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################################ | |
# (c) Daniel Fürth, 2016 | |
# Spatial Transcriptomics with WholeBrain | |
################################ | |
#set the anterior poster coordinate of brin section in millimeter | |
coordinate.for.section<- -0.42 | |
#set filter for Cy3 spots | |
feature.filter <-structure(list(alim = c(120, 1000), threshold.range = c(14L, 255 | |
), eccentricity = 1000L, Max = 70, Min = 0, brain.threshold = 1L, | |
resize = 0.08*0.25, blur = 4L, downsample = 0.125/2), .Names = c("alim", | |
"threshold.range", "eccentricity", "Max", "Min", "brain.threshold", | |
"resize", "blur", "downsample")) | |
#set filter for H&E nuclei and the background of the brain section | |
cell.body.filter <-structure(list(alim = c(3, 50), threshold.range = c(140L, | |
255L), eccentricity = 1000L, Max = 200, Min = 10, brain.threshold = 50L, | |
resize = 0.08*0.20, blur = 4L, downsample = 0.25), .Names = c("alim", | |
"threshold.range", "eccentricity", "Max", "Min", "brain.threshold", | |
"resize", "blur", "downsample")) | |
#file paths | |
HandE.file<-'~/Downloads/160919_SE2_St&Th_ID3_E1_H&E_AJu.jpg' | |
Cy3.file<-'~/Downloads/161006_SE2_St&Th_ID3_E1_Cy3_AJu.jpg' | |
temp<-spatial.transcriptomics(HandE.file, Cy3.file, feature.filter, cell.body.feature) | |
#registration | |
regi<-registration(temp$filename, coordinate= coordinate.for.section, filter=cell.body.filter, right.hemisphere=FALSE) | |
#EDIT the registration: | |
regi <-remove.corrpoints(regi, 1:32) #remove all 32 corrpoints and overwrite original registration | |
regi<-add.corrpoints(regi, 32) #manually add 32 unique corrpoints both in Target (right, purple) and in Reference (orange, left) | |
#regi<-change.corrpoints(regi, c(13,14,16)) #if I just want to change corrpoint 13 and 14 and 16 in the Target image | |
#rerun the registration with the new corrpoints by adding correspondance=regi | |
regi<-registration(temp$filename, coordinate= coordinate.for.section, filter=cell.body.filter, right.hemisphere=FALSE, correspondance=regi) | |
#get the data set | |
dataset<-inspect.registration(regi, temp$features, forward.warps=TRUE, draw.trans.grid=FALSE) | |
head(dataset) | |
dataset$animal<-'ID3_E1' | |
#plot the section | |
schematic.plot(dataset) |
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