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@ekatrukha
Created February 7, 2019 18:03
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ImageJ macro making a tilted movie out of Z-stack
//ImageJ macro making a tilted movie out of stack
//uses shear transform + rotation
//Eugene Katrukha katpyxa at gmail.com
requires("1.48h");
sTitle=getTitle();
sMovieTitle=sTitle+"_tilt_movie";
setBatchMode(true);
//Dialog
Dialog.create("Tilt parameters:");
Dialog.addNumber("Tilt radius in X (px):", 20);
Dialog.addNumber("Tilt radius in Y (px):", -20);
Dialog.addNumber("Rotation angle:", 15);
Dialog.addNumber("Number of movie frames:", 40);
sZChoice=newArray("Last frame is top","First frame is top");
Dialog.addChoice("Z direction:", sZChoice);
Dialog.show();
nCurrStepX=Dialog.getNumber();
nCurrStepY=Dialog.getNumber();
nCurrRotAngle=0.5*Dialog.getNumber();
nSteps=Dialog.getNumber();
sChoice=Dialog.getChoice();
nStepX=(-2)*nCurrStepX/nSteps;
nStepY=(-2)*nCurrStepY/nSteps;
//nRotationRange = 20;
nRotStep = (-2.0)*nCurrRotAngle/nSteps;
init=getImageID();
bNotFirstIt=false;
print("Starting movie generation...");
for (i=0;i<nSteps;i++)
{
run("Duplicate...", "duplicate");
copyx=getImageID();
for (j=0;j<nSlices;j++)
{
if(startsWith(sChoice, "Last"))
{ setSlice(nSlices-j);}
else {
setSlice(j+1);}
//making shear transform with respect to stack center
dx=2.*((j-nSlices*0.5)*nCurrStepX/nSlices);
dy=2.*((j-nSlices*0.5)*nCurrStepY/nSlices);
runstring="x="+toString(dx)+" y="+toString(dy)+" interpolation=Bilinear slice";
run("Translate...", runstring);
}
//adding some rotation
run("Z Project...", "projection=[Max Intensity]");
runstring="angle="+toString(nCurrRotAngle)+" grid=1 interpolation=Bicubic";
run("Rotate... ", runstring);
if(bNotFirstIt)
{
sCurrTitle=sTitle+"_frame"+toString(i);
rename(sCurrTitle);
run("Concatenate...", " title=["+sMovieTitle+"] image1=["+sMovieTitle+"] image2=["+sCurrTitle+"]");
sMovieID=getImageID();
}
else
{
rename(sMovieTitle);
sMovieID=getImageID();
bNotFirstIt=true;
}
//updating rotate/shear counters
nCurrStepX=nCurrStepX+nStepX;
nCurrStepY=nCurrStepY+nStepY;
nCurrRotAngle= nCurrRotAngle+nRotStep;
selectImage(copyx);
close();
selectImage(init);
print("Frame " +toString(i+1) +" out of "+toString(nSteps));
}
selectImage(sMovieID);
setBatchMode(false);
print("Done");
@maciejmotyka
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Hi! Thank you both for this useful tool.
I have some confocal z-stacks with slices apart by 10.5 pixels. Does this macro/plugin take into account slice spacing?
So far I've been using the 3D Project plugin, which has an option to specify the slice spacing. With 3DTilt is it enough to set the voxel size to 1x1x10.5, or is it necessary to alter the code?

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