miura

macro"drawGrids"{
        newImage("Untitled", "8-bit black", 400, 400, 1);
        y1=0;
        y2=399;
        setColor("white");
        setLineWidth(1);
        for (x1=20;x1<400;x1+=20){
                drawLine(x1,y1,x1,y2);
        }
        x2=0;

miura

macro "grid_perp" {
	width = getNumber("width?",400);
	height = getNumber("height?",400);
	factor = getNumber("how many lines?",10)
	newImage("grid", "8-bit black", width, height, 1);
	setColor("white");
	for (i = width/factor; i < width; i+=width/factor) 
		drawLine(i, 0, i, height);
	for (i = width/factor; i < height; i+=height/factor) 
		drawLine(0, i, width, i);

miura

from ij.plugin import ChannelSplitter as CS

imp = IJ.getImage()
chs = CS.split(imp)
for aimp in chs:
        aimp.show()

miura

macro "delete even frames" {
  for (i=2; i<=nSlices; i++) {
		setSlice(i);
		run("Delete Slice");
	}
}

miura

var Gtitle = "map";
var Rtitle = "nuc";

twoImageChoice();
selectWindow(Rtitle);
  
//makeLine(0, 0, 0, 0);
run("Gaussian Blur...", "sigma=0.75 scaled stack");
//setAutoThreshold("IsoData dark");
//setOption("BlackBackground", false);

miura

from fiji.threshold import Auto_Local_Threshold as ALT

# nucleus selection 

#imp = IJ.getImage()
imp = IJ.openImage("/Users/miyanari/Desktop/EMBL_with Kota/FISH_data/DNA-FISH_Demo.tif")
#IJ.run(imp, "Split Channels", "")
imps = ChannelSplitter.split(imp)
nucimp = imps[0]
#nucimp.show()

miura

imp = IJ.getImage()
midslice = int(imp.getStackSize() / 2)
imp.setSlice(midslice)
#IJ.setThreshold(-50, -0.62)
ip.setAutoThreshold(AutoThresholder.Method.Default, False) 
IJ.setThreshold(ip.getMinThreshold(), ip.getMaxThreshold())
print ip.getMaxThreshold()
print ip.getMinThreshold()
#th = ip.getMaxThreshold()
IJ.run("Convert to Mask", "method=Default background=Light black")

miura

def floatStackThresholder(ip, pix, th):
  for i in range(pix):
		if ip.get(i) > th:
			ip.setf(i, 255.0)
		else:
			ip.setf(i, 0.0)
	ip = ip.convertToByte(False)
	return ip
	
imp = IJ.getImage()

miura

def stacklistGenerate(imp):
        stk = imp.getStack()
	imglist = []
	print len(imglist)
	for i in range(imp.getStackSize()):
		ip = stk.getProcessor(i+1)
		title = "img" + str(i+1)
		impsingle = ImagePlus(title, ip.duplicate())

miura

'''
Opens series of .lsm files as a single hyperstack

20130712 Kota Miura (cmci.embl.de)

Choose a file among the file series, and this script searchs all the 
files with a pattern

	(basename)_R(fixed)_GR(.*)_B(block number)_L(location number)\.lsm