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Research data and scripts for manuscript "Beyond Lux: Methods for Species and Photoreceptor-Specific Quantification of Ambient Light for Mammals"

journal contribution
posted on 2023-10-23, 15:22 authored by Richard McdowellRichard Mcdowell, Altug DidikogluAltug Didikoglu, Tom WoeldersTom Woelders, Mazie Gatt, Timothy M. Brown, Robert J Lucas, Roelof Hut

These files contain the raw data, analysis and scripts used to create the figures for the paper: Beyond Lux: Methods for Species and Photoreceptor-Specific Quantification of Ambient Light for Mammals

Figure 1 Data - Mammalian melanopsin spectral sensitivities

Raw & normalised cell response data:

  • Figure 1 - cell responses & lmax.xlsx

lmax fitting script:

  • Opsin_Fit-README.md
  • opsin-receptor-fitting-analysis.Rproj
  • 1.extract_and_transform.R
  • 2.fitting_procedure.R
  • 3.fig_bootstrap_results.R
  • 4.fig_RSS_per_lmax.R
  • 5.sigmoind_fits_plots.R
  • calc_sum_log_photons_gov.R
  • create_govardovskii_template.R
  • lmax_based_5p_fitting.R
  • power_to_photons.R
  • responses.xlsx
  • spectra.xlsx


Figure 2 Data - Cross-species light dosimeter validation

  • Figure 2 - ReadMe.txt

Functions:

  • plotspecs.m
  • plotvalidation.m
  • calculateerrors.m

Workspaces (Used by functions above):

  • calibration.mat
  • validation.mat


Figure 3 Data - Irradiance response curves for circadian phase shifting in C57 wild-type mouse

  • Figure 3 - raw data.xlsx


Figure 4 Data - Cross-species α-opic EDIs across different light sources

  • Figure 4 - raw data.xlsx
  • Figure 4 - SolarAngle.R
  • Figure 4 - SolarAngle.Rdata


Supplementary Figure 1 - Pre-Receptoral Filtering Data

  • Pre_R_Filter-Cornea-1-Norm_cornea_trans_data.csv
  • Pre_R_Filter-Cornea-2-Transf_Norm_Spline_Norm_cornea_trans_data.csv
  • Pre_R_Filter-Cornea-2-Transf_Norm_SplineCubic_Norm_cornea_trans_data.csv
  • Pre_R_Filter-Cornea-3-cornea.trans.data.csv
  • Pre_R_Filter-Lens-1-Norm_lens_trans_data.csv
  • Pre_R_Filter-Lens-2-Transf_Norm_Spline_Norm_lens_trans_data.csv
  • Pre_R_Filter-Lens-2-Transf_Norm_SplineCubic_Norm_lens_trans_data.csv
  • Pre_R_Filter-Lens-3-lens.trans.data.csv
  • Pre_R_Filter-Vitreous-1-Norm_vitreous_trans_data.csv
  • Pre_R_Filter-Vitreous-2-Transf_Norm_Spline_Norm_vitreous_trans_data.csv
  • Pre_R_Filter-Vitreous-2-Transf_Norm_SplineCubic_Norm_vitreous_trans_data.csv
  • Pre_R_Filter-Vitreous-3-vitreous.trans.data.csv



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