Posted by
kb011 on
Aug 21, 2014; 3:18pm
URL: http://imagej.273.s1.nabble.com/Manual-tracking-tp5009287p5009291.html
Hello,
You can easily use R to transfer your data and process it. For example, I
use the tracking plug-in TrackMate which give a lot of data, and what I do
is I just select the Track ID, X and Y positions and time using data.table.
Here is my sample code:
##name the file into s1
library (data.table)
##direct input from trackmate
NT=data.table(s1, key="TRACK_ID")
NT=NT[, list(A=TRACK_ID, X=POSITION_X, Y=POSITION_Y, T=FRAME),
by=c("TRACK_ID")]
s1a= NT[order(A, T)]
s1=s1a[,list(T=T, X=X, Y=Y, V=c(0, sqrt(diff(X)^2+diff(Y)^2))), by=c("A")]
and then just use write.table to save it:
write.table (s1, "the directory where you want to save it.csv",
sep=";", col.names=T, row.names=F)
Hope this helps.
Cheers,
Karen
ᐧ
On Thu, Aug 21, 2014 at 3:21 PM, Daniel Roberts <
[hidden email]
> wrote:
> I havent used ImageJ in a while for animal movement studies, but I find
> Spatial Ecology (formerly Hawthes Tools) useful, however, it is platformed
> to ArcGIS 10x.... But the approach and concepts may be useful.
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> Guilherme Barbosa
> Sent: Thursday, August 21, 2014 6:32 AM
> To:
[hidden email]
> Subject: Manual tracking
>
> Hello,
>
> After colecting a whole dataset on manual tracking plugins on IMAGEJ does
> anybody has a good idea on how to easily process all the data? Maybe a R
> script or something like this.,.
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
*Karen Grace V. Bondoc | Ph.D. Student*
*International Max Planck Research School *
*Institute for Inorganic and Analytical Chemistry *
*Bioorganic Analytics, Friedrich-Schiller-Universität Jena*
*Lessingstr. 8 (R 228)*
*D-07743 Jena*
*Tel.: 03641 948956*
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html