FRET Simulation Dataset

Datafiles contain over 3 million simulated noisy FRET spectra which can be used for validating FRET analysis approaches. The same data is formatted for both matlab and python. The matlab file can be read in with each of the components as a separate variable. The python numpy array can be read in and then converted to a dictionary containing each component using numpy.load(‘YourFilepath’).item().Matlab Variable/Python Dictionary Entry: ’Simulated Pixels’: These are simulated noisy spectra covering a range of SNR and FRET efficiencies, organized in the following manner: Simulated_Pixels[N,Power,Efficiency,Excitation,Emission], where N are repeat simulations to calculate statistics with (1000 simulations for every condition). Has an overall shape of (1000, 150, 11, 2, 32). ’sRET luxFRET Calibration Spectra’: These are noiseless calibration spectra organized in the following manner: sRET luxFRET Calibration Spectra[Power,Donor or Acceptor,Excitation,Emission], with an overall shape of (150, 2, 2, 32). These spectra can also be used to calculate the normalized emission spectra and gamma parameter needed for sensorFRET, but we also included those values separately for convenience. ’Power Vector’: The vector relating the indices in the 2nd dimension of ‘Simulated Pixels’ to the simulated power used ranging from 0.1-1000 (arbitrary units) in 150 logarithmic steps to change the SNR and provide normalized residuals in the approximate range of 0.001 to 0.1. ’Efficiency Vector’: The vector relating the indices in the 3rd dimension of ‘Simulated Pixels’ to the simulated FRET efficiency ranging from 0 to 1 in 11 linear steps. ’Excitation Wavelength Vector’: The vector relating the indices of the 4th dimension of ‘Simulated Pixels’ to the simulated Excitation wavelength, either 405 or 458. ’Emission Wavelength Vector’: The vector relating the indices of the 5th dimension of ‘Simulated Pixels’ to the simulated Emission Wavelengths, ranging from 416 to 718 in 32 linear steps to match the spectral resolution of our experiments. ’Normalized Emission Spectra’:An array containing the normalized emission shapes for the Cerulean and Venus fluorophores (shape of (2, 32)). ’Gamma’: the sensorFRET gamma parameter for the Cerulean/Venus-405/458 pairing, 0.0605 (from experiment) ’Qd’: the quantum efficiency of Cerulean, 0.62. ’Qa’: the quantum efficiency of Venus, 0.57.