Boston Bioimage Analysis Course (BoBIAC)

Teaching materials for Boston Bioimage Analysis Course (BoBIAC).

Install juv

After installing uv:

uv tool install juv

Then to use any command you run:

juv [OPTIONS] COMMAND [ARGS]...

If you do not want to install it, you can run juv with:

uvx juv [OPTIONS] COMMAND [ARGS]...

Create a notebook

juv init notebook.ipynb
juv init --python=3.12 notebook.ipynb # specify a minimum Python version

Add dependencies to the notebook

juv add notebook.ipynb "ndv[vispy,jupyter]" tifffile

# or

juv add notebook.ipynb package-name --requirements=requirements.txt

Launch the notebook

# Launch the notebook
juv run notebook.ipynb

# or

juv run --with=pyqt6 notebook.ipynb # additional dependencies for this session (not saved)
juv run --jupyter=nbclassic notebook.ipynb -- --no-browser # pass additional arguments to Jupyter

Course Structure

The course materials are organized in the following folders:

• 00_intro_bioimage_analysis/: Introduction to bioimage analysis concepts and tools
• 01_intro_fluorescence_microscopy/: Basics of fluorescence microscopy
• 02_intro_python_1/: First part of Python programming introduction
• 03_intro_python_2/: Second part of Python programming introduction

Each folder contains Jupyter notebooks, both the teacher version and the student version.