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

run("Fresh Start");
run("Options...", "iterations=1 count=1 black");
run("Boats");
setBatchMode(true);
run("Duplicate...","title="+getTitle);
makeOval(100,100,300,300);
w=getWidth;h=getHeight;
roiManager("add");
newImage("temp", "8-bit black", w, h, 1);
size = 10;

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

sourcedir=getDirectory("select source directory with lsm files");
destdir=getDirectory("select or create destination directory");
list = getFileList(sourcedir);

Dialog.create("New LSM Batch color converter options");
	Dialog.addChoice("Export format  ", newArray("Tiff", "Jpeg"));
	Dialog.addCheckbox("Output merged channels image(s) ", true);
	Dialog.addCheckbox("Process all time points ", false);
	Dialog.addCheckbox("Process all slices ", false);
	Dialog.addCheckbox("Convert to 8-bit ", false);

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);

mutterer

/*
 * Making a pretty fluorogram
 * Olivier Burri, BioImaging & Optics Platform, EPFL
 */

run("Fluorescent Cells (400K)");

image = getTitle();
run("Split Channels");

mutterer

// written at the request of S.Mingle.
// https://gist.github.com/mutterer/8fc04d0bdcc72a56072c

var baselineIndex=0;

macro "Help Action Tool - C00cT0f18?" {
  help = setup();
}

macro "Define BaseLine Action Tool - C00cT0f18BTaf18l" {

mutterer

macro "MultiFreehand Tool - C00cT0f18M" {
  xs = newArray(1);
  ys = newArray(1);
  getCursorLoc(x, y, z, flags);
  xs[0]=x; ys[0]=y;
  lastx=x;lasty=y;
  leftclick=16;
  while (flags&leftclick>0) {
   getCursorLoc(x, y, z, flags);
   if ((x!=lastx)||(y!=lasty)) {