hyperspectral

Finding the limit of the number fluorescent molecules we can distinguish

Imaging model

We illuminate the four fluorophores with four wavelengths. We generate the Fisher information matrix and calculate figures of merit to access how well each fluorophore can be imaged.

Overview

The main scripts are Model.ipynb and demo.ipynb. View these scripts in action with by running

streamlit run User_Interface.py

Directory structure

fluoro_spectra

• fluorophore excitation and emission spectra data in CSV files
• downloaded from FPbase

fluorophore-spectra

• repeat of fluoro_spectra with an added test file

FOM

• calculated figures of merit for each fluorophore
• generated from Model.ipynb

Figures

• variation of plots generated from plotting/* and Model.ipynb

playground

• scripts for temporary testing and comparison

quantum-efficiency-data

• detector quantum efficiency data in CSV files
• ORCA-Fusion BT camera
• script generating plots of the data

Dependencies

• numpy
• pandas
• matplotlib
• notebook/ipython
• streamlit