mutterer

// This tool draws a line, and overlays its profile and some infos
 
 macro "Line and Profile Tool -C00bL1de0L1ee1" {
        getCursorLoc(x, y, z, flags);
        xstart = x; ystart = y;
        x2=x; y2=y;        
        while (true) {
            getCursorLoc(x, y, z, flags);
            if (flags&16==0) {
                dx=x2-xstart; dy=y2-ystart;

mutterer

var tags   = newArray("nucleus-1","nucleus-2","cyto-1", "cyto-2");
var colors = newArray("red",      "green",    "blue",   "magenta");
var commands = newArray("Select by tag...");
var menu = Array.concat(commands, tags);
var pmCmds = newMenu("Popup Menu", menu);
 
macro "Popup Menu" {
	cmd = getArgument();
	if (cmd=="Select by tag...") {
		Dialog.create("Title");

mutterer

// CZI batch project macro
// parses the file metadata to work around a bioformat bug
// that assigns wrong channel colors.
// edit the first two lines to use DIC in the projection or not
// and what projection mode is needed (see Image>stacks>Z project...)

useDic = true;
projectionMode = "Max Intensity";

var r,g,b;

mutterer

// creates series of montages
// use case: input stack of 200 images
// user wants 4x5 montage: 10 pages output.

source = getImageID;
slices=nSlices;
cols = 4;
rows = 5;
imagesPerPage = cols*rows;
for (i=0; i<slices/imagesPerPage; i++) {

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");
}

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

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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);

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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

// yet another multichannel profile plotter
// with smart(?) lookuptables
// 20181114 : works as a macro Tool thanks to Sophie Allart
// plot x-axis is calibrated thanks to Christian Rouviere
// works with 16-bit images thanks to Tiago Ferreira (https://gist.github.com/tferr/863b630d7da2dbcdbed0/revisions)
// Add Image popup menu with Inverted Background command to get dark mode plots (Christian Rouvière)
// Add standard line adjusting behavior (Christian Rouvière)
// Works with RGB or Composite images

macro "multichannel profile plotter Tool - Cf00D02D13D14D24D25D26D27D38D46D47D56D65D75D85D95Da5Db5Dc5Dc6Dd6Dd7Dd8De7De8Df6Df7C00fD09D1aD1bD2cD2dD2eD3eD3fD4dD4eD5cD6bD7bD7cD8bD9aDabDbaDcaDdbDdcDddDecDedDfbC000T06102"{