Behavioral tracking

[jesusmartin-cortecero]

Hi Peter.

Is CellExplorer Compatible with Deeplabcut?

[petersenpeter]

Hi Jesus

To what extent do you mean compatible? If you save the output from DeepLabCut to a behavior struct, then yes:
https://cellexplorer.org/datastructure/data-structure-and-format/#behavior

[petersenpeter]

Here is a tutorial on working with behavior data in CellExplorer:
https://cellexplorer.org/tutorials/behavior-tutorial/

[jesusmartin-cortecero]

In the tutorial i see that i need OptiTrack files, i have behavioral data analyzed with deeplabcut, and i was wondering if i can import this data to cellExplorer.

[petersenpeter]

You don't need optitrack files. The tutorial just captures how to import data from that format. If you have position data from DeepLabCut you create a behavior struct with that data.

[jesusmartin-cortecero]

if i understand correctly the required data is:

optitrack.timestamps timestamps from optitrack
% optitrack.position.x x-position
% optitrack.position.y y-position
% optitrack.position.z z-position
% optitrack.speed speed
% optitrack.sr samplingrate

when i use the session-Gui, i see and option to add a file

should i add there the mat structure that contains the data mentioned above?

thank you very much in advance

[petersenpeter]

The structure you suggested is correct. You don't need to use the GUI - this section is for describing your raw data (could be used to describe the DeepLabCut files). Save the behavior structure with an appropriate name, it could also be:

deeplabcut.timestamps = 1:100; % In seconds
deeplabcut.position.x = 1:100
deeplabcut.position.y = 1:00
deeplabcut.position.z = 1:100
deeplabcut.sr = 1;  %1 Hz

Not all fields are required. Then save the Matlab structure as basename.deeplabcut.behavior.mat
Then create a firingratemap structure as described in the tutorial.
Finally, rerun ProcessCellMetrics for that session, and it will import the rate maps to the cell_metrics, and you can view them in CellExplorer.

[jesusmartin-cortecero]

This is very useful, many thanks