Posted by
chris elliott on
Sep 14, 2010; 5:27pm
URL: http://imagej.273.s1.nabble.com/Mtracck2-problems-tp3686926p3686927.html
Please see comments below:
On Sep 13 2010, Vinay sj wrote:
>Dear All,
>
> I am writing a macro to track nuclei from a live cell imaging movie. I am
> using Mtrack2 to automate the tracking. I am having several problems with
> this macro. It seems that the macro is not able to generate tracks from
> binary images of DAPI stained nuclei. However, when I invert the images
> to a white foreground, the Mtrack2 algorithm works when i use it manually
> with the imagej. However, when I run Mtrack2 from my own macro. The
> tracking does not work. Please help.
>
>I have put my code below. stackpath is the path to the stack of
>images(binary images of nuclei)
>
>stackPath = stackFolder + "Stack.tif";
>
are you sure that stackFolder ends with a directory separator ? / or \\ ?
>open(stackPath);
>
>run("Invert","stack");
>
>
>call("MTrack2_.setProperty","minSize","50");
>call("MTrack2_.setProperty","maxSize","2000");
>call("MTrack2_.setProperty","minTrackLength","3");
>call("MTrack2_.setProperty","maxVelocity","4");
>call("MTrack2_.setProperty","saveResultsFile","false");
>call("MTrack2_.setProperty","showPaths","true");
>call("MTrack2_.setProperty","showPathLengths","true");
>call("MTrack2_.setProperty","showLabels","false");
>call("MTrack2_.setProperty","showPositions","true");
>call("MTrack2_.setProperty","skipDialogue","true");
>
>run("MTrack2");
I did run("MTrack2 ", "minimum=6 maximum=999999 maximum_=100 save
save=&path4");
see
http://biolpc22.york.ac.uk/drosophila/larvae/ for analysing a directory
full of avi (rather than tif) stacks; I did the task in two parts, one to
convert all the images to black/white, and the other to do the tracking.
Any comments appreciated chris