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function photoreceptors = DefaultPhotoreceptors(kind)
% photoreceptors = DefaultPhotoreceptors(kind)
%
% Return a structure containing default sources
% for photoreceptor complements of various kinds.
%
% Available kinds
% LivingHumanFovea (Default) - Human foveal cones in the eye
% CIE2Deg - Leads to CIE 2-Deg fundamentals
% CIE10Deg - Leads to CIE 10-Deg fundamentals
% LivingHumanMelanopsin - Most recent melanopsin spectral sensitivity in living eye.
% LivingHumanMelanopsinTsujimura2010 - Older estimate of melanopsin gc spectral sensitivity in living eye
% LivingDog - Canine
% GuineaPig - Guinea pig in dish
%
% See also: FillInPhotoreceptors, PrintPhotoreceptors, RetIrradianceToIsoRecSec
% IsomerizationsInEyeDemo, IsomerizationsInDishDemo, ComputeCIEConeFundamentals,
% RodFundamentalTest, MelanopsinFundamentalTest.
%
% 7/25/03 dhb Wrote it.
% 12/04/07 dhb Added dog parameters
% 8/14/11 dhb Added fieldSizeDegrees and ageInYears fields to photoreceptors for LivingHumanFovea case.
% These defaults match the CIE standard.
% 4/20/12 dhb Add LivingHumanMelanopsin
% 5/10/12 dhb Changed name for LivingHumanMelanopsin to postpend Tsujimura2010
% 8/12/13 dhb Change field order to make printouts look nicer.
% 11/13/13 dhb Add 'LivingHumanRod' and 'LivingHumanMelanopsin' options.
% 5/26/14 dhb Add pupilDimater.value = [] to fix FillInPhotoreceptors.
% 1/11/21 dhb Comment tuning.
% Default
if (nargin < 1 || isempty(kind))
kind = 'LivingHumanFovea';
end
% Fill it in
switch (kind)
% CIE 2-Deg fundamentals
case 'CIE2Deg'
photoreceptors.species = 'Human';
photoreceptors.types = {'FovealLCone' 'FovealMCone' 'FovealSCone'};
photoreceptors.nomogram.S = WlsToS((390:5:780)');
photoreceptors.OSlength.source = 'None';
photoreceptors.ISdiameter.source = 'Rodieck';
photoreceptors.specificDensity.source = 'None';
photoreceptors.axialDensity.source = 'CIE';
photoreceptors.nomogram.source = 'None';
photoreceptors.quantalEfficiency.source = 'Generic';
photoreceptors.fieldSizeDegrees = 2;
photoreceptors.ageInYears = 32;
photoreceptors.pupilDiameter.value = 3;
photoreceptors.eyeLengthMM.source = 'Rodieck';
photoreceptors.absorbance = 'log10coneabsorbance_ss';
photoreceptors.lensDensity.source = 'CIE';
photoreceptors.macularPigmentDensity.source = 'CIE';
% CIE 10-Deg fundamentals
case 'CIE10Deg'
photoreceptors.species = 'Human';
photoreceptors.types = {'LCone' 'MCone' 'SCone'};
photoreceptors.nomogram.S = WlsToS((390:5:780)');
photoreceptors.OSlength.source = 'None';
photoreceptors.ISdiameter.source = 'Webvision';
photoreceptors.specificDensity.source = 'None';
photoreceptors.axialDensity.source = 'CIE';
photoreceptors.nomogram.source = 'None';
photoreceptors.quantalEfficiency.source = 'Generic';
photoreceptors.fieldSizeDegrees = 10;
photoreceptors.ageInYears = 32;
photoreceptors.pupilDiameter.value = 3;
photoreceptors.eyeLengthMM.source = 'Rodieck';
photoreceptors.absorbance = 'log10coneabsorbance_ss';
photoreceptors.lensDensity.source = 'CIE';
photoreceptors.macularPigmentDensity.source = 'CIE';
% LivingHumanRod
%
% The choices of values here were chosen in the Brainard
% lab (by Manuel Spitschan) to provide a pretty good fit to the CIE
% 1924 scotopic sensitivity curve. Many combinations of lambda max,
% nomogram, and axial densitiy will provide a good fit. We chose the ones
% below because the lambda-max and axial density parameters seem
% in accord with values in the literature and the fit is quite good.
% Ref [1] gives lambda max of 491, and the average of the rod axial density values in
% [2] and [3] is the value 0.334.
%
% See RodFundamentalTest to obtain a plot of the agreement with the tabulated 1924 function.
%
% Depending on what you are using this for, you may want to override the default 3 mm pupil.
%
% [1] Baylor DA, Nunn BJ, Schnapf JL. The photocurrent, noise, and spectral
% sensitivity of rods of the monkey Macaca fascicularis. J Physiol. 1984; 357: 575?607.
%
% [2] Alpern, M. & Pugh, E.N. (1974). The density and photosensitivity of human rhodopsin in
% the living retina. Journal of Physiology, London, 237, 341-370. [0.342 from densitometry]
%
% [3] Zwas, F. & Alpern, M. (1976). The density of human rhodopsin in the rods. Vision Research 16,
% 121-127. [0.318 from brightness matching, 0.342 from dark adaptation curves]
case 'LivingHumanRod'
photoreceptors.species = 'Human';
photoreceptors.types = {'Rod'};
photoreceptors.nomogram.S = WlsToS((390:5:780)');
photoreceptors.OSlength.source = 'None';
photoreceptors.ISdiameter.source = 'Webvision';
photoreceptors.specificDensity.source = 'None';
photoreceptors.axialDensity.source = 'Value Provided Directly';
photoreceptors.axialDensity.value = 0.334;
photoreceptors.nomogram.source = 'Govardovskii';
photoreceptors.nomogram.lambdaMax = 491;
photoreceptors.quantalEfficiency.source = 'Generic';
photoreceptors.fieldSizeDegrees = 10;
photoreceptors.ageInYears = 32;
photoreceptors.pupilDiameter.value = 3;
photoreceptors.eyeLengthMM.source = 'Rodieck';
photoreceptors.lensDensity.source = 'CIE';
photoreceptors.macularPigmentDensity.source = 'CIE';
% LivingHumanMelanopsin
%
% The choices of values here were chosen in the Brainard
% lab to privde an estimate of a reasonable fundamental for
% melanopin ipRGCs. We follow work from the Lucas lab [1,2]
% and use a very low (essentially zero) axial density and no
% macular pigment (because the ipRGCs are in front of most of
% the macular pigment, as we understand it [3]. We inherit the
% CIE standard for lens density, and this can be adjusted via
% the CIE formulae by overriding the default age and pupil size
% parameters.
%
% [1] Enezi, J, Revell, V, Brown, T, Wynne, J, Schlangen, L. & Lucas, R. (2011).
% A "melanopic" spectral efficiency function predicts the sensitivity of melanopsin
% photoreceptors to polychromatic lights. J Biol Rhythms 26(4), 314-23.
% doi: 10.1177/0748730411409719
%
% [2] Brown, T, Allen, A, Al-Enezi, J., Wynne, J., Schlangen, L., Hommes, V. & Lucas, R. (2013).
% The Melanopic Sensitivity Function Accounts for Melanopsin-Driven Responses in Mice under
% Diverse Lighting Conditions. PLoS One, 8(1), e53583. doi: 10.1371/journal.pone.0053583.
%
% [3] Vienot, F., Brettel, H., Dang, T.V., Le Rohellec, J. (2012). Domain of metamers exciting
% intrinsically photosensitive retinal ganglion cells (ipRGCs) and rods. J Opt Soc Am A Opt
% Image Sci Vis. 29(2): A366-76. doi: 10.1364/JOSAA.29.00A366.
case 'LivingHumanMelanopsin'
photoreceptors.species = 'Human';
photoreceptors.types = {'Melanopsin'};
photoreceptors.nomogram.S = WlsToS((390:5:780)');
photoreceptors.axialDensity.source = 'Value provided directly';
photoreceptors.axialDensity.value = 0.015;
photoreceptors.nomogram.source = 'Govardovskii';
photoreceptors.nomogram.lambdaMax = 480;
photoreceptors.quantalEfficiency.source = 'Generic';
photoreceptors.fieldSizeDegrees = 10;
photoreceptors.ageInYears = 32;
photoreceptors.pupilDiameter.value = 3;
photoreceptors.lensDensity.source = 'CIE';
photoreceptors.macularPigmentDensity.source = 'None';
case 'LivingHumanFovea'
photoreceptors.species = 'Human';
photoreceptors.types = {'FovealLCone' 'FovealMCone' 'FovealSCone'};
photoreceptors.nomogram.S = [380 1 401];
photoreceptors.OSlength.source = 'Rodieck';
photoreceptors.ISdiameter.source = 'Rodieck';
photoreceptors.specificDensity.source = 'Rodieck';
photoreceptors.nomogram.source = 'StockmanSharpe';
photoreceptors.nomogram.lambdaMax = [558.9 530.3 420.7]';
photoreceptors.quantalEfficiency.source = 'Generic';
photoreceptors.fieldSizeDegrees = 2;
photoreceptors.ageInYears = 32;
photoreceptors.pupilDiameter.source = 'PokornySmith';
photoreceptors.pupilDiameter.value = [];
photoreceptors.eyeLengthMM.source = 'Rodieck';
photoreceptors.lensDensity.source = 'StockmanSharpe';
photoreceptors.macularPigmentDensity.source = 'Bone';
% This creates Tsujiumura's (2010) estimate of the melanopsin gc
% spectral sensitivity in the human eye. The quantal efficiency
% is just made up, though, so that the code runs.
%
% Tsujimura has used different lambda-max in different papers.
% The 482 value given here is from the 2010 paper. His email
% suggests he may have used 489 and 502 at different times. Also
% by email, he used Stockman-Sharpe not Govardovskii nomogram
% for the 2010 paper, despite what the paper says.
%
% The value Tsujimura uses for axial density seems way too high,
% given what the physiologists tell us about the fact that
% the melanopsin receptors live in a very thin layer in the ganglion
% cells.
case 'LivingHumanMelanopsinTsujimura2010'
photoreceptors.species = 'Human';
photoreceptors.types = {'Melanopsin'};
photoreceptors.nomogram.S = [380 1 401];
photoreceptors.axialDensity.source = 'Tsujimura';
photoreceptors.axialDensity.value = 0.5;
photoreceptors.nomogram.source = 'StockmanSharpe';
photoreceptors.nomogram.lambdaMax = [482]';
photoreceptors.quantalEfficiency.source = 'None';
photoreceptors.quantalEfficiency.value = 1;
photoreceptors.fieldSizeDegrees = 10;
photoreceptors.ageInYears = 32;
photoreceptors.lensDensity.source = 'CIE';
photoreceptors.macularPigmentDensity.source = 'CIE';
case 'LivingDog'
photoreceptors.species = 'Dog';
photoreceptors.types = {'LCone' 'SCone' 'Rod'};
photoreceptors.nomogram.S = [380 1 401];
photoreceptors.OSlength.source = 'PennDog';
photoreceptors.ISdiameter.source = 'PennDog';
photoreceptors.specificDensity.source = 'Generic';
photoreceptors.pupilDiameter.source = 'PennDog';
photoreceptors.pupilDiameter.value = [];
photoreceptors.eyeLengthMM.source = 'PennDog';
photoreceptors.nomogram.source = 'Govardovskii';
photoreceptors.nomogram.lambdaMax = [555 429 506]';
photoreceptors.quantalEfficiency.source = 'Generic';
photoreceptors.lensDensity.source = 'None';
photoreceptors.macularPigmentDensity.source = 'None';
case 'GuineaPig'
photoreceptors.species = 'GuineaPig';
photoreceptors.types = {'MCone' 'SCone' 'Rod'};
photoreceptors.nomogram.S = [380 1 401];
photoreceptors.OSlength.source = 'SterlingLab';
photoreceptors.OSdiameter.source = 'SterlingLab';
photoreceptors.ISdiameter.source = 'SterlingLab';
photoreceptors.specificDensity.source = 'Bowmaker';
photoreceptors.pupilDiameter.source = 'None';
photoreceptors.pupilDiameter.value = [];
photoreceptors.eyeLengthMM.source = 'None';
photoreceptors.nomogram.source = 'Govardovskii';
photoreceptors.nomogram.lambdaMax = [529 430 500]';
photoreceptors.quantalEfficiency.source = 'Generic';
photoreceptors.lensDensity.source = 'None';
photoreceptors.macularPigmentDensity.source = 'None';
otherwise
error('Unknown photoreceptor kind specified');
end
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