1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
|
function densities = PhotopigmentSpecificDensity(receptorTypes,species,source)
% densities = PhotopigmentSpecificDensity(receptorTypes,[species],[source])
%
% Return estimates of photopigment specific densities.
%
% 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), GuineaPig.
%
% Supported sources:
% Rodieck (Human) (Default).
% Bowmaker (GuineaPig).
% Generic
% None (returns empty matrix as value)
%
% The Generic source returns a single number for all species and receptor types.
% This number is 0.015 /um.
%
% 7/11/03 dhb Wrote it.
% 8/9/13 dhb Comment clean up, allow 'None' to return empty as the value.
% Fill in defaults
if (nargin < 2 || isempty(species))
species = 'Human';
end
if (nargin < 3 || isempty(source))
source = 'Rodieck';
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 {'None'}
densities = [];
case {'Generic'}
densities(i) = 0.015;
case {'Bowmaker'}
switch (species)
case 'GuineaPig',
% Specific density measured in Guinea Pig.
% In Parry JWL, Bowmaker JK, 2002 paper
% transverse measurement: OD in table Table 1
% in the order of [M, S, Rod]
%
% Note communication with Dr. J. Bowmaker:
% "The OD values measured in msp are always somewhat suspect
% snd this is more so for mammalian cones - the outer segments
% tend to collapse and because of their small size it is difficult
% to ensure that the measuring beam is totally within the outer segment.
%
% "Because we use light polarized perpendicular to the long axis of
% the os, you can simply multiply the specific density by the length
% of the OS to give an axial OD. The values will be in the right order of
% magnitude, but could be out be a factor of 2 or 3."
%
% Also see http://cvrl.ucl.ac.uk, section on photopigment optical density.
% Start with the transverse optical densities
% and use to calculate an estimate of the specific densities. The
% diameter in the transverse measurement is roughly the pathlength,
% so we divide by that to get the specific density.
switch (type)
case {'MCone'}
transverseOD = 0.009;
OSdiameter = PhotoreceptorDimensions('MCone','OSdiam','GuineaPig','SterlingLab');
densities(i) = transverseOD/OSdiameter;
case 'SCone',
transverseOD = 0.008;
OSdiameter = PhotoreceptorDimensions('SCone','OSdiam','GuineaPig','SterlingLab');
densities(i) = transverseOD/OSdiameter;
case 'Rod'
transverseOD = 0.021;
OSdiameter = PhotoreceptorDimensions('Rod','OSdiam','GuineaPig','SterlingLab');
densities(i) = transverseOD/OSdiameter;
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 {'Rodieck'}
switch (species)
case {'Human'},
% Rodieck, The First Steps in Seeing, p. 472 gives a value for
% axial specific density for rods and cones as about 0.015 /um.
% Here we compute these numbers from his estimate of outersegment
% length and axial optical density. This enforces consistency
% across different ways of getting the same number.
switch (type)
case {'FovealLCone','FovealMCone','FovealSCone','Rod'}
OSlength = PhotoreceptorDimensions(type,'OSlength',species,source);
axialOpticalDensity = PhotopigmentAxialDensity(type,species,source);
densities(i) = axialOpticalDensity ./ OSlength;
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
|
