hand_tracking

In Dr. Daniel O'Connor's lab, we are interested in haptic shape perception in primates. We use our hands to grasp, recognize, and manipulate objects. To understand how we perceive 3D shapes using tactile signals, it is critical to track how hands interact with objects. This repository is created for markerless 3D tracking of monkey hand from multiple camera views. It leverages the machine learning approach Lightning Pose / DeepLabCut to track keypoints in 2D and Anipose / NCams to estimate 3D pose. We then can apply musculoskeletal modeling (OpenSim).

Notes:

• DeepLabCut and Lightning Pose are 2D CNNs. I'm exploring other 3D tracking tools that use 3D CNNs (DANNCE) or hybrid 2D/3D CNNs JARVIS.

Workflow

1. Camera calibration
   Both Jarvis and Anipose require camera calibration.See below sections and corresponding folders for detailed instructions.

2. Annotation
   Jarvis provides a great annotation tool that leverages the multi camera recordings by projecting manual annotations on a subset of those cameras to the remaining ones, significantly reducing the amount of tedious manual annotations needed.
   Jarvis GitHub: https://github.com/JARVIS-MoCap/JARVIS-AnnotationTool

3. Model training
   Lightning Pose improves pose estimation through (1) unsupervised losses (2) temporal context network and (3) post hoc refinement (Kalman smoothing).
   Lightning Pose GitHub: https://github.com/danbider/lightning-pose
   Lightning Pose paper: https://www.nature.com/articles/s41592-024-02319-1

4. Triangulation
   Following camera calibration, Anipose can triangulate 2D outpupts from Lightning Pose and refine estimation using spatiotemporal filters.
   Anipose GitHub: https://github.com/lambdaloop/anipose
   Anipose paper: https://doi.org/10.1016/j.celrep.2021.109730

5. Inverse kinematics
   OpenSim is a platform for modeling humans, animals, robots, and the environment, and simulating their interaction and movement. https://simtk.org/projects/opensim/

Prerequisites

• Software
  Please install the software listed in the workflow section.

• Hardware
  To study haptic shape perception from, experiments are designed to be conducted in the dark to minimize visual information of 3D objects. Therefore, in this study, infrared illuminators and cameras are used to capture images in the dark.

  • Cameras:
    FLIR Blackfly S3 cameras (4 mono-color cameras with 25mm focal length lens and 2 color cameras with 12mm focal length lens).
    Remove IR filters if needed.
  • Illuminators:
    Edmundoptics IR Spot Lights (940 nm)

Camera Calibration

• Calibration Videos

  • Print a checker or charuco board.
    See an example 6*8 charuco board.

  • For intrinsic calibration, take videos for individial cameras.

  • For extrinsic calibration, take videos for all cameras (Anipose) or pairs of cameras (Jarvis).

  • Notes:

    • A charuco board is recommended.

    • We can use ncams.camera_tools.create_board to create a checker or charuco board (see Step 2 in Camera_calibration_pipeline).

    • Try to cover several distances and all parts of views.

    • For checker board calibration, keep the orientation consistent. Do not roate the checker board more than 30 degrees.

    • More tips can be found here.

• Camera Calibration
  Please see the instructions in the Jarvis and Anipose folders.

Hand Anatomy

Video Recording

• Cameras are set up to cover all key points of monkey hand, and each key point is viewed by at least 2 cameras.
• Synchronize multiple cameras. (See hardware-triggered cameras)
• Save videos from multiple hardware-triggered cameras(See FLIR_multi_cam)