Excitation Spectrum with MATLAB

Shows the range of wavelengths that can excite a fluorophore and induce fluorescence. Each fluorophore has a unique excitation spectrum that depends on its molecular structure.

Fluorescence Excitation | ViaDean亚图跨际 on Notion

🌵MATLAB snippet

To create or analyze an excitation spectrum using MATLAB, you need to plot the intensity of fluorescence as a function of excitation wavelength. Below is an outline of how to generate such a spectrum in MATLAB:

Steps to Plot an Excitation Spectrum in MATLAB:

1. Collect Data: Gather experimental data or simulate data where you have excitation wavelengths and corresponding fluorescence intensities.

2. Load Data into MATLAB: You can manually input data or import it from a file (e.g., .csv or .txt).

3. Plot the Data: Use MATLAB's plotting functions to create the excitation spectrum.

Sample MATLAB Code:

Here's a basic script to plot an excitation spectrum from data.

 % Sample data for demonstration (replace with actual data)
 excitation_wavelengths = 300:10:700; % Example wavelengths (in nm)
 fluorescence_intensities = rand(1, length(excitation_wavelengths)) * 100; % Replace with your data
 ​
 % Plot the excitation spectrum
 figure;
 plot(excitation_wavelengths, fluorescence_intensities, '-o', 'LineWidth', 1.5);
 title('Excitation Spectrum');
 xlabel('Excitation Wavelength (nm)');
 ylabel('Fluorescence Intensity (a.u.)');
 grid on;
 xlim([min(excitation_wavelengths), max(excitation_wavelengths)]);

Explanation:

• excitation_wavelengths: Replace this vector with your actual excitation wavelengths.

• fluorescence_intensities: Replace with the fluorescence intensity data for each wavelength.

• The plot function is used to create a line plot, with optional markers for clarity.

• Adjust the LineWidth and markers as needed for better visualization.

Loading Data from a File:

If you have data in a file, such as a CSV:

 % Load data from a CSV file (assumes two columns: wavelengths and intensities)
 data = csvread('excitation_data.csv', 1, 0); % Skip the first row if it has headers
 excitation_wavelengths = data(:, 1); % First column: wavelengths
 fluorescence_intensities = data(:, 2); % Second column: intensities
 ​
 % Plot the data
 plot(excitation_wavelengths, fluorescence_intensities, '-o', 'LineWidth', 1.5);
 title('Excitation Spectrum');
 xlabel('Excitation Wavelength (nm)');
 ylabel('Fluorescence Intensity (a.u.)');
 grid on;

Customizing the Plot:

• title, xlabel, ylabel: Add labels and a title to provide context.

• Grid and Line Customization: grid on improves readability, and you can adjust the line style (e.g., '-', '--', '-.').

• Color Customization: Add ,'Color', [0 0.5 0.8] to set a specific color.

Additional Features:

• Smoothing: Use smooth or movmean to reduce noise in the data.

• Fitting: Fit a curve to the data using fit or polyfit to identify peaks and characteristics of the spectrum.

 % Example of smoothing data
 smoothed_intensity = smooth(fluorescence_intensities);
 plot(excitation_wavelengths, smoothed_intensity, '-r', 'LineWidth', 2);

With these steps, you can generate and customize an excitation spectrum plot in MATLAB, aiding in the visualization and analysis of fluorescence excitation data.