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Gait kinematics

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Annette Z edited this page Sep 2, 2021 · 1 revision

Based on bodypart coordinates predicted by a markerless pose tracking program such as DeepLabCut, automatically extract kinematic parameters for treadmill or spontaneous overground walk experiments.

In a treadmill set-up, the program assumes (at least) labels of one hind limb: iliac crest, hip, knee, ankle, MTP joint (mtp), and toe.

In a spontaneous walking set-up, the program assumes (at least) labels of left and right hind limbs: crestL / crestR, hipL / hipR, kneeL / kneeR, ankleL/ankleR, mtpL / mtpR, and toeL / toeR.

  1. Import the csv output from a DeepLabCut model including the estimated bodypart coordinates (or a spreadsheets containing the same header and column structures as a DLC output file). The file should contain the coordinates of joints on one hind limb, labelled "toe", "mtp", "ankle", "knee", "hip", and "iliac crest". (*We are working on additional features to include kinematic analysis with different setups, including front limb and tail, as well as to adapt the program to data in other formats, e.g., when the bodyparts are named differently, and experimental conditions, e.g., spontaneous kinematics without treadmill [the spontaneous walk functions are currently being tested].)

  2. Alternatively, select a folder that contains multiple csv files that contain the estimated bodypart coordinates in the appropriate format, for data obtained with the same experimental setup (most importantly, distance from camera, and - if using semi-automated mode - treadmill speed).

  3. In semi-automated mode, the program requires the cm/s speed of the treadmill. Additional relevant parameters such as px-cm ratio will be calculated immediately and displayed, prior to starting the analysis, for validation.

(Semi-automated analysis requires user input of treadmill speed in cm/s. )

  1. If the conversion ratio between the px/frame speed and the cm/s speed of the treadmill is known (to be calculated during calibration outside the toolbox or estimated using the semi-automated function using known cm/s treadmill speeds), you can select "Fully automated" mode and input the conversion ratio. In this case, bulk processing allows for analysis of data with different treadmill speed settings.

(Fully-automated analysis requires user input of the conversion ratio from px/frame to cm/s, which can be manually calculated or through the output of the semi-automated method, e.g., using a linear regression on the conversion ratio of several treadmill speed settings. Comparing the displayed parameters with those based on the semi-automated method reveals similar estimates for px-to-cm length conversion ratio by both methods and a reliable estimate of the cm/s speed using the fully-automated method - without inputting the speed.)

  1. Extract kinematic parameters and export the results as csv files.
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