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function densities = PhotopigmentAxialDensity(receptorTypes,species,source,fieldSizeDegrees)
% densities = PhotopigmentAxialDensity(receptorTypes,[species],[source],[fieldSizeDegrees])
%
% Return estimates of photopigment axial density, sometimes called peak
% absorbance.
%
% Allowable receptor types depend on species and source, but the general
% list is:
% SCone, MCone, LCone, FovealSCone, FovealMCone, FovealLCone, Rod.
%
% The type argument may be a single string or a cell array of strings. If it
% is an array, a column vector of values is returned.
%
% The foveal version of cone types is sensible only for primates. Not all
% estimate sources support all receptor types.
%
% Note that the following three numbers are overdetermined: photopigment
% specific density (sd), photopigment axial density (ad), and outer segment
% length osl. In particular, ad = sd*osl. Depending on the measurement
% method, different sources provide different pairs of these numbers.
% We have attempted to enforce this consistency in the set of routines
% PhotopigmentSpecificDensity, PhotopigmentAxialDensity, and PhotoreceptorDimensions.
% That is to say, for the same source, species, and cone type, you should get
% a consistent triplet of numbers.
%
% Supported species:
% Human (Default).
%
% Supported sources:
% Rodieck (Human) (Default).
% StockmanSharpe (Human).
% CIE (Human).
% Tsujimura (Human; melanopsin-containing RGCs)
%
% The CIE method takes a field size argument. This
% overrides the specified foveal or not part of the
% cone string. If the field type is not passed and
% the method is CIE, it is set to 10-degrees for SCone, MCone,
% and LcCne, and to 2-degrees for FovealSCone, FovealMCone, and
% FovealLCone.
%
% The fieldSizeDegrees argument is ignored for sources other than
% CIE.
%
% 7/11/03 dhb Wrote it.
% 8/12/11 dhb Added CIE source, and allow passing of fieldSizeDegrees.
% 4/20/12 dhb Add Tsujimura's estimate of melanopsin optical density in human.
% 12/16/12 dhb, ms Add Alpern's rod estimates from CVRL table.
% Fill in defaults
if (nargin < 2 || isempty(species))
species = 'Human';
end
if (nargin < 3 || isempty(source))
source = 'Rodieck';
end
if (nargin < 4 || isempty(fieldSizeDegrees))
fieldSizeDegrees = [];
end
% Fill in specific density according to specified source
if (iscell(receptorTypes))
densities = zeros(length(receptorTypes),1);
else
densities = zeros(1,1);
end
for i = 1:length(densities)
if (iscell(receptorTypes))
type = receptorTypes{i};
elseif (i == 1)
type = receptorTypes;
else
error('Argument receptorTypes must be a string or a cell array of strings');
end
switch (source)
case {'Rodieck'}
switch (species)
case {'Human'},
% Rodieck, The First Steps in Seeing, Appendix B.
switch (type)
case {'FovealLCone','FovealMCone','FovealSCone'}
densities(i) = 0.50;
case 'Rod'
densities(i) = 0.47;
otherwise,
error(sprintf('Unsupported receptor type %s for %s estimates in %s',type,source,species));
end
otherwise,
error(sprintf('%s estimates not available for species %s',source,species));
end
case {'Alpern'}
% This value from the CVRL table of receptor optical density. There are 3 papers from
% Alpern's lab cited, with values of 0.342 (Alpern & Pugh, 1974), 0.342 (Zwas & Aloper, 1976), and
% 0.318 (Zwas & Alpern, 1976). The value of 0.333 here is roughly the mean of these.
switch (species)
case {'Human'}
switch (type)
case 'Rod'
densities(i) = 0.333;
otherwise,
error(sprintf('Unsupported receptor type %s for %s estimates in %s',type,source,species));
end
otherwise
error(sprintf('%s estimates not available for species %s',source,species));
end
case {'StockmanSharpe'}
switch (species)
case {'Human'},
% Foveal values from Note c, Table 2, Stockman and Sharpe (2000), Vision Research. These
% are the values they used to produce a fit to their 2-degree fundamentals. The peripheral
% values were provided to me by Andrew Stockman, and were used to produce a fit to their
% 10-degree fundamentals.
switch (type)
case {'FovealLCone','FovealMCone'}
densities(i) = 0.50;
case 'FovealSCone'
densities(i) = 0.40;
case {'LCone', 'MCone'}
densities(i) = 0.38;
case {'SCone'}
densities(i) = 0.3;
otherwise,
error(sprintf('Unsupported receptor type %s for %s estimates in %s',type,source,species));
end
otherwise,
error(sprintf('%s estimates not available for species %s',source,species));
end
case {'CIE'}
switch (species)
case {'Human'},
% These values computed according to formulae in CIE 170-1:2006.
switch (type)
case {'FovealLCone','FovealMCone'}
if (isempty(fieldSizeDegrees))
fieldSizeDegrees = 2;
end
densities(i) = 0.38+0.54*exp(-fieldSizeDegrees/1.333);
case 'FovealSCone'
if (isempty(fieldSizeDegrees))
fieldSizeDegrees = 2;
end
densities(i) = 0.30+0.45*exp(-fieldSizeDegrees/1.333);
case {'LCone', 'MCone'}
if (isempty(fieldSizeDegrees))
fieldSizeDegrees = 10;
end
densities(i) = 0.38+0.54*exp(-fieldSizeDegrees/1.333);
case {'SCone'}
if (isempty(fieldSizeDegrees))
fieldSizeDegrees = 10;
end
densities(i) = 0.30+0.45*exp(-fieldSizeDegrees/1.333);
otherwise,
error(sprintf('Unsupported receptor type %s for %s estimates in %s',type,source,species));
end
otherwise,
error(sprintf('%s estimates not available for species %s',source,species));
end
case {'Tsujimura'}
switch (species)
case {'Human'},
switch (type)
case {'Melanopsin'}
densities(i) = 0.50;
otherwise,
error(sprintf('Unsupported receptor type %s for %s estimates in %s',type,source,species));
end
otherwise,
error(sprintf('%s estimates not available for species %s',source,species));
end
otherwise
error(sprintf('Unknown source %s for specific density estimates',source));
end
end
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