BAR 1.5.1

This is the largest update so far. Highlights:

• Several IJ1 plugins rewritten as IJ2 Scijava commands
• Several improvements to Commander, including a system-wide shortcut: You can now press F1 anywhere in IJ to activate/hide Commander's frame
• All core files are now distributed inside a single jar, and are no longer spread across the ImageJ directory
• Offline help displays the README.md files displayed by GitHub when browsing directories in the repository
• Several routines for time series analysis (such as calcium imaging experiments)
• Several scripts are now installed in the Script Editor Templates menu
• User scripts are now placed in a more convenient location: the /scripts/BAR/ directory in ImageJ root directory (rather than the convoluted /plugins/scripts/BAR/(...) location
• My Routines supersedes My Snippets
• BAR is now more polyglot with code written in more languages e.g., Clojure and Groovy
• Support for multichannel profiles for images with more than 7 channels

[Uploaded to the BAR update site on 2017.04.05]

BAR 1.1.14

Most relevant changes:

• Fixed an overlay issue in Multi ROI Profiler
• Optimizations in Multichannel Z/T-axis Profile (including an issue reported by Jacob Keller in which y-axis range was not always optimized)

[Uploaded to the BAR update site on 2017.03.12]

BAR 1.1.13

Most relevant changes:

• New routine: Multi ROI Profiler that plots ROI intensities over time. Allows ROIs to be pre-filtered and is aware of multi-dimensional images. Designed for monitoring iGluSnFR fluorescence and calcium imaging experiments.
• Fix a bug in Multichannel Z/T-axis Profile that mixed averages from consecutive frames (reported by Jacob Keller)
• Allow log transforms in ROI Color Coder (#22)

[Uploaded to the BAR update site on 2017.03.10]

BAR 1.1.12

Most relevant changes:

• Improvements to Multichannel_ZT-axis_Profile.bsh
• JARified tutorial files (plugin)
• Maintenance fixes

[Uploaded to the BAR update site on 2017.02.24]

BAR 1.1.11

Most relevant changes

• Several improvements in LoG_DoG_Spot_Counter.py
• New Java plugin: Runner
• Made Scripts more aware of IJ2
• Fixed an issue with scripts loading data from Results table
• Extended JARification to scripts in Analysis, Annotation, and Segmentation

[Uploaded to the BAR update site on 2016.11.24]

BAR 1.1.10

Fixed an issue that did not allow scripts to import Scijava's Script Editor (unnoticed when 1.1.9 was released)

[Uploaded to the BAR update site on 2016.11.14]

BAR 1.1.9

• Script for interactive plotting is now a much more powerful and responsive Java plugin
• Data Analysis routines can retrieve tables from PlotWindows
• Started taking advantage of SciJava discovering scripts within JAR files (Right now just Data Analysis scripts, other directories will follow)
• Several scripts were simplified through the usage of script parameters
• New routine: LoG_DoG_Spot_Counter.py
• New routine: Create_Polar_Plot
• Improvements in Create BoxPlot, Distribution Plotter, ROI Color Coder, and Wipe Background
• Non-Fiji installations are no longer supported and Java 8 is now required

[Uploaded to the BAR update site on 2016.11.13]

BAR 1.1.8

Thanks to Mark Hiner, Jenkins integration!

BAR 1.1.7

Additions:

• Thanks to Mark Hiner, the first BAR Op!
• New snippets: Extract_Bouts_From_Tracks.py and List_BARs.groovy

Improvements:

• Data Analysis routines got smarter: In addition to the Results table, BAR scripts can now import data from other sources, including the clipboard, external files (.csv/.txt), or ANY ImageJ table.
• Plot Results, now Plot XY Data, is now fully interactive due to new API and allows for e.g., include data from different sources in a single plot.
• Multi-channel_ZT profile: Add support for StdDev statistics (thanks to Nicolas Vanderesse)
• Multichannel ZT-axis Profile: It is now possible to trigger custom routines in Live Mode.

Bug fixes:

• Distribution plotter: Fix exception when ignoring zero data points.

Changes:

• Plot Results as been renamed to Plot XY Data
• The Strahler Analysis script has been converted into a java plugin, now part of the hIPNAT repository
• The now deprecated Clipboard_to_Results.py is no longer listed in the BAR> menu hierarchy

Documentation:

• Updated API, Markdown, and User documentation

BAR 1.1.6

• Routines:
  • New script: Create Boxplot, a BeanShell script that creates box-and-whisker plots from ImageJ measurements
  • Plot Results has been re-written: It is now a full-fledged interactive plotting GUI
  • Updated ROI Manager Tools for IJ 1.45b (The ROI Manager can now store ROIs with the same name).
• API:
  • New class PlotUtils (Javadoc), providing utility methods for plotting operations, including exporting of JFreeChart plots as vector graphics (PDF or SVG)
  • Added new methods to the Utils class for interacting with the ImageJ Results table (Javadoc)
• Bug Fixes:
  • Fixed an issue that did not allow Groovy lib to be recognized by the ImageJ updater
  • Fixed an issue in which Clipboard to Results could terminate a calling script
  • Fixed an issue (#13) in ROI Manager Tools in which labels were not properly reset
  • Suppressed the "Ignoring unsupported output" Consoled warnings triggered by several routines
  • Fixed and issue that in which exiting messages of Segmentation macros could not be read in the ImageJ status bar
• Documentation:
  • Updated API, Markdown, and User documentation