Tools to cut down on manual intervention in my PhD.
Installation of this package gives you the following command-line tools:

Stack many tiff files.
From this:

experiment1/
├── image0000.tif
├── image0001.tif
├── ...
├── image0999.tif
└── image1000.tif

To this

experiment1/
├── stack0.tif
└── stack1.tif

by running tiff-stacker experiment1.
You must have ImageMagick installed.