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
- (py) LoG-DoG Spot Counter
- (bsh) Multichannel Plot Profile
- (bsh) Multichannel ZT-axis Profile
- (bsh) Smoothed Plot Profile
- (groovy) Multi ROI Profiler
- (groovy) Normalize Against F0
- (groovy) Register Against Average
Operations related to statistics, profiles, histograms and curve fitting.
- (bsh) Create Boxplot
- (bsh) Create Polar Plot
- (ijm) Distribution Plotter
- (bsh) Find Peaks
- (bsh) Fit Polynomial
- (java) Interactive Plotting
- (py) NN Distances
Aiders for the annotation of scientific images.
- (ijm) Combine Orthogonal Views
- (bsh) Cumulative Z-Project
- (ijm) ROI Color Coder
- (ijm) ROI Magnifier Tool
Routines for partitioning images into analyzable parts.
- (ijm) Apply Threshold To ROI
- (ijm) Clear Thresholded Pixels
- (bsh) Remove Isolated Pixels
- (ijm) Segment Profile Tool
- (java) Shen-Castan Edge Detector
- (ijm) Threshold From Background
- (ijm) Wipe Background
- (java) Commander
- (ijm) Calibration Menu
- (ijm) List Folder Menu
- (java) New Snippet
- (ijm) Shortcuts Menu
- (ijm) ROI Manager Tools
- (ijm) Toolset Creator
An infrastructure to help users tinkering with ImageJ.
- Multi-language libs:
- Boilerplate Scripts, multi-language skeletons
for new scripts that load lib files.
- Script Templates, multi-language snippets
Maven project implementing the backbone of BAR, including several IJ1 plugins and IJ2
commands, External Ops,
and the BAR API.
Introduction to Scripting:
101 of (IJ1) scripting using BeanShell and Python (Jython)
External Ops: Advanced tutorial exemplifying how to
provide ImageJ Ops
- Want to Contribute to BAR?
- Having problems? Found a bug? Need to ask a question?
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
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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