Installation

without bioformats

Install Python 3.10.0, following the instructions on the official website (https://www.python.org/downloads/release/python-3100/)
Install Anaconda (https://docs.anaconda.com/free/anaconda/install/index.html)
Install the latest git version via your terminal (see https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
In the terminal window, navigate to the folder where you want to save the required code.
Type git clone https://github.com/IPMI-ICNS-UKE/DARTS.git into the terminal window and press enter. The github repository should now be cloned to your local machine. Alternatively, download the .zip file on the github-page.
In your file explorer, go to the folder “DARTS/src” and delete the (empty) folder ‘TDEntropyDeconvolution’
In the terminal window, navigate to the subfolder “src” inside the DARTS folder
Type git clone https://github.com/IPMI-ICNS-UKE/TDEntropyDeconvolution.git to clone this module to your ‘src’ folder
In the terminal window, create a conda environment DARTS with a specific python version: conda create --name DARTS python=3.10.0
Activate the conda environment: conda activate DARTS

Install the necessary packages and their dependencies by executing this command in the terminal:

pip install matplotlib stardist trackpy tomli tensorflow alive-progress openpyxl pystackreg tkcalendar tomlkit simpleitk-simpleelastix

Alternatively, install the packages separately (pip install )

with bioformats

This includes the bioformats library, which allows the import and processing of common microscopy imaging formats.

After running the steps in the section “without bioformats”, follow these steps to install python-bioformats:

Java Development Kit (JDK) needs to be installed. You can download the JDK from the official Oracle website or use OpenJDK.
The JAVA_HOME environment variable needs to be set correctly to point to the directory of your JDK installation. On Linux or MacOS you can set it temporarily with
```
export JAVA_HOME=/path/to/your/jdk
```
On Windows, you’d set it via the System Properties > Environment Variables dialog. To point to a specific version: Make sure to point to the correct version of jdk, since newer ones are not compatible. We tested successfully using v8.

After installing the JDK and setting the environment variable correctly, execute the following code in the terminal while the conda environment “DARTS” is still activated:

pip install python-bioformats

JDK installation on MacOS using homebrew

As an example, we provide here a step-by-step guide to install the java dependencies for bioformats using homebrew.

We were successfull using v8 of JDK. Install it by running

   brew install adoptopenjdk/openjdk/adoptopenjdk8

You can check which versions of Java you have installed by running

/usr/libexec/java_home -V

To set JAVA_HOME for a particular version, you can use the following

export JAVA_HOME=$(/usr/libexec/java_home -v 8)

Or add the above line to your shell configuration file (e.g., ~/.bashrc, ~/.bash_profile, ~/.zshrc) to make the change persistent across sessions.

Alternatively, you can install jenv to switch between java versions.

Install by

brew install jenv

Then integrate into shell (Use ~/.zshrc if you’re using the Zsh shell.)

echo 'export PATH="$HOME/.jenv/bin:$PATH"' >> ~/.bash_profile
echo 'eval "$(jenv init -)"' >> ~/.bash_profile
source ~/.bash_profile

Add java versions to jenv

jenv add $(/usr/libexec/java_home -v 8)

Now you can switch with

jenv global 8

Update DARTS

How to update DARTS:

Navigate to the DARTS folder in the terminal
Activate the conda env: “conda activate DARTS”
git checkout main
git pull origin main