TiffStack

PIMS can read most TIFF files out of the box, so you should try reading you files pims.open('my_tiff_file.tif') and revisit this section if you encounter an error.

A tiff stack is a single file (.tif or .tiff) containing several images, often a time series or “Z stack.”

TiffStack expects a single filename. To load a collection of many single-image tiff files (e.g., img-1.tif, img-2.tif) see ImageSequence.

Dependencies

There are several Python packages for reading TIFFs. Our default reader, built around Christoph Gohlke’s tifffile.py, handles all the formats we have personally encountered. But we have alternative TIFF readers built around Pillow (see above) and libtiff. To use a specific reader, use TiffStack_tifffile, TiffStack_libtiff, or TiffStack_pil, which depend, respectively, on the packages below. The “default” reader, TiffStack is an alias. At import time, it is pointed to the first reader for which the required package is installed.

• tifffile

• pylibtiff

• Pillow or PIL

Tifffile is installed with the PIMS conda package.