BioimagingTutorial_2025

IT introduction for BioimagingTutorial (summer 2025)

Installation of Miniconda

1. Open a web browser and visit https://docs.conda.io/en/latest/miniconda.html.
2. Download the correct software version for your operating system.
3. Start the installation and follow the instructions

Create a virtual environment for Python

Windows user should execute conda commands from the anaconda prompt (has been installed together with miniconda). Linux and macOS users may use their default terminals

• Windows: From the start menu, search for "Anaconda Prompt" and open it.
• macOS and Linux: Open a terminal

Execute the following command in your command prompt:

conda create -n napari python=3.9

Once the virtual environment has been generated, activate it with this command:

conda activate napari

Access to BioimagingTutorial_2025 folder and install the requirements

Make sure that your virtual environment is activated. Execute the following commands in your command prompt:

cd BioimagingTutorial_2025
pip install -r requirements.txt

all the required python packages listed in the file "requirements.txt" will be installed.

Start Jupyter Lab

Start jupyter lab from the console within the bio325_2024 folder:

jupyter-lab