Saving 16-bit tiff files using Python
When dealing with microscopy data it is not uncommon to be dealing with image
files that have 16-bit channels. This presents a difficulty when
working with Python as many imaging libraries struggle to save
To illustrate the problem let us create a white 50x50 pixel 16-bit image using
>>> import numpy as np >>> ar = np.ones((50,50), dtype=np.uint16) >>> ar = ar * np.iinfo(np.uint16).max
>>> from PIL import Image >>> img = Image.fromarray(ar) Traceback (most recent call last): ... TypeError: Cannot handle this data type
SciPy does save the file, but it converts it to 8-bit. Personally I do not like this behaviour as it has caused me confusion on several occasions as subsequent steps of the analysis has read the file and tried to extract meaningful information from it.
>>> import scipy.misc >>> scipy.misc.imsave('scipy.tiff', ar) >>> ar2 = scipy.misc.imread('scipy.tiff') >>> ar2.dtype dtype('uint8') >>> np.max(ar2) 0
PyLibTiff to the rescue
PyLibTiff is a package that provides a
wrapper to the libtiff library. To use
it simply make sure that you have the libtiff library installed on your system
and then you can use
pip to install PyLibTiff. On a Debian based system.
sudo apt-get install libtiff-dev sudo pip install libtiff
Now let us look at how to save a file using PyLibTiff.
>>> from libtiff import TIFF >>> tiff = TIFF.open('libtiff.tiff', mode='w') >>> tiff.write_image(ar) >>> tiff.close()
To show that everything is working as expected let us open the tiff file and read in the image from it.
>>> tiff = TIFF.open('libtiff.tiff', mode='r') >>> ar = tiff.read_image() >>> tiff.close() >>> ar.dtype dtype('uint16') >>> np.max(ar) 65535
Another option for working with 16-bit tiff files is OpenCV-Python. I also believe that tiffile.py can handle them, although I have not tested this myself. The reason I prefer PyLibTiff over these is that it can be installed into a virtual environment using pip.