Example of extracting a tile from a BioFormats-readable file (e.g. Zeiss CZI) using python

bioformats-extract-tile.py

# Requires both javabridge and python-bioformats:
#   pip install python-bioformats

# On e.g. Ubuntu you may need to add JAVA_HOME to /etc/profile:
#   JAVA_HOME=/usr/lib/jvm/default-java
#   PATH=$PATH:$HOME/bin:$JAVA_HOME/bin
#   export JAVA_HOME
#   export JRE_HOME
#   export PATH

import sys
import os
from PIL import Image
import javabridge as jv
import bioformats as bf
jv.start_vm(class_path=bf.JARS)

path = sys.argv[1]
# print(dir(bf))
TILE_SIZE = 256

with bf.ImageReader(path, perform_init=True) as reader:
    rdr = reader.rdr
    # data = reader.rdr.openBytes(0, 0, 0, 256, 256)
    image_x = rdr.getSizeX()/2
    image_y = rdr.getSizeY()/2
    image_data = reader.rdr.openBytesXYWH(
        0, image_x, image_y, TILE_SIZE, TILE_SIZE)
    # print(bytearray(image_data))
    i = Image.frombytes('RGB', (TILE_SIZE, TILE_SIZE), image_data)
    filename = '_'.join([os.path.splitext(path)[0], str(image_x),
                         str(image_y), str(TILE_SIZE), str(TILE_SIZE)]) + '.png'
    i.save(filename, 'PNG')

jv.kill_vm()