Freehand ultrasound without external trackers (original) (raw)

Published November 9, 2022 | Version v2

Dataset Open

Authors/Creators

• 1. Centre for Medical Image Computing, Wellcome/EPSRC Centre for Interventional and Surgical Sciences, Department of Medical Physics and Biomedical Engineering, University College London, London, U.K.
• 2. Centre for Medical Image Computing, Wellcome/EPSRC Centre for Interventional and Surgical Sciences, Department of Medical Physics and Biomedical Engineering, University College London, London, U.K., State Key Laboratory of Robotics and System, Harbin Institute of Technology, Harbin, China
• 3. School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K.

Description

We have collected a new large freehand ultrasound dataset and are organising a MICCAI2024&2025 Challenges (TUS-REC Challenge). Check Part 1 and Part 2 of the training dataset for TUS-REC2024, and Train Data for TUS-REC2025.

Freehand US scans were acquired on both left and right forearms from 19 volunteers, using Ultrasonix machine (BK, Europe) with a curvilinear probe (4DC7-3/40), tracked by an NDI Polaris Vicra (Northern Digital Inc., Canada). On each forearm, the US probe was moved, for the study purpose, in a straight line, a ‘C’ shape and a ‘S’ shape, in a distal-to-proximal direction. These three scans were repeated, with the curvilinear transducer held (thus the US planes) perpendicular of and parallel to the forearm. B-mode images with median level of speckle reduction were recorded at ~20 fps. Each scan included frames between 36 and 430 with a size of 480×640 pixels, equivalent to a probe travel distance approximately between 100 and 200 mm.

A total of 12 scans were acquired from each volunteer, recorded in a single ‘*.mha’ file, with the filename indicating the acquisition time. For example, “LH_Ver_S_20220425_141454.mha” means a scan acquired on 14:14:54 April 25th, 2022. The ‘valid_frames.csv’ file contains the 6 “protocols” with each arm from each volunteer: 1) RH_Par_L (right arm, straight line shape with the probe parallel to the forearm); 2) RH_Par_C (right arm, ‘C’ shape with the probe parallel to the forearm); 3) RH_Par_S (right arm, ‘S’ shape with the probe parallel to the forearm); 4) RH_Ver_L (right arm, straight line shape with the probe perpendicular of the forearm); 5) RH_Ver_C (right arm, ‘C’ shape with the probe perpendicular of the forearm); 6) RH_Ver_S (right arm, ‘S’ shape with the probe perpendicular of the forearm); 7) LH_Par_L (left arm, straight line shape with the probe parallel to the forearm); 8) LH_Par_C (left arm, ‘C’ shape with the probe parallel to the forearm); 9) LH_Par_S (left arm, ‘S’ shape with the probe parallel to the forearm); 10) LH_Ver_L (left arm, straight line shape with the probe perpendicular of the forearm); 11) LH_Ver_C (left arm, ‘C’ shape with the probe perpendicular of the forearm); 12) LH_Ver_S (left arm, ‘S’ shape with the probe perpendicular of the forearm). The ‘start’ and ‘end’ denote the start and end frame indices of a scan, respectively, in each ‘*.mha’ file.

US images, transformation matrix obtained from the tracker, and corresponding csv file, for each scan can be found in Freehand_US_data.zip. In the “calib_matrix.csv” file, we provide a calibration matrix and a time difference in sec, obtained from our calibration experiments.

A baseline code is provided in this repo.

If you find this data set useful for your research, please consider citing some of the following works:

• 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, 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. "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

calib_matrix.csv

Files (8.5 GB)