Published May 12, 2024 | Version 1.0.0
Dataset Restricted

Trackerless 3D Freehand Ultrasound Reconstruction Challenge - Train Dataset (Part 1)

Creators

  • 1. University College London
  • 2. King's College London

Description

This is the first part of the Challenge train dataset. Link to second part; Link to third part. Link to validation dataset.

Acquisition devices and config: The 2D US images were acquired using an Ultrasonix machine (BK, Europe) with a curvilinear probe (4DC7-3/40). The associated position information of each frame was recorded by an optical tracker (NDI Polaris Vicra, Northern Digital Inc., Canada). The acquired US frames were recorded at 20 fps, with an image size of 480×640, without speckle reduction. The frequency was set at 6MHz with a dynamic range of 83 dB, an overall gain of 48% and a depth of 9 cm. 

Scanning protocol: Both left and right forearms of volunteers were scanned. For each forearm, the US probe moves in three different trajectories (straight line shape, "C" shape, and "S" shape), in a distal-to-proximal direction followed by a proximal-to-distal direction, with the US plane perpendicular of and parallel to the scanning direction. The train dataset contains 1200 scans in total, 24 scans associated with each subject.

For detailed information please refer to the Challenge website. Baseline code is also provided, which can be found at this repo.

Dataset structure: 

  • The dataset contains 50 folders (one subject per folder), each with 24 scans. Each .h5 file corresponds to one scan, storing image and transformation of each frame within this scan. Key-value pairs in each .h5 file are explained below.

    • “frames”  - All frames in the scan; with a shape of [N,H,W], where N refers to the number of frames in the scan, H and W denote the height and width of a frame. 

    • “tforms” - All transformations in the scan; with a shape of [N,4,4], where N is the number of frames in the scan, and the transformation matrix denotes the transformation from tracker tool space to camera space. 

    • Notations in the name of each .h5 file: “RH”: right arm; “LH”: left arm; “Per”: perpendicular; “Par”: parallel; “L”: straight line shape; “C”: C shape; “S”: S shape; “DtP”: distal-to-proximal direction; “PtD”: proximal-to-distal direction; For example, “RH_Per_L_DtP.h5” denotes a scan on the right forearm, with ultrasound probe perpendicular of the forearm sweeping along straight line, in distal-to-proximal direction.

  • Calibration matrix: The calibration matrix was obtained using a pinhead-based method. The "scaling_from_pixel_to_mm" and "spatial_calibration_from_image_coordinate_system_to_tracking_tool_coordinate_system" are provided in the “calib_matrix.csv”. 

Data Usage Policy:

  • The training and validation data provided may be utilized within the research scope of this challenge and in subsequent research-related publications. However, commercial use of the training and validation data is prohibited. In cases where the intended use is ambiguous, participants accessing the data are requested to abstain from further distribution or use outside the scope of this challenge.
  • Please note the following publication policy mentioned in the Challenge proposal:
    We are planning to submit a paper including challenge dataset summary and results analysis. Members of the top five participating teams will be invited as co-authors.
    The participating teams can only publish their novel methodology without discussion of data and obtained results if the above mentioned paper is not published (submission to arXiv is considered as a sufficient waiting period). Once the challenge paper from the organising team is published, the participants should cite this challenge paper if their work has not been published.
  • After we publish the summary paper of the challenge, if you use our dataset in your publication, please cite the summary paper (reference will be provided once published) and some of the following articles:  
    • Qi Li, Ziyi Shen, Qianye Yang, Dean C. Barratt, Matthew J. Clarkson, Tom Vercauteren, and Yipeng Hu. "Nonrigid Reconstruction of Freehand Ultrasound without a Tracker." In International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 689-699. Cham: Springer Nature Switzerland, 2024. doi: 10.1007/978-3-031-72083-3_64.
    • Qi Li, Ziyi Shen, Qian Li, Dean C. Barratt, Thomas Dowrick, Matthew J. Clarkson, Tom Vercauteren, and Yipeng Hu. "Long-term Dependency for 3D Reconstruction of Freehand Ultrasound Without External Tracker." IEEE Transactions on Biomedical Engineering, vol. 71, no. 3, pp. 1033-1042, 2024. doi: 10.1109/TBME.2023.3325551.
    • Qi Li, Ziyi Shen, Qian Li, Dean C. Barratt, Thomas Dowrick, Matthew J. Clarkson, Tom Vercauteren, and Yipeng Hu. "Trackerless freehand ultrasound with sequence modelling and auxiliary transformation over past and future frames." In 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), pp. 1-5. IEEE, 2023. doi: 10.1109/ISBI53787.2023.10230773.
    • Qi Li, Ziyi Shen, Qian Li, Dean C. Barratt, Thomas Dowrick, Matthew J. Clarkson, Tom Vercauteren, and Yipeng Hu. "Privileged Anatomical and Protocol Discrimination in Trackerless 3D Ultrasound Reconstruction." In International Workshop on Advances in Simplifying Medical Ultrasound, pp. 142-151. Cham: Springer Nature Switzerland, 2023. doi: https://doi.org/10.1007/978-3-031-44521-7_14.

Files

Restricted

The record is publicly accessible, but files are restricted to users with access.

Request access

If you would like to request access to these files, please fill out the form below.

You need to satisfy these conditions in order for this request to be accepted:

Participants of the challenge will be given access to the dataset. We ask participants to formally register by filling in this registration form. If you have successfully registered, please fill in the request form below and leave your team name in the "Request message" field. Access link will be sent via email.

We kindly request all participants to familiarize themselves with our Publication Policy, prior to participating in the challenge.

Please contact qi.li.21@ucl.ac.uk if you encounter any problem.

 

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Additional details

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