_____________This entire fork merely adds 4 extended versions of the BAR color coding script and one for color coding lines.

###BAR_ROI_Color_Coder+autoprefs_ASC

 Additional features include:

1. The measured range of values is shown for all measurements in the Measurement selector (this makes it easier to manually select a range for the color ramp).

2. The selected LUT (color lookup table) can be reversed.

3. An automatic suggested value for the decimal places can be selected (based on the magnitude and range of the values).

4. A ramp height is suggested base on the image height.

5. Parameter and unit labels added to the top an bottom of ramp respectively.

6. Overrun labels are added to the ramp if the true range exceeds the range chosen for the ramp (see example below). This is useful when there are just a few outliers that would otherwise reduce the contrast variation for the majority of the features.

7. Any previous ramp is closed before creation of a new ramp.

8. Provides an option at the end to create a new merged image combining labeled image and legend (the legend/ramp height is scaled to match the height of the image).

9. Select any system font (and have favorites list).

10. LUTs list has preferred LUTs at top (edit getLutsList function).

###BAR_ROI_Color_Coder53+autoprefs+summary

Additional feature over those listed above:

A summary list can be added in the corners, center or a selected location listing up to 6 lines of statistics.

###BAR_ROI_Color_Coder_with_ROIManagerLabels

    Additional features over the autoprefs macro listed above:

      Each ROI is renamed with the chosen feature value and these are used as labels.

  

###BAR_ROI_Color_Coder_with_ScaledLabels

      Additional features over the autoprefs macro listed above:

    Each ROI is labeled with the chosen feature value using extensive formatting options. If Gabriel Landini's "Morphology" plugin is installed it will allow you to center the labels at the morphological centers of the objects (better than centroids for complex shapes because these points are always inside the original objects).

###BAR_ROI_Color_Coder+ScaledLabels+Summary

      As above but now also has the Summary table option.

Color Coder example for scaled labels and summary version using asc-silver LUT with ramp frequency plot and ln stats

###LineColorCoder

      Inspired by the BAR ROI Color Coder this macro color codes lines according to any Results table parameter.

_________________________________________________________________

_________________________________________________________________

The original BAR README.................

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, download the latest version of Fiji and subscribe to the BAR update site. For more details refer to the BAR documentation page.

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

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

Image Annotation

Aiders for the annotation of scientific images.

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

Image Segmentation

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

Tools and Toolsets

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

Snippets

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

1. (py) Extract Bouts From Tracks
2. (groovy) List BARs
3. (py) Median Filter
4. (py) NN Distances
5. Batch Processors 1. (ijm) Process Folder IJM 2. (py) Process Folder PY
6. (bsh) Search BAR

lib

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

Utilities

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)

Java Classes

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

Tutorials

1. Introduction to Scripting Tutorials used in the workshop Scripting with BAR, at the 2015 ImageJ User & Developer Conference.
2. External Ops: Tutorial exemplifying how to provide ops.

Misc

Scripts that are not distributed through the BAR update site:

1. Capture Window
2. Clipboard to Results

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

Citations

• To cite BAR:

  

• 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

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 by the 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 and Jan Eglinger. 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.

Analysis	Data Analysis	Annotation	Segmentation	Tools	Plugins	lib	Snippets	IJ