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@ackman678 ackman678/dFoverFmovie.txt
Last active May 23, 2018

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An ImageJ macro to make a dF/F movie from a calcium imaging recording.Works best if file extension is changed to '.ijm' and saved in your ImageJ folder at plugins/Macros/dFoverFmovie.ijm
//dF/F image stack, James B. Ackman 2012-02-14, update 2014-02-21 09:44:13
// this macro will (1) reduce an open image stack in half
// (2) create an average image in the z-dimension
// (3) calc dF/F image stack
// Uncomment the lines 21 run("Size..." ...) as well as the filenames at line 14,32 if you want to downsample the movie size
// To run without the autosave option, comment out the lines 62
// Comment out lines 41-58 if you don't want to auto adjust the contrast
name1=getTitle;
//selectWindow(name1)
directory=getInfo("image.directory");
//name=getInfo("image.filename");
nn=replace(name1, ".tif", "-dFoF-50fps.avi");
//nn=replace(name1, ".tif", "-dFoF-50fps-halfsz.avi");
fnm=directory+nn;
//print(fnm)
n = nSlices;
w = getWidth/2;
h = getHeight/2;
//run("Size...", "width=w height=h depth=n constrain interpolation=None");
run("Z Project...", "start=1 stop=n projection=[Average Intensity]");
name2=getTitle;
imageCalculator("Subtract create 32-bit stack", name1,name2);
name3=getTitle;
run("Jet");
imageCalculator("Divide create 32-bit stack", name3,name2);
name4=getTitle;
selectWindow(name2)
nn2=replace(name1, ".tif", "_AVG.tif");
//nn2=replace(name1, ".tif", "_AVG-halfsz.tif");
fnm2=directory+nn2;
saveAs("Tiff", fnm2);
name2=getTitle;
selectWindow(name4)
rename(nn)
name4=getTitle;
Stack.getStatistics(voxelCount, mean, min, max, stdDev)
print("stats");
print(" voxels: "+voxelCount);
print(" min: "+min);
print(" max: "+max);
print(" mean: "+mean);
print(" std dev: "+stdDev);
newMin=-3*stdDev
newMax=7*stdDev
//print(" new min: "+newMin);
//print(" new max: "+newMax);
//run("Brightness/Contrast...");
setMinAndMax(newMin, newMax)
getMinAndMax(min, max)
print(" new min: "+min);
print(" new max: "+max);
close(name1);
close(name3);
run("AVI... ", "compression=JPEG frame=50 save=&fnm");
doCommand("Start Animation [\\]");
//close(name2);
//close(name4);
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