Dear Edouard, Following is my way to collect landmark coordinate using ImageJ and R (for *R* user) 1. to set scale: Analyze/set Scale (record the distance in px and adding known distance) 2. Collecting the coordinate of landmark point: 2.1 Analyze/Set Measurements -> check on Display label (to record image name as specimen code) 2.2 Open image, then using multi-point Tools to mark your landmark points 2.3 Click m or Analyze Measure to print the result to Results window (repeat step 2.2 and 2.3 for all specimen you have) 2.4 (save your results) On Results window: File/Save As --> save result to an *.txt file. 2.5 Using R code which I wrote below to import landmark coordinate into R (PLEASE check attach file): (with *readtps(filename, nland = number of landmark points)*)
On Mon, Jun 15, 2015 at 7:59 PM, Edouard Masson-MacLean < e.massonmacl...@gmail.com> wrote: > Hello, > > Is there a guide for the complete beginner on how to use ImageJ instead of > tpsdig, especially on how to set the scale before digitizing? > > Many thanks > > Edouard > > > ----------------------------------------------------- > Edouard Masson-MacLean > PhD Candidate > Room 119 > Department of Archaeology > School of Geosciences > University of Aberdeen > St. Mary's, Elphinstone Road > Aberdeen, AB24 3UF > Scotland, UK > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- DangMau *Trinh.* Website: http://pideas.org Blog: Sharing Knowledge <http://sharingknowledge-2w.blogspot.com> Email: dmautr...@pideas.org Yahoo: trinhdangmau Skype: trinhdangmau (+84) 948765483 (+66) 816191394 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
#### read tps data from imageJ #### readtps<-function(filepath, nland = 12){ tempdata<-read.table(filepath) ##### get lable and check correspond nlandmark point to all specimen label <- tempdata["Label"] l.table<-table(label) if(length(l.table[l.table!=nland])!=0){ err<-l.table[l.table!=nland] print(err) stop("The number of landmark not equal to all specimen") } ### get x and y coordinate X<-round(tempdata["X"], 0) Y<-round(tempdata["Y"],0) XY<-cbind(X, Y) XY<-as.vector(t(XY)) n = nland m = 2 k = nrow(tempdata)/nland coords<-aperm(array(XY, c(m, n, k)), c(2,1,3)) v.names<-names(l.table) dimnames(coords)<-list(paste("LM", 1:nland, sep=""),c("X", "Y"), v.names) return(coords) }