🧬 JupyterHub Bioimage Environment

A JupyterHub-based Docker image with a pre-configured Python environment, including a wide range of tools for bioimage analysis such as:

• CellProfiler
• Cellpose
• Fiji
• Ilastik
• QuPath

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📦 Overview

This repository outlines the Docker image configuration and Jupyter proxy integration used to support image analysis tools.

Currently, the image is based on the University of Münster JupyterHub. However, we are planning to build a separate, standalone image to ensure accessibility and compatibility with various JupyterHub instances.

To build the image yourself, you can start with either:

• A standard Linux base image (e.g., ubuntu, debian)
• A JupyterHub notebook base image (e.g., from Jupyter Docker Stacks)

Make sure to install the necessary components, including:

• noVNC
• X11
• Other required dependencies for your image analysis tools

This setup enables support for GUI-based applications within the Jupyter notebook interface.

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🚀 Usage

Build the Docker Image

docker build -t bioimage-jupyter .

Run the Docker Image

docker run --name bioimage --rm --net=host -w "/usr/local/src" -e HOME="/tmp" -p 8888:8888 bioimage-jupyter:latest

Then open your browser and go to:

http://localhost:8888

The Jupyter Notebook interface will open. From there, you can access terminal, notebooks, and any installed GUI-based image analysis tools

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🧰 Installed Bioimage Tools and Plugins

No.	Tool	Version	Plugins
1	CellProfiler	v4.2.7	cellpose, imagejscript, omnipose
2	Cellpose	v2.0.5	–
3	Fiji	2.14.0	OMERO-Fiji (v5.8.6), MorphoLibJ, simple-omero-client, omero-macro-extension
4	Ilastik	v1.4.0	–
5	QuPath	v0.5.1	Cellpose (0.9.6), StarDist, OMERO extension

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🔗 Useful Links

• JupyterHub
• Jupyter Docker Stacks
• OMERO

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