3D coordinates in video

Hello everyone!

First of all, I apologize if my question is easy to solved, I begin with imageJ… And i am apparently not so good with it.

I have an issue regarding a manual 3D videoTracking.
I recorded two video, from 2 sides of an aquarium (one front with x and y, one side with y and z). I would like to use MTrackJ to follow manually the movement of my fish. Apparently, MTrackJ is able to manage 3D coordinates from video analyzed frame by frame.
My problem: I didn’t manage to tell him how the coordinates x, y and z are defined and which axis they follow.
I tried the add-on Sync Windows and sync measure 3D (https://imagej.nih.gov/ij/plugins/sync-windows.html), but it doesn’t do what I would like.

Is there a way to define the 3D coordinates on two sync videos ?

Thank you for your help!

PS: I saw this topic from 2016 with more or less exactly my question, but he received no answer: Manual tracking: 3D alternative to "retrieve z coordinates"?

Hi Trantsyx,

I guess that MTrackJ expect a 4D stack. In microscopy we can acquire sequential xy planes among the z axis (resulting in a 3D stack). So for each time point you get a 3D stack that you can repeat in time and get a 4D stack.

In your case you have 2 simultaneous planes xy and xz (or yz).
I’ m sorry but I don’t know any imageJ plugin or opensource software that could do the job.
I only found theses commerical tools : (http://www.viewpoint.fr/en/p/software/zebralab & http://www.noldus.com/animal-behavior-research/products/track3d)

Furthermore a similar topic can be found here : Tracking in 3d with stereo camera setup




Thank you very much for your answer, Romain!
I will try to find a solution from the two 2D datasets.