🎭 FaceMap data in SimBA

CREATE A FACEMAP PROJECT IN SIMBA

Before working with FaceMap data in SimBA, make sure you have the latest version of SimBA installed.

If you have SimBA installed on your system, you can make sure you have the latest version by typing pip install simba-uw-tf-dev --upgrade.

To work with FaceMap tracking data in SimBA, first create a FaceMap project in SimBA.

Follow Scenario 1 tutorial up-to the Generate Project Config section.

Next, under TYPE OF TRACKING select Classic tracking. Under BODY PART CONFIGURATION, select FaceMap as in the screenshot below.

image

Once selected, click the CREATE PROJECT CONFIG button to create the project in your chosen directory.

IMPORT FACEMAP VIDEO TO YOU SIMBA PROJECT

After clicking on the CREATE PROJECT CONFIG button, head to the [IMPORT VIDEOS] tab to import the videos representing your FaceMap data into your new FaceMap SimBA project: For more information on video import, see the Scenario 1 documentation.

The import of videos is not a strict requirement, but recommended, for amongst others, visualization puposes and the ability to read video meta data relevant for data smoothing if selected (see next step).

image

IMPORT FACEMAP DATA TO YOU SIMBA PROJECT

Next, we need to import the FaceMap tracking data to the project. Click on the [Import tracking data] tab. Here, select H5 (FaceMap) from the DATA TYPE dropdown:

image

(i) If the FaceMap data contains missing data, you can interpolate it using one of the options available in the INTERPOLATION METHOD dropdown. For more information on interpolation, see the interpolation section in the Scenario 1 tutorial.

(ii) If the FaceMap data is β€œjittery”, we may want to smooth the tracking data using one of the options available in the SMOOTHING dropdown. For more information on interpolation, see the smoothing section in the Scenario 1 tutorial.

Note

If you are performing smoothing, it is required that you import the videos first (so SimBA can read the FPS frame-rate from the video file meta-data).

(iii) Next, to import a directory of FaceMap H5 files, select a directory containing .h5 files and hit the import button. Alternatively, to import a single FaceMap .h5 file, go to the labelframe IMPORT FACEMAP h5 file and hit the import single file button. You can follow the progress in the main SImBA terminal.

Once complete, close the PROJECT CONFIGURATION window and load the project as documented HERE

Important

When working with FaceMap data in SimBA, there is no need to correct outliers (or no need click skip outlier correction).