🔬 Fluorescence ΔF/F₀ Notebook

A compact Jupyter notebook for analyzing calcium imaging data that:

1. Loads GFP (or other wide‑field) video acquisitions via imageio.
2. Computes mean fluorescence per frame.
3. Normalises to the 10th‑percentile baseline so ΔF/F₀ = 0 % means no change.
4. Computes and plots the ΔF/F₀ per frame.

Simple kick-starter for python analysis of MCAM video data!

Setup

Conda

1. Create the environment

conda env create -f environment.yml

2. Activate the environment

conda activate cardiac_organoid_deltaF

3. Start Jupyter Lab

jupyter lab fluorescence_analysis.ipynb

---

uv

uv run --with jupyter jupyter lab fluorescence_analysis.ipynb

License

MIT