#variable numbers
RESOLUTION_var <- 512
SPIN_resolution <- 64
my_lambda <- 0.001
# Run retistruct()
# Markup the retina's incisions
# Set eye to Left or Right eye
# Set a most dorsal, or most nasal point on the retina
# 'Save' and close the retistruct GUI
Ntae_381_coords <- data.frame( minX = 42, #the leftmost counting frame's X value
maxX = 597, #the rightmost counting frame's X value (from the ImageJ outline PNG)
deltaX = ((597-42)/17), #the average ImageJ pixel distance (in the X axis) between counting frame locations from the outline image.
minY = -584, #bottommost counting frame's Y value
maxY = -32, #the topmost counting frame's Y value
deltaY = (584-32)/17 ) #the average ImageJ pixel distance (in the Y axis) between counting frame locations from the outline image.
Ntae_381<- retina_object(
path = system.file(package = "retina", 'extdata/Ntae_381'),
#Eye Measurements
LD = NULL,
ED = 4.508 , #ED EYE DIAMETER (at the hemisphere) in mm
AL = 3.1395 ,#AL Axial Length (from front to back of eye) in mm
#Stereology Parameters
height = 25 ,# height of the counting frame in microns
width = 25, # width of the counting frame in microns
#Plotting Parameters
lambda=my_lambda ,#defines the smoothing parameter for thin plate spline interpolation (see fields::Tps for more information)
extrapolate=TRUE ,#when true, the plotter will create a full representation of the hemisphere even outside of the bounds of measured points.
spatial_res=RESOLUTION_var, #number of pixels wide the plotter will use. a value of 1000 will create a 1000x1000 pixel plot
rotation_ccw= -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.
#ImageJ Datapoint Calibration Measurements
IJcoords = Ntae_381_coords,
plot_suppress=TRUE
#End parameter Specification
)
Pmol_753_coords <- data.frame( maxX=1437,
maxY=-45,
minX=469,
minY=-1029,
deltaX=60,
deltaY=61) #the average ImageJ pixel distance (in the Y axis) between counting frame locations from the outline image.
Pmol_753 <- retina_object(
path = system.file(package = "retina", 'extdata/Pmol_753'),
#Eye Measurements
ED = 4.8,
AL = 3.43,
LD = 1.8,
#Stereology Parameters
height = 25 ,# height of the counting frame in microns
width = 25, # width of the counting frame in microns
#Plotting Parameters
lambda = my_lambda ,#defines the smoothing parameter for thin plate spline interpolation (see fields::Tps for more information)
extrapolate = TRUE ,#when true, the plotter will create a full representation of the hemisphere even outside of the bounds of measured points.
spatial_res = RESOLUTION_var, #number of pixels wide the plotter will use. a value of 1000 will create a 1000x1000 pixel plot
rotation_ccw = -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.
plot_suppress=TRUE,
#ImageJ Datapoint Calibration Measurements
IJcoords = Pmol_753_coords)
Pmol_752_coords <- data.frame(maxX=848,
maxY=-48,
minX=40,
minY=-965,
deltaX=(848-40)/15,
deltaY=(965-48)/17) #the average ImageJ pixel distance (in the Y axis) between counting frame locations from the outline image.
## this part demonstrates how to combine sampling site count data, with your manually recorded XY location of each sampling site.
ssites <- read.csv(system.file(package = "retina", 'extdata/Pmol_752/Pmol_752_ssite_locations.csv'))
counts <- read.csv(system.file(package = "retina", 'extdata/Pmol_752/Pmol_site_counts.csv'))
colnames(ssites) <- c("x", "y", "samplingsite")
colnames(counts) <- c("samplingsite", "count")
Pmol_752_xyz <- ssite_merge(ssites,counts)
colnames(Pmol_752_xyz) <- c("x","y","z")
write.csv(Pmol_752_xyz, system.file(package = "retina", 'extdata/Pmol_752/xyz.csv'), row.names=FALSE)
Pmol_752 <- retina_object(
path = system.file(package = "retina", 'extdata/Pmol_752'),
ED=5.225,
AL=3.9,
LD=2.05,
height = 25,
width = 25,
lambda = my_lambda,
extrapolate=TRUE,
spatial_res = RESOLUTION_var,
rotation_ccw = -90,
plot_suppress=TRUE,
IJcoords = Pmol_752_coords)
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