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@bdunnette
bdunnette / bioformats-extract-tile.py
Last active March 17, 2022 09:02
Example of extracting a tile from a BioFormats-readable file (e.g. Zeiss CZI) using python
# 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