mutterer

// creates a stack, duplicating the source image
// after an idea by Mathieu Fallet

x=getNumber("no of Slices", 10);
run("Select All");
run("Copy");
for(i=1;i<x;i++){
  run("Add Slice");
  run("Paste");
}

mutterer

run("Blobs (25K)");
run("Smooth");
run("Mean...", "radius=2");
setAutoThreshold("Intermodes");
run("Analyze Particles...", "exclude clear add");

mutterer

resetThreshold();
run("Remove Overlay");
n = roiManager("count");
Dialog.create("Choix");
Dialog.addChoice("paramètre", newArray("Area","Mean","Circ."),"");
Dialog.show();
param = Dialog.getChoice();
m=moy(param);
for (i=0;i<n;i++) {
	roiManager("select",i);

mutterer

dir = File.directory;
data = dir+ File.nameWithoutExtension+".txt";
if (File.exists(data)) { 
  data=File.openAsString(data);
  setMetadata("Info", data);
  List.setList(data);
  size=split(List.get('$CM_FULL_SIZE'));
  makeRectangle(0,0,size[0],size[1]);
  run("Crop");
  pixels = List.get('$$SM_MICRON_BAR');

mutterer

// fixes the display range of lsm files with pixelDepth>8

macro "fix display range [f]" {
  Stack.getDimensions(width, height, channels, slices, frames);
  for (c=0;c<channels;c++){
    Stack.setChannel(c+1);
    getStatistics(area, mean, min, max, std, histogram);
    setMinAndMax(min, max);
  }
}

mutterer

// Fix funny LUT for LSM or CZI files opened with Bioformats
// parses the file metadata to work around a bioformat bug
// that assigns wrong channel colors.

var r,g,b;
title = getTitle();
id=getImageID;
 
Stack.getDimensions(width, height, channels, slices, frames);
 

mutterer

// On windows, permanently delete files:
// * of a certain type
// * older than a certain year
// * that do not have one of a set of keywords

type="lsm";
keepFrom = 2014;
words= newArray("config","setting");

  dir = getDirectory("Choose a Directory ");

mutterer

run("RGB Stack"); 							// convert RGB image in a stack
run("32-bit"); 								// make it 32 bit for computations
run("Multiply...", "value=-1 stack"); 					// invert values for r,g,b
setSlice(2); 								// go to the green channel
run("Multiply...", "value=-2 slice"); 					// -g*-2 = +2g
run("Z Project...", "start=1 stop=3 projection=[Sum Slices]"); 		// sum all channels result= -r + 2g -b
setAutoThreshold("Intermodes dark"); 					// auto thresholding now works 

mutterer

// grab the Viridis (option-d) colormap from Berkeley Institute for Data Science GitHub repo
// and parse it to an ImageJ LUT
// Viridis colormap presented @ SciPy 2015 by Nathaniel Smith and Stéfan van der Walt
s=File.openUrlAsString("https://raw.githubusercontent.com/BIDS/colormap/master/option_d.py");
s=substring(s,indexOf(s,"[[")+1,indexOf(s,"]]")+1);
s=replace(s,'\n\n','\n');
s=replace(s,' ','');
s=split(s,'\n');
length = s.length;
reds = newArray(length);

mutterer

var xp = newArray();
var yp = newArray();

macro "tick marks Tool - C00cT0f16T" {
	if (roiManager('count')<1) exit("add at least one ROI the the roiManager");
	roiManager("Show All");
	getCursorLoc(x, y, z, flags);
	roiManager('select',0);
	run("Interpolate", "interval=1 adjust");
	getSelectionCoordinates(xp, yp);