Setup

Setting up an environment for converting images

The conversion tools need access to the bioformats2raw executable. There are various ways to install this, the easiest is probably via conda.

Once installed, the environment variables BIOFORMATS2RAW_JAVA_HOME and BIOFORMATS2RAW_BIN are used to specify the install location.

These can be set by adding them to a .env file in the tools directory, for example:

BIOFORMATS2RAW_JAVA_HOME=/Users/matthewh/miniconda3/envs/bf2zarr/lib/jvm
BIOFORMATS2RAW_BIN=/Users/matthewh/miniconda3/envs/bf2zarr/bin/bioformats2raw