Create highly compressed MP4 movie from a TIFF stack with scalebar and a timestamp

make_tirf_movie.ijm

Dialog.create("pTIRF movie creator");
Dialog.addNumber("Time interval between frames", 500, 0, 6, "ms");
Dialog.addNumber("Brightness/contrast: black level", 400, 0, 6, "counts");
Dialog.addNumber("Brightness/contrast: white level", 1000, 0, 6, "counts");
Dialog.addNumber("Time point of injection", 10, 1, 6, "s");
Dialog.show();

exp_time = Dialog.getNumber() / 1000.0;
low = Dialog.getNumber();
high = Dialog.getNumber();
injection = -Dialog.getNumber();

setMinAndMax(low, high);
run("8-bit");

run("Set Scale...", "distance=1152 known=250 unit=µm");
run("Scale Bar...", "width=50 height=20 thickness=8 font=32 color=White background=Black location=[Lower Right] horizontal bold label");
run("Time Stamper", "starting=injection interval=exp_time x=10 y=10 font=50 decimal=1 anti-aliased or=s");
run("Image Sequence... ", "format=TIFF name=img");

Dialog.create("pTIRF movie creator");
Dialog.addString("Now invoke ffmpeg with these arguments", "./ffmpeg -i frames/img%04d.tif -c:v libx264 -crf 30 <movie name>.mp4", 60)
Dialog.show();

Open a TIFF stack in ImageJ. Figure out what brightness/contrast setting you want to use and remember the lower/upper limits.
Then run this script, plug in the numbers, and it will save individual annotated 8-bit frames in a folder of your choice.

After that, you can run ffmpeg from the command line to create an MP4 file from these exported frames.