====== 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 [[http://fiji.sc/BAR|BAR]].
Keywords Analyze particles, heat-map, lookup table, non-destructive image overlay, BAR
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=== Output ===
{{ :macro:roicolorcoderoutput.png |blobs.gif in which the Area of segmented particles was matched to the fire LUT (filled ROIs) and Feret lengths to a custom heat-map LUT (contours)}}
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=== Prompt ===
{{ :macro:rcc:roicolercoder05.png | Dialog prompt of ROI Color Coder}}
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=== Requirements ===
ImageJ 1.46h or later. Use ''Help>Update ImageJ...'' to upgrade to a newer version.
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=== Installation ===
- Subscribe to the [[http://fiji.sc/BAR#Installation|BAR update site]] in [[http://fiji.sc/|Fiji]]. Alternatively, download the latest version of ''ROI_Color_Coder.ijm'' from [[https://github.com/tferr/Scripts/blob/master/Annotation/ROI_Color_Coder.ijm?raw=true|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''.
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=== 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 [[http://rsb.info.nih.gov/ij/download/luts/luts.zip|ImageJ web site]] (direct link)
* You can easily customize lookup tables using the ''Edit>Color>Edit LUT'' command.
* The [[http://rsb.info.nih.gov/ij/download/luts/glasbey.lut|glasbey.lut]] (direct link) can be used to colorize selections randomly (although other strategies would probably perform better in this task, e.g., [[http://rsb.info.nih.gov/ij/macros/js/RoisToOverlay.js|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 [[https://github.com/tferr/Scripts/#scripts|GitHub]] for more details
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=== Change History ===
* 2014.01.31 v.5.1
* Added support for the Angstrom symbol
* Moved file to [[https://github.com/tferr/Scripts/#scripts|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
--- //[[:users:tferreira|Tiago Ferreira]] 2014/06/19 23:10//