<code>

//A simple tool that tracks objects by selecting them with the magic wand
//A new image stack of the tracked object is also recorded
//Place Wand_Track_Tool.ijm in /fiji/macros/toolsets and restart
//Clicking the first button acivates the tool
//Clicking the second starts a new track
//Results are recorded in the same format as the manual tracking tool (http://rsbweb.nih.gov/ij/plugins/track/track.html)


//Global variables for cell tracking
var gtrack = 1;
var number = 1;
var count = 1;

macro "Wand Track MB Tool - CfffD00D01D02D03D04D05D06D07D0bD0cD0dD0eD0fD10D11D12D13D14D15D16D17D19D1bD1cD1dD1eD1fD20D21D22D23D24D25D26D2bD2cD2dD2eD2fD30D31D32D33D34D39D3aD3bD3cD3dD3eD3fD40D41D42D43D50D51D52D53D60D61D62D68D69D6aD70D71D77D78D79D7aD7bD7cD7dD84D87D88D89D8aD8bD8cD8dD8eD8fD91D93D94D97D98D99D9aD9bD9cD9dD9eD9fDa3Da4Da7Da8Da9DaaDabDacDadDaeDafDb0Db1Db2Db3Db4Db8Db9DbaDbbDbcDbdDbeDbfDc0Dc1Dc2Dc3Dc4Dc9DcaDcbDccDcdDceDcfDd0Dd1Dd2Dd3Dd4Dd9DdaDdbDdcDddDdeDdfDe0De1De2De3De4De5DeaDebDecDedDeeDefDf0Df1Df2Df3Df4Df5DfbDfcDfdDfeDffC48dD4dD6cDc8Dd7Dd8De6De7Df6C37dD7fDfaC69eDa5C777D45C58dD6dDc6Dd5C999D27D36D37D38D54D63D64D72D73D74D83C8beD5eD75C48dD6bDb7Dc7Dd6C48dD4eDf7C8aeD49D4aD58D59C888D28D46D55D82C59eD96Db6C9beD57C47dD4fD7eDe8De9Df8Df9C7aeD5fD6fC59dDb5Dc5C8beD5aD66C69dD47D65C69eD76D86Da6C9beD5bD5cD5dD85C7aeD48D4bC59eD4cC59dD67C8beD95C6aeD6e" 
{

//some variables
    track = gtrack;
    slice = getSliceNumber();
    Image = getTitle();
    width = getWidth();
    height = getHeight();
//draws the tracking table
    requires("1.38m");
    title1 = Image+"_Tracking Table";
    title2 = "["+title1+"]";
    f = title2;
    if (isOpen(title1)) {
    }
    else {
        if (getVersion>="1.41g")
            run("Table...", "name="+title2+" width=1000 height=300");
        else
            run("New... ", "name="+title2+" type=Table width=250 height=600");
        print(f, "\\Headings: \tTrack\tSlice\tX_R\tY_R\tX_M\tY_M\tWidth\tHeight\tX_B\tY_B");
    }
    run("Colors...", "foreground=white background=white selection=cyan");
    autoUpdate(false);
    getCursorLoc(x, y, z, flags);
    doWand(x, y, 100, "8-connected");
    wait(150);
//Checkpoint for ROI size so that if you accidently click outside the intended region the macro stops and warns you
    run("Set Measurements...", "center area redirect=None decimal=4");
    run("Clear Results");
    run("Measure");
    area=(getResult("Area"));
    if (area>3000)
    {
        selectWindow("Results");
        run("Close");
        Dialog.create("ROI ERROR!");
        Dialog.addMessage("ROI too large! Did you click outside the cell? Please repeat");
        Dialog.show();
    }
    else{
        selectWindow("Results");
        run("Close");
        selectWindow(Image);
        run("Copy");
        
            if (isOpen(Image+"_Track"+track))
            {
                selectWindow(Image+"_Track"+track);
                run("Add Slice");
            }
            else{
                newImage(Image+"_Track"+track, "8-bit Black", width, height, 1);
            }
            run("Restore Selection");
            run("Paste");
            selectWindow(Image);
//Make measurements on ROI
            run("Set Measurements...", "center redirect=None decimal=4");
            run("Clear Results");
            run("Measure");
//Rounded results are designed to be compatible with Ibidi Chemotaxis tool. The exact results are recorded too.
            COM_X=round(getResult("XM"));
            COM_Y=round(getResult("YM"));
            X_M=getResult("XM");
            Y_M=getResult("YM");
            getSelectionBounds(x, y, width, height);
            if (isOpen("Results")) {
                selectWindow("Results");
                run("Close");
            }
            run("Select None");       
        
            print(f,(number++)+"\t"+(track)+"\t"+(slice)+"\t"+(COM_X)+"\t"+(COM_Y)+"\t"+(X_M)+"\t"+(Y_M)+"\t"+(width)+"\t"+(height)+"\t"+(x)+"\t"+(y));
        
//advance to next slice
        run("Next Slice [>]");
        selectWindow(Image);
    }
}

//You do not need to click it before you start tracking as gtrack is set to 1 in the first instance.
macro "Add Track Action Tool - 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"
{
    setTool("rectangle");
    waitForUser("Select stack", "Select the master image stack, then click OK");
    Image = getTitle();
    dir = File.directory();
    gtrack++;
    Dialog.create("New Track Added");
    Dialog.addMessage("A new track has been added to the analysis. New Track = Track "+gtrack);
    Dialog.show();
    setSlice(1);
    last_track = gtrack-1;
    if (isOpen(Image+"_Track"+last_track))
    {   selectWindow(Image+"_Track"+last_track);
        save(dir+Image+"_Track"+last_track);
        selectWindow(Image+"_Track"+last_track);
        run("Close");
    }
    else
    {}
}
//Icons used courtesy of: http://www.famfamfam.com/lab/icons/silk/
//Richard Mort 29/01/2013

</code>