ROI Color Coder

Colorizes selections listed in the ROI Manager by matching measurements to a color of a lookup table (LUT), generating particle-size heat maps. It complements the Analyze>Analyze Particles… command. ROI Color Coder is part of the BAR.

Keywords Analyze particles, heat-map, lookup table, non-destructive image overlay, BAR

Output

Prompt

Requirements

ImageJ 1.46h or later. Use Help>Update ImageJ… to upgrade to a newer version.

Installation

Subscribe to the BAR update site in Fiji. Alternatively, download the latest version of ROI_Color_Coder.ijm from GitHub (direct link).
Place the file in the ImageJ/plugins/ or Fiji.app/plugins/ folder (or subfolder).
The command ROI Color Coder will be listed in the Plugins> menu after running Help>Refresh Menus.

Tips

Rename your preferred LUTs in the ImageJ/luts/ directory with a numeric prefix (e.g. '00-Gold.lut') to have them listed first in the LUT dropdown menu
Check “Labels” in the ROI Manager to toggle ROI labeling. Adjust ROI labels using the ROI Manager More»Labels… command
Use the ROI Manager Flatten [F] command to obtain an RGB image with the overlay rendered as pixel data. The image overlay is also embedded when saving the image in PNG or JPEG format (File>Save As> submenu)
A zip folder containing several 'heat-map' LUTs can be downloaded from the ImageJ web site (direct link)
You can easily customize lookup tables using the Edit>Color>Edit LUT command.
The glasbey.lut (direct link) can be used to colorize selections randomly (although other strategies would probably perform better in this task, e.g., RoisToOverlay.js)
Once installed in the Plugins menu, ROI Color Coder can be called from other macros, e.g.:
```
run("ROI Color Coder", "measurement=Area lut=Ice width=10 opacity=80");
```
See GitHub for more details

Change History

2014.01.31 v.5.1
- Added support for the Angstrom symbol
- Moved file to GitHub
2012.03.01 v.5
- Min value is no longer restricted to zero
- Legend is now fully customizable
2010.12.06 v.4
- Accepts all LUT files recognized by ImageJ (previous versions accepted only tab-delimited text LUT files)
- Fixed an issue caused by files without extension saved in the luts directory
2009.12.14 v.3
- Added options for transparency, contours width, ROI filling
- Results table is cleared and ROIs (re)measured if needed
2009.12.01 v.2
- Fixed labels misalignment in legend

— Tiago Ferreira 2014/06/19 23:10