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// This macro converts a 26x26 8-bit image to a tool macro icon
// string. Ideally, the image should have no more than 16 colors.
// Includes seven examples that, with the exception of the 
// "Lena Tool", were created by converting website favicons
// (http://en.wikipedia.org/wiki/Favicon).
// v1.0 : 4 April 2006
// v1.1 : 17 January 2021 : works with 26x26px images.

macro "Convert 26x26 Image to Tool Icon..." {
  requires("1.35r");

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// this example uses the Toolbar.setIcon(toolName,icon) method
// This example action tool uses the Toolbar.setIcon() method,
// added in v1.53h, to dynamically update its icon.
// uses extended hex icon coordinates

var icons = newArray( "Ca30N44V00nn","C037N44F00nn");
var colors = newArray( "Cf00","C0f0","C00f","Cf0f");
var xs = newArray(4);
var ys = newArray(4);
var xbs = newArray(4);

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// Providing an image and polyline, macro illustrates
// (creates a stack with animation)
// "Straighten" ROI function of ImageJ
// 2021.01.15 Eugene Katrukha / katpyxa at gmail dot com

if (nImages<1)
{
	exit("This macro needs an input image. Open something");
}
if(selectionType()!=6)

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id=getImageID;
Stack.getDimensions(width, height, channels, slices, frames);
for(i=1; i<=slices; i++) {
    selectImage(id);
    Stack.setSlice(i)
    run("Duplicate...", "duplicate slices=&i-&i");
    run("Set Label...", "label=Hue");
    run("RGB Color","");
    run("Set Label...", "label=");
}

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// This macro creates an animation by interpolating ROI coordinates
// and drawing each step and fading and blurring the image.
// The active ROI is hidden if batch mode is true.

run("Fresh Start");
newImage("2021", "8-bit black", 256, 256, 1);
run("Fire");

setBatchMode(true); // hide ROIs on active image, requires 1.53h21

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// colours of 2021

call("ij.gui.ImageWindow.centerNextImage");
newImage("2020 LUTs demo", "8-bit black", 512, 256, 1);
r=10;
setForegroundColor(255,255,255);
luts = getList("LUTs");
lut=0;
makeLine(78,90,97,61,134,63,149,91,76,174,66,157,139,180,170,160);
run("Fit Spline");

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// suggested by @noodlyscientist Liat Adler 
// this script nicely organizes windows for screen recording
// save this script in the plugins folder

IJ.run("Fresh Start","");
IJ.getInstance().setLocation(0,0);
IJ.run("Macro","");
b=GUI.getScreenBounds()
x=b.width/2; y=b.height/2;
f=WindowManager.getFrame("Macro.ijm")

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run("Fresh Start"); run("Blobs (25K)"); 
selectWindow('blobs.gif');setLocation(0, 100);
setThreshold(192, 255);
makeRectangle(56, 132, 68, 61);
run("To Selection");
doWand(80, 175);
run("Set Measurements...", "area redirect=None decimal=3");
run("Measure");
print(Table.get('Area',Table.size-1),'Measure, no options');
run("Set Measurements...", "area limit redirect=None decimal=3");

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// cutepeaks exports ab1 files as tab delimited csv
// this macro replaces tabs with commas
// reopens peaks file
// and builds a nucleotide plot
// v 1.0 : 20201109
//   1.1 : 20201207 handles csv files with different columns ordering

s=File.openAsString("");
name = File.name;
s=s.replace('\t',',');

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// this is what it takes to make a red/geen image
// colorblind friendly

run("Make Composite");
setSlice(1);
run("Magenta");
setSlice(2);
run("Green");
// optional: remove blue channel completely
// (some jpgs have residual blue channel which decrease contrast)