Beginner: tracking ellipses

object-tracking
trackmate
Tags: #<Tag:0x00007fd54215f418> #<Tag:0x00007fd54215f2d8>

#1

im new at track mate and have the task to detect and track flies in free flight. what is the proper way to detect and track ellipses? i found that there is a Spot Morphology script on github, but it is several years old and unsupported(also no idea how to add it to my track mate). thanks in advance.

edit: also why do i get RGB is invalid when i try to open certain videos in track mate?
edit: ok that was silly enough. converted the image to 8 bit grayscale and stuff works now. still no clue how to do the ellipse tracking.

regards.


#2

Can you be a bit more specific?

So you’re using TrackMate. Are you using one of its built-in spot detectors?

Which script are you refering to? The only thing I was able to find is this, but it’s a CellProfiler module written in Python.

So I’m not sure what exactly it is that you’re after.

Also, an example image/video would certainly help.


#3

Please provide some sample images :slight_smile:


#4

Greetings. first thanks for the replies and apology for the delay in my response(was away for a week) :slight_smile:

@imagejan yes, i am doing my work with trackmate. so far i have used the built in log detector due to the size in pixels.
the script i am refering to is this one: https://github.com/fiji/TrackMate/blob/master/src/main/java/fiji/plugin/trackmate/features/spot/SpotMorphologyAnalyzer.java

here is what i am working on:
https://postimg.org/image/ruaxrc7af/
as you see i have cleared the background and inverted the grayscaled image. my objects are elipses as can be seen. trackmate has done a fantastic job of tracking them due to the fact that the arena does not allow overlapping and the detector represents objects as points. the objects however can move in all directions and not just forward. ideally i want to be able to get the length of their axis and determine their orientation.
regards


#5

I am also interested in this question (orientation). Additionally, I would like to know how you initially managed to get the log detector to identify your ellipses? I cannot get the automatic detector to find my objects. Any hints of how to deal with it? What settings have you made?
In my case, the program detects pixels at the edge of some of the ellipses, but not the entire ellipse, despite me changing the estimated blob diameter and threshold.
Thanks in advance!