IJ BAR

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:

Analysis

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

Utilities

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.

Tutorials

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

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

Help?

• 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, IJ FAQs and Bug reporting best practices. Then, you can either:
    • Open an issue on this repository
    • Report it on the ImageJ forum

Citations

• To cite BAR:

• BAR scripts are known to have contributed to the following publications:

  1. Parinejad et al. Disruption of an EAAT-Mediated Chloride Channel in a Drosophila Model of Ataxia (2016), 36(29):7640-7. PMID 27445142
  2. Bouvier et al. High Resolution Dissection of Reactive Glial Nets in Alzheimer's Disease (2016), 19;6:24544. PMID 27090093
  3. Ferreira et al. Neuronal morphometry directly from bitmap images. Nature Methods (2014), 11(10):982–984. PMID 25264773
  4. 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
  5. 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
  6. Ferreira et al. Dendrite architecture is organized by transcriptional control of F-actin nucleation. Development (2014), 141(3):650–60. PMID 24449841
  7. Dobens and Dobens. FijiWings: an open source toolkit for semiautomated morphometric analysis of insect wings. G3 (Bethesda) (2013), 3(8):1443-9. PMID 23797110
  8. 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
  9. Soulet et al. Automated filtering of intrinsic movement artifacts during two-photon intravital microscopy. PLoS ONE (2013), 8(1):e53942. PMID 23326545
  10. Paolicelli et al. Synaptic pruning by microglia is necessary for normal brain development. Science (2011), 9;333(6048):1456-8. PMID 21778362
  11. Carnevalli et al. S6K1 plays a critical role in early adipocyte differentiation. Developmental Cell (2010), 18(5):763-74. PMID 20493810

License

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.

Contributors

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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