embryonic stem cell-derived pericytes inside a microfluidic device. Lab Chip (2013), 13(18):3562-8. PMID 23702711
7. Soulet et al. Automated filtering of intrinsic movement artifacts during two-photon intravital microscopy. PLoS ONE (2013), 8(1):e53942. PMID 23326545
8. Paolicelli et al. Synaptic pruning by microglia is necessary for normal brain development. Science (2011), 9;333(6048):1456-8. PMID 21778362
9. Carnevalli et al. S6K1 plays a critical role in early adipocyte differentiation. Developmental Cell (2010), 18(5):763-74. PMID 20493810

This program is free software: you can redistribute them and/or modify them under the terms of the GNU General Public License as published by the 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, Jerome Mutterer and Kota Miura. 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.