Welcome to the IJ BAR: A collection of Broadly Applicable Routines for ImageJ/Fiji, 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.

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

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

Aiders for the annotation of scientific images.

1. (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. (ijm) Segment Profile Tool
5. (ijm) Set Threshold From Background
6. (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) ROI Manager Tools
3. (ijm) Segment Profile Tool
4. (ijm) Shortcuts Menu
5. (ijm) Toolset Creator

Maven project implementing the Java plugins bundled with BAR. The files organizing the BAR menu are also described in this section.

A depository of generic and reusable scripts to be used as scripting templates, such as:

1. (py) Median Filter
2. (ijm) Process Folder

• 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:

• 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) vol. 4 (1) pp. 20130046 PMID 24501674
• Dobens and Dobens. FijiWings: an open source toolkit for semiautomated morphometric analysis of insect wings. G3 (Bethesda) (2013) vol. 3 (8) pp. 1443-9 PMID 23797110
• 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) vol. 13 (18) pp. 3562-8 PMID 23702711
• Soulet et al. Automated filtering of intrinsic movement artifacts during two-photon intravital microscopy. PLoS ONE (2013) vol. 8 (1) pp. e53942 PMID 23326545
• Carnevalli et al. S6K1 plays a critical role in early adipocyte differentiation. Developmental Cell (2010) vol. 18 (5) pp. 763-74 PMID 20493810

• Shen and Castan. An optimal linear operator for step edge detection. CVGIP: Graphical Models and Image Processing (1992) vol. 54 (2) pp. 112-133 DOI: 10.1016/1049-9652(92)90060-B

These scripts are 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. This project would not have been possible without the support of the outstanding ImageJ community.