mutterer’s gists

mutterer / LineAndProfileTool.txt

Last active December 25, 2015 01:58

// This ImageJ macro tool draws a line, and overlays it's profile. // see https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;197bef78.1310

	// 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 / RoiClassesTest.ijm

Last active April 3, 2019 21:57

A sample image menu macro that allows manually assigning classes to ROIs

	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.ijm

Last active December 30, 2015 05:39

	// 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 / multipage_montage.ijm

Created January 15, 2014 20:39

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

	// 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 / sameImageToStack.ijm

Created March 17, 2014 10:33

creates a stack, duplicating the source image

	// 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 / macro1.ijm

Last active August 29, 2015 13:57

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

mutterer / macro2.ijm

Last active August 29, 2015 13:57

	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 / calibrer_SEM.ijm

Last active August 29, 2015 13:59

	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 / Fix_display_range.ijm

Created September 11, 2014 08:31

Fix display range of multichannel images with bitdepth>8

	// 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 / multichannel_profile_plot.ijm

Last active September 23, 2021 11:09

	// 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"{