πŸ” SuperAnimal-Topview data in SimBA

CREATE A SuperAnimal-Topview PROJECT IN SIMBA

Before working with SuperAnimal-Topview 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 SuperAnimal-Topview tracking data in SimBA, first create a SuperAnimal-Topview project in SimBA.

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

Next, under TYPE OF TRACKING select Multi tracking. Under BODY PART CONFIGURATION, select SuperAnimal-Topview as in the screenshot below.

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

IMPORT SuperAnimal-Topview VIDEOS TO YOU SIMBA PROJECT

After clicking on the CREATE PROJECT CONFIG button, head to the [IMPORT VIDEOS] tab to import the videos representing your SuperAnimal-Topview data into your new SuperAnimal-Topview 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). If you have many animals tracked, it is required as we physically have to identify each track across videos with an ID.

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IMPORT SuperAnimal-Topview DATA TO YOU SIMBA PROJECT

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

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(i) If the SuperAnimal-Topview 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 SuperAnimal-Topview 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, select the number of animals beeing tracked in your SuperAnimal-Topview tracking data, and give them names.

(iv) Next, to import a directory of SuperAnimal-Topview H5 files, select a directory containing .h5 files and hit the import button. Alternatively, to import a single SuperAnimal-Topview tracking data .h5 file, go to the labelframe IMPORT SuperAnimal-Topview h5 file and hit the import single file button. You can follow the progress in the main SImBA terminal.

(v) If you are tracking multiple animals using SuperAnimal-Topview, then you will be assigned track identities manually, as described HERE.

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