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macro:roi_color_coder [2019/04/12 11:13] (current)
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 +====== 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]].
  
 +<​html>​
 +  <div class="​level1"​ style="​margin-bottom:​ 20px;">​
 +    <​b>​Keywords</​b>​ &nbsp; Analyze particles, heat-map, lookup table, non-destructive image overlay, BAR
 +  </​div>​
 +</​html>​
 +----
 +=== 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)}}
 +----
 +=== Prompt ===
 +{{ :​macro:​rcc:​roicolercoder05.png | Dialog prompt of ROI Color Coder}}
 +----
 +=== Requirements ===
 +ImageJ 1.46h or later. Use ''​Help>​Update ImageJ...''​ to upgrade to a newer version.  ​
 +----
 +=== 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''​.
 +
 +----
 +=== 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.:<​code>​run("​ROI Color Coder",​ "​measurement=Area lut=Ice width=10 opacity=80"​);</​code>​
 +  * See [[https://​github.com/​tferr/​Scripts/#​scripts|GitHub]] for more details
 +
 +\\ 
 +----
 +=== 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//
macro/roi_color_coder.txt ยท Last modified: 2019/04/12 11:13 (external edit)