// **********************************************************************
// declare global variable
//var mypath="c:/";
  
// **********************************************************************
// "0gel_analysis"
// Macro for quantifying gels
// Fabrice Duprat april 2013
//  INPUT: Image of the gel
// The macro ask to check that background value is close to zero and foreground is higher (otherwise you need to Edit/Invert and Image/Lookup table/Invert LUT)
// The macro ask you to draw a rectangle in an enpty line of the gel to measure the background to be substracted
//  Then, for each lane, draw a rectangle  and press Ctrl+M to measure
// OUTPUT:  All the Integrated density measurements are in the Results window
// 
// ********************************************************************************

//
// If you are using this script for a research article, please cite this web page: https://www.ipmc.cnrs.fr/~duprat/scripts/
//


macro "gel_analysis"

{

run("Colors...", "foreground=black background=white selection=red");

run("Set Measurements...", "  mean integrated display redirect=None decimal=2");

run("Clear Results");

waitForUser("Please check that the white background value is close to zero and black foreground is higher");

setTool("rectangle");

waitForUser("Select the BACKGROUND to be substracted");

run("Measure");
backgr = getResult("Mean", 0);

backgrd = round(backgr);

run("Select None");

run("Subtract...", "value="+backgrd );

run("Clear Results");

run("Set Measurements...", "  integrated display redirect=None decimal=2");

waitForUser("Select the BLOTS and press Ctrl+M to measure");


}