Model-Based Treatment Planning for Focused Ultrasound Surgery

Lead Research Organisation: University College London
Department Name: Medical Physics and Biomedical Eng

Abstract

Cancer is one of the most prevalent diseases in the UK. Each year it accounts for nearly 1 in 3 of all deaths. For patients with late-stage cancer, the cancer cells often spread to other parts of the body. This process is called metastasis, and the secondary tumours that form are called metastases. One of the most common sites for metastases to develop is bones. Around 2 in 3 patients with late-stage breast and prostate cancer, and 1 in 3 with late-stage lung, thyroid, and kidney cancer will develop bone metastases. This can cause debilitating pain, which has a significant impact on patients' quality of life. The most common treatment for reducing pain from bone metastases is external beam radiation therapy. This is aimed at relieving symptoms and controlling the growth of the cancer to improve quality of life, rather than trying to cure the patient (this is known as palliative care). However, as many as 1 in 3 patients treated with radiation therapy do not experience adequate pain relief, and the treatment cannot be repeated due to the toxicity of radiation to healthy tissue inside the body.

A very promising alternative therapy for pain palliation is focused ultrasound surgery, also known as high-intensity focused ultrasound or HIFU. This technique works by sending a tightly focused beam of ultrasound into the tissue. At the focus, the ultrasound energy is sufficient to heat the tissue and cause cell death in a very localised region, while the surrounding tissue is not harmed. This is akin to focusing sunlight through a magnifying glass, where only in the focus is the energy high enough to singe an object. Focused ultrasound surgery can be used to alleviate the pain from bone metastases by treating the layer of nerves and connective tissue that surrounds the bone. The major challenge is to ensure the focus is accurately placed at the desired target within the body. This is difficult because bones and other organs can significantly distort the path of the ultrasound beam.

The aim of this fellowship is to develop, validate, and apply new computer models to simulate how sound waves travel inside the human body. These models will be based on innovative advances in theoretical acoustics and numerical methods, and will use state-of-the-art computing facilities that have only recently become available. The computer models will allow the position of the focus and the heating of bones during focused ultrasound surgery to be accurately predicted for the first time. This will allow physicians to carefully plan and optimise the treatment parameters to eliminate the pain arising from bone metastases. This is expected to increase the effectiveness of focused ultrasound surgery, reduce the time it takes to treat patients, and extend the range and location of cancers that are eligible for treatment. As part of the fellowship, the models will be rigorously validated using patient data from previous clinical treatments, along with carefully planned laboratory experiments using phantom materials designed to mimic human tissue.

Planned Impact

The direct beneficiaries of this project are cancer patients with metastatic bone disease. These patients often experience excruciating and unrelenting pain. This can have a significant impact on quality of life, including causing functional impairment, physical debilitation, and psychological distress. The number of people affected by pain from bone metastases in the UK is continuing to grow due to the rising incidence of cancer. This is directly related to the ageing population, with the number of people in the UK over 65 expected to rise to 1 in 4 by 2050. Critically, nearly two-thirds of all new cancers are diagnosed in people in this age group. Moreover, two of the most common cancers in the elderly, prostate cancer and breast cancer, are also the most likely to lead to bone metastases.

Coupled with the appropriate treatment planning tools, focused ultrasound surgery offers the potential to deliver pain palliation to these patients with significantly less side effects than existing radiotherapy treatments. The therapy is completely non-invasive, delivered as a day procedure, and can be repeated if necessary without the dose tolerance and toxicity limits associated with radiation. It is hypothesised that the model-based treatment planning tools proposed in this fellowship will significantly accelerate the application of this technology for the treatment of skeletal lesions. In particular, these tools will provide detailed insight into the delivered ultrasound dose under different treatment conditions; increase the targeting accuracy by allowing the delivery parameters to be optimised; and extend the range of skeletal metastases that are eligible for treatment (the skull and the majority of the spine are currently excluded from clinical trials). In the context of delivering value-based healthcare, these tools could also play a significant role in decreasing procedural costs and optimising clinical outcomes.

The enhanced computational performance, unprecedented levels of physical accuracy, extensive validation, and clinician-led translation of the modelling tools developed in this fellowship will provide a significant competitive edge over the simulation packages currently used in academia and in industry. These advances will make the software commercially attractive to the manufacturers of focused ultrasound devices, one of whom is already directly engaged with the project through the expert advisory panel. It is expected the generated IP will lead to licensing agreements or the development of new start-ups, with the UK becoming a base for future international investment into treatment planning technology. The developed software tools will also act as a platform technology for other research areas that require large-scale acoustic models, including seismology, architectural acoustics, and sonar.
 
Description The primary objective of this fellowship was to develop, validate, and apply new computer models to simulate how sound waves travel inside the human body. These models are used for model-based treatment planning in focused ultrasound surgery, particularly for the neuromodulation of deep brain structures. The project is now complete, and significant progress has been made towards these objectives. First, new models coupling elastic wave propagation and heating have been developed to allow the study of bone heating under different sonication conditions. These results give new insights into the mechanisms of heating for different types of ultrasound transducer and different bone geometries. Second, new numerical methods based on novel domain-decomposition approaches have allowed these models to be parallelised on clusters containing large numbers of graphical processing units (GPUs). This has allowed predictions with unprecedented scale and realism. Third, new techniques for measuring high-intensity ultrasound waves have been developed to allow these models to be validated. In particular, we have developed a system that can map the pressure fields from ultrasound therapy devices at clinical levels at unprecedented speeds and signal-to-noise ratios. This will allow the models to be tested under clinical conditions, a critical step towards their translation into the clinical workflow. Finally, we have conducted a series of careful validation experiments to ensure that the acoustic outputs produced by the software are correct.
Exploitation Route The developed modelling and measurement tools are likely to generate impact both on the targeted delivery of ultrasound therapy, as well as academics working to understand wave physics and ultrasound metrology. This impact is likely to come about through our open-source software and dataset releases, as well as the development of new measurement and modelling approaches that can be applied in many other fields.
Sectors Digital/Communication/Information Technologies (including Software),Healthcare

 
Description The impact arising from this grant arises in four key areas: Model development: We developed new models to address the challenges of physical complexity and computational scale. In particular, we: (1) developed new governing equations that describe ultrasound absorption in bones, (2) developed a new open-source elastic wave model based on Fourier spectral methods, (3) developed new domain decomposition techniques that allow ultrasound simulations to efficiently scale over thousands of computer cores or hundreds of GPUs, (4) developed adaptive moving-mesh schemes based on local bandwidth that allow simulations to be performed with significantly less computer memory, (5) generalised the idea of k-space methods to establish non-standard PSTD schemes that allow the exact solution of time-dependent partial differential equations, (6) applied the non-standard PSTD framework to develop a highly-efficient solver for Pennes' bioheat equation that allows tissue-realistic coupled acoustic and thermal simulations, and (7) developed fast one-step methods for rapidly calculating the acoustic field from continuous wave sources. These developments represent a significant contribution to the state-of-the-art. The acoustic models are being used by ultrasound and acoustic companies in the private sector, including for transducer design, image reconstruction, and ultrasound dose calculations. Model validation using lab-based experiments: We validated the developed numerical models using carefully controlled phantom experiments. In particular, we: (1) experimentally validated the models for linear and nonlinear ultrasound propagation through fluid and solid heterogeneities, (2) performed a systematic investigation into factors affecting transcranial simulation accuracy, (3) quantified the effects of image-related homogenisation on simulations of transcranial ultrasound, and (4) developed a novel technique for the rapid measurement of FUS transducers based on a robust planar Fabry-Perot interferometer. The latter allows wide-bandwidth and low-noise measurements at clinical intensities for the first time while significantly reducing scan times. Treatment optimisation: We applied the developed forward models to solve the treatment-planning inverse problem. In particular, we: (1) applied an evolutionary strategy to find the optimal focal position and sonication time for a series of FUS ablations to target a given planning volume while avoiding organs at risk, (2) developed adjoint methods to efficiently solve gradient-based optimisation problems in ultrasound computed tomography, photoacoustic imaging, and equivalent source holography, and (3) applied the modelling tools to study FUS ablation in the liver, kidney, brain, and prostate. These tools have allowed systematic studies of ultrasound beam distortions using patient specific images for the first time-a critical step towards individualised model-based treatment planning. Translation and planning interface: We translated the treatment planning tools into a software suite that can be used by clinicians and researchers. The developed software package, called k-Plan, is an advanced modelling tool for precision planning of transcranial ultrasound procedures. It uses a streamlined and intuitive workflow that allows users to select an ultrasound device, position the device using a template or medical image, and specify the sonication parameters. High-resolution calculations of the ultrasound field and temperature inside the skull and brain are then automatically calculated in the cloud with a single click. No knowledge of numerical modelling or high-performance computing is required.
First Year Of Impact 2015
Sector Digital/Communication/Information Technologies (including Software),Education,Healthcare,Manufacturing, including Industrial Biotechology
Impact Types Economic

 
Description Capital Award for Core Equipment at UCL
Amount £650,000 (GBP)
Funding ID EP/T023651/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 11/2019 
End 05/2021
 
Description Capital Award for Core Equipment at UCL
Amount £650,000 (GBP)
Funding ID EP/T023651/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 11/2019 
End 05/2021
 
Description From the cluster to the clinic: Real-time treatment planning for transcranial ultrasound therapy using deep learning (Ext.)
Amount £952,159 (GBP)
Funding ID EP/S026371/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 07/2019 
End 08/2022
 
Description Spectral element methods for fractional differential equations, with applications in applied analysis and medical imaging
Amount £103,887 (GBP)
Funding ID EP/T022280/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 06/2021 
End 06/2024
 
Description ThUNDDAR Network Pilot Funding
Amount £49,298 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 08/2018 
End 02/2019
 
Description UCL Knowledge Exchange and Innovation Fund
Amount £28,163 (GBP)
Organisation UCL Business 
Sector Private
Country United Kingdom
Start 03/2018 
End 09/2018
 
Description UCL Knowledge Exchange and Innovation Fund
Amount £86,087 (GBP)
Funding ID EPSRC IAA 2017-20 Discovery-To-Use 
Organisation University College London 
Sector Academic/University
Country United Kingdom
Start 01/2021 
End 12/2021
 
Title Experimental Assessment of Skull Aberration and Transmission Loss at 270 kHz for Focused Ultrasound Stimulation of the Primary Visual Cortex 
Description This data was collected in order to assess acoustic field aberrations and transmission loss induced by human skulls in the context of focused ultrasound stimulation of the primary visual cortex (V1) region of the brain. A 2 element spherically focusing annular array ultrasound transducer (H115, driven at 270 kHz, Sonic Concepts) was used to generate an acoustic field. Measurements were performed with a 0.2 mm PVDF needle hydrophone (Precision Acoustics) with right angle connector to reduce its length so it could be accommodated within the skull cavity. The transducer was driven under quasi continuous wave conditions at low drive level to produce a linear field. The transducer was held in a fixed position, the skull was positioned to obtain the correct focal alignment and the hydrophone was held in a 3D printed mount with manual alignment in the axial direction and automated scanning in the lateral directions. Measurements were performed inside 3 human skulls which had previously had the superior section of the parietal and frontal bones removed. Measurements were made with the transducer positioned at two locations for each skull corresponding to the focal region intersecting with the positions of the left and right V1 regions of the brain, with a 1 cm separation between source and skull. For each position, the hydrophone was aligned with the focus inside the skull, then a planar scan was performed covering the largest possible area while avoiding collision of the hydrophone with the skull bone. The skull was then removed and a 2nd scan was performed in water as a reference, the axial position was determined from time of flight in free field during these reference water scans. The study consists of 6 datasets, each of which contains a planar scan made within the skull cavity, and a reference planar scan in water after the skull was removed, preserving the coordinates. File 1: skull 2120, left V1 File 2: skull 2120, right V1 File 3: skull 2150, left V1 File 4: skull 2150, right V1 File 5: skull 2125, left V1 File 6: skull 2125, right V1 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://rdr.ucl.ac.uk/articles/dataset/Experimental_Assessment_of_Skull_Aberration_and_Transmission_...
 
Title Experimental Assessment of Skull Aberration and Transmission Loss at 270 kHz for Focused Ultrasound Stimulation of the Primary Visual Cortex 
Description This data was collected in order to assess acoustic field aberrations and transmission loss induced by human skulls in the context of focused ultrasound stimulation of the primary visual cortex (V1) region of the brain. A 2 element spherically focusing annular array ultrasound transducer (H115, driven at 270 kHz, Sonic Concepts) was used to generate an acoustic field. Measurements were performed with a 0.2 mm PVDF needle hydrophone (Precision Acoustics) with right angle connector to reduce its length so it could be accommodated within the skull cavity. The transducer was driven under quasi continuous wave conditions at low drive level to produce a linear field. The transducer was held in a fixed position, the skull was positioned to obtain the correct focal alignment and the hydrophone was held in a 3D printed mount with manual alignment in the axial direction and automated scanning in the lateral directions. Measurements were performed inside 3 human skulls which had previously had the superior section of the parietal and frontal bones removed. Measurements were made with the transducer positioned at two locations for each skull corresponding to the focal region intersecting with the positions of the left and right V1 regions of the brain, with a 1 cm separation between source and skull. For each position, the hydrophone was aligned with the focus inside the skull, then a planar scan was performed covering the largest possible area while avoiding collision of the hydrophone with the skull bone. The skull was then removed and a 2nd scan was performed in water as a reference, the axial position was determined from time of flight in free field during these reference water scans. The study consists of 6 datasets, each of which contains a planar scan made within the skull cavity, and a reference planar scan in water after the skull was removed, preserving the coordinates. File 1: skull 2120, left V1 File 2: skull 2120, right V1 File 3: skull 2150, left V1 File 4: skull 2150, right V1 File 5: skull 2125, left V1 File 6: skull 2125, right V1 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Experimental measurements are critical for the development of medical ultrasound software and devices, including for validation of modelling tools and for comparison of measurement equipment and protocols. Data sharing encourages reproducibility and consistency across labs, and provides access to other researchers who may not have the equipment or expertise to conduct their own measurements. 
URL https://rdr.ucl.ac.uk/articles/dataset/Experimental_Assessment_of_Skull_Aberration_and_Transmission_...
 
Title Experimental Validation of k-Wave: Nonlinear Wave Propagation in Layered, Absorbing Fluid Media 
Description The data was collected for characterisation of the source, a single element spherically focusing ultrasound transducer driven with a 4 cycle burst at 1.1 MHz (H151, Sonic Concepts), and validation of simulation of the source propagating into water at a number of different drive levels. Measurements were also made for experimental validation of simulation of a nonlinear ultrasound field propagating through planar and wedge shaped glycerol filled phantoms. All measurements were made with a PVDF needle hydrophone in an automated scanning tank. The study data contains 3 files: 1 containing measurements made in water, 1 with a planar glycerol filled phantom and 1 with a wedge shaped glycerol filled phantom. File 1, medium: water only: Axial scans cover 30 to 200 mm, lateral scans cover -20 to 20 mm. 1: XY planar scan for source characterisation at low drive level, measured at z = 40 mm over a 52 by 52 mm plane. 2 - 7: Axial scans from 30 to 200 mm, at the lowest drive level (as used in 1), 6 repeats. (Fig 2,3) 8: lateral scan, level 1 (Fig 2,3) 9-11: Axial scans, level 2 (Fig 3) 12-13: lateral scans level 2 (Fig 3) 14-16: axial scans level 3 (Fig 3) 17-18: lateral scans level 3 (Fig 3) 19-21: axial scans level 4 (Fig 3) 22-23: lateral scans level 4 (Fig 3) 24-26: Axial scans level 5 (Fig 3) 27-28: lateral scans level 5 (Fig 3) 29-33: axial scans level 6 (Figs 3, 4) 34-38: lateral scans level 6 (Figs 3, 4) File 2: medium: water background with planar glycerol phantom 1: XZ planar scan from x = -20 mm to 20 mm, z = 60 to 200 mm (beyond phantom) (Figs 5-7) File 3: medium: water background with wedge shaped glycerol phantom 1: XZ planar scan from x = -20 to 20 mm, z = 70 to 200 mm (beyond phantom) (Figs 8-10) 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Experimental measurements are critical for the development of medical ultrasound software and devices, including for validation of modelling tools and for comparison of measurement equipment and protocols. Data sharing encourages reproducibility and consistency across labs, and provides access to other researchers who may not have the equipment or expertise to conduct their own measurements. 
URL https://rdr.ucl.ac.uk/articles/dataset/Experimental_Validation_of_k-Wave_Nonlinear_Wave_Propagation_...
 
Title Experimental Validation of k-Wave: Nonlinear Wave Propagation in Layered, Absorbing Fluid Media 
Description The data was collected for characterisation of the source, a single element spherically focusing ultrasound transducer driven with a 4 cycle burst at 1.1 MHz (H151, Sonic Concepts), and validation of simulation of the source propagating into water at a number of different drive levels. Measurements were also made for experimental validation of simulation of a nonlinear ultrasound field propagating through planar and wedge shaped glycerol filled phantoms. All measurements were made with a PVDF needle hydrophone in an automated scanning tank. The study data contains 3 files: 1 containing measurements made in water, 1 with a planar glycerol filled phantom and 1 with a wedge shaped glycerol filled phantom. File 1, medium: water only: Axial scans cover 30 to 200 mm, lateral scans cover -20 to 20 mm. 1: XY planar scan for source characterisation at low drive level, measured at z = 40 mm over a 52 by 52 mm plane. 2 - 7: Axial scans from 30 to 200 mm, at the lowest drive level (as used in 1), 6 repeats. (Fig 2,3) 8: lateral scan, level 1 (Fig 2,3) 9-11: Axial scans, level 2 (Fig 3) 12-13: lateral scans level 2 (Fig 3) 14-16: axial scans level 3 (Fig 3) 17-18: lateral scans level 3 (Fig 3) 19-21: axial scans level 4 (Fig 3) 22-23: lateral scans level 4 (Fig 3) 24-26: Axial scans level 5 (Fig 3) 27-28: lateral scans level 5 (Fig 3) 29-33: axial scans level 6 (Figs 3, 4) 34-38: lateral scans level 6 (Figs 3, 4) File 2: medium: water background with planar glycerol phantom 1: XZ planar scan from x = -20 mm to 20 mm, z = 60 to 200 mm (beyond phantom) (Figs 5-7) File 3: medium: water background with wedge shaped glycerol phantom 1: XZ planar scan from x = -20 to 20 mm, z = 70 to 200 mm (beyond phantom) (Figs 8-10) 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Experimental measurements are critical for the development of medical ultrasound software and devices, including for validation of modelling tools and for comparison of measurement equipment and protocols. Data sharing encourages reproducibility and consistency across labs, and provides access to other researchers who may not have the equipment or expertise to conduct their own measurements. 
URL https://rdr.ucl.ac.uk/articles/dataset/Experimental_Validation_of_k-Wave_Nonlinear_Wave_Propagation_...
 
Title Rapid Spatial Mapping of Focused Ultrasound Fields Using a Planar Fabry-Pérot Sensor 
Description The data was acquired in order to investigate the potential of a robust planar Fabry-Pérot sensor for measurement of high acoustic pressures. The sensor was formed from all hard dielectric materials, and designed to operate at 1550 nm, coupled with a C-L (1516-1610 nm) band wavelength tunable laser and rapid scanning system. A set of measurements of the field of a single element spherically focusing HIFU transducer (H101, Sonic Concepts) driven at 1.1 MHz with a 4 cycle burst, was made with the sensor at a variety of drive levels, which at the lower end was compared against hydrophone measurements (0.2 mm PVDF needle hydrophone, Precision Acoustics), and at the higher end was beyond the damage threshold of conventional commercially available PVDF hydrophones, and was compared with KZK simulations of the field. Volume scans were also performed to demonstrate the feasibility of these given the rapid scan times. The transducer was mounted pointing downwards into a small temperature controlled tank filled with degassed, deionised water, with manually adjustable xyz position. The Fabry-Perot sensor was mounted in the bottom of the tank in a fixed position, and measurements were taken over the sensor area by scanning the interrogation laser beam. The directional frequency response of the sensor is included in the frequency response field in the sensor dataset. This has size [1002, 978, 3], where [:, 1, :] contains the frequency, [1, :, :] contains the angles, [2:end, 2:end , 1] is the magnitude response, [2:end, 2:end, 2] is the phase response, and [2:end, 2:end, 3] is the smoothed/corrected magnitude correction (1/mag response) that as applied to the data. In total, this records contains 5 data files: 1. Planar field scan acquired with the Fabry Perot sensor at the focal plane at low level, for comparison with hydrophone scans (Fig4). 2. Planar scans at the focal plane at three drive levels (Fig 5). 3. Small area planar scans at the focal plane at 22 different drive levels, 6 repeats up to level 13, 3 repeats at levels 13-22: 94 datasets (Fig 6). 4. Planar scans at three different axial positions at an intermediate drive level. (Fig 7). 5. Hydrophone scans: a planar scan used to define the source boundary condition for KZK simulations performed as a comparison with scans in file 2. A lateral line scan acquired for comparison with the Fabry-Perot scan in file 1. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://rdr.ucl.ac.uk/articles/dataset/Rapid_Spatial_Mapping_of_Focused_Ultrasound_Fields_Using_a_Pl...
 
Title Rapid Spatial Mapping of Focused Ultrasound Fields Using a Planar Fabry-Pérot Sensor 
Description The data was acquired in order to investigate the potential of a robust planar Fabry-Pérot sensor for measurement of high acoustic pressures. The sensor was formed from all hard dielectric materials, and designed to operate at 1550 nm, coupled with a C-L (1516-1610 nm) band wavelength tunable laser and rapid scanning system. A set of measurements of the field of a single element spherically focusing HIFU transducer (H101, Sonic Concepts) driven at 1.1 MHz with a 4 cycle burst, was made with the sensor at a variety of drive levels, which at the lower end was compared against hydrophone measurements (0.2 mm PVDF needle hydrophone, Precision Acoustics), and at the higher end was beyond the damage threshold of conventional commercially available PVDF hydrophones, and was compared with KZK simulations of the field. Volume scans were also performed to demonstrate the feasibility of these given the rapid scan times. The transducer was mounted pointing downwards into a small temperature controlled tank filled with degassed, deionised water, with manually adjustable xyz position. The Fabry-Perot sensor was mounted in the bottom of the tank in a fixed position, and measurements were taken over the sensor area by scanning the interrogation laser beam. The directional frequency response of the sensor is included in the frequency response field in the sensor dataset. This has size [1002, 978, 3], where [:, 1, :] contains the frequency, [1, :, :] contains the angles, [2:end, 2:end , 1] is the magnitude response, [2:end, 2:end, 2] is the phase response, and [2:end, 2:end, 3] is the smoothed/corrected magnitude correction (1/mag response) that as applied to the data. In total, this records contains 5 data files: 1. Planar field scan acquired with the Fabry Perot sensor at the focal plane at low level, for comparison with hydrophone scans (Fig4). 2. Planar scans at the focal plane at three drive levels (Fig 5). 3. Small area planar scans at the focal plane at 22 different drive levels, 6 repeats up to level 13, 3 repeats at levels 13-22: 94 datasets (Fig 6). 4. Planar scans at three different axial positions at an intermediate drive level. (Fig 7). 5. Hydrophone scans: a planar scan used to define the source boundary condition for KZK simulations performed as a comparison with scans in file 2. A lateral line scan acquired for comparison with the Fabry-Perot scan in file 1. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Experimental measurements are critical for the development of medical ultrasound software and devices, including for validation of modelling tools and for comparison of measurement equipment and protocols. Data sharing encourages reproducibility and consistency across labs, and provides access to other researchers who may not have the equipment or expertise to conduct their own measurements. 
URL https://rdr.ucl.ac.uk/articles/dataset/Rapid_Spatial_Mapping_of_Focused_Ultrasound_Fields_Using_a_Pl...
 
Title Repeatability and reproducibility of hydrophone measurements of medical ultrasound fields 
Description This data was collected in order to study the repeatability and reproducibility of hydrophone measurements of ultrasound fields. Sets of independent measurements were made with two probe (0.2 mm, 40 µm) and two membrane hydrophones (0.4 mm, 0.2 mm differential) (all from Precision Acoustics) to examine the repeatability of measurements. The pressures measured by these hydrophones in three different ultrasound fields, with both linear and nonlinear, pulsed and steady state driving conditions, were acquired to assess the reproducibility of measurements between hydrophones. Repeatability measurements: Sets of five independent measurements were made with each hydrophone of the field generated by a single element focusing bowl transducer (Sonic Concepts H151) driven at a frequency of 1.1 MHz, with both a 4 cycle burst and under quasi steady state conditions. Axial and lateral line scans passing through the focus were acquired at a drive level which generated a weakly nonlinear field. Reproducibility measurements: Two single element focusing bowl transducers (H151 at 1.1 MHz, and H101 at 3.3 MHz, Sonic Concepts) and one diagnostic linear array (L14-5 at 5 MHz, Ultrasonix) sources were used. For the single element transducers, axial and lateral line scans passing through the focus were acquired with each hydrophone at two drive levels to generate both a linear and a weakly nonlinear field, with both a 4 cycle burst and under quasi steady state conditions. For the diagnostic linear array, lateral line scans were acquired passing through the beam axis at an axial distance of 40 mm. The transducer was driven with a 4 cycle burst at a power level that generated harmonics up to 30 MHz.All measurements were acquired using an automated scanning tank filled with degassed, deionised water. The transducers mounted in a fixed xyz position with automated tilt, rotate adjustment. Hydrophones were mounted on an automated xyz stage, with manual tilt, rotate adjustment. In total this study contains 12 datasets, the corresponding figure or table in the paper is given in brackets: 1-4: Repeatability and reproducibility - H151 x 4 hydrophones (Figs 1-4, Table 3) Each dataset contains axial and lateral line scans at 2 drive levels, with a 4 cycle and a 40 cycle burst, with 5 sets of scans at the high drive level and one set of scans at the low drive level 5-8: Reproducibility - H101 x 4 hydrophones (Figs 4-5, Table 3) Each dataset contains a single set of axial and lateral line scan at each of 2 drive levels, with a 4 cycle and a 120 cycle burst. 9-12: Reproducibility - L14-5 x 4 hydrophones (Fig 6, Table 3) Each dataset contains lateral scans at 1 power level. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Experimental measurements are critical for the development of medical ultrasound software and devices, including for validation of modelling tools and for comparison of measurement equipment and protocols. Data sharing encourages reproducibility and consistency across labs, and provides access to other researchers who may not have the equipment or expertise to conduct their own measurements. 
URL https://rdr.ucl.ac.uk/articles/dataset/Repeatability_and_reproducibility_of_hydrophone_measurements_...
 
Title Repeatability and reproducibility of hydrophone measurements of medical ultrasound fields 
Description This data was collected in order to study the repeatability and reproducibility of hydrophone measurements of ultrasound fields. Sets of independent measurements were made with two probe (0.2 mm, 40 µm) and two membrane hydrophones (0.4 mm, 0.2 mm differential) (all from Precision Acoustics) to examine the repeatability of measurements. The pressures measured by these hydrophones in three different ultrasound fields, with both linear and nonlinear, pulsed and steady state driving conditions, were acquired to assess the reproducibility of measurements between hydrophones. Repeatability measurements: Sets of five independent measurements were made with each hydrophone of the field generated by a single element focusing bowl transducer (Sonic Concepts H151) driven at a frequency of 1.1 MHz, with both a 4 cycle burst and under quasi steady state conditions. Axial and lateral line scans passing through the focus were acquired at a drive level which generated a weakly nonlinear field. Reproducibility measurements: Two single element focusing bowl transducers (H151 at 1.1 MHz, and H101 at 3.3 MHz, Sonic Concepts) and one diagnostic linear array (L14-5 at 5 MHz, Ultrasonix) sources were used. For the single element transducers, axial and lateral line scans passing through the focus were acquired with each hydrophone at two drive levels to generate both a linear and a weakly nonlinear field, with both a 4 cycle burst and under quasi steady state conditions. For the diagnostic linear array, lateral line scans were acquired passing through the beam axis at an axial distance of 40 mm. The transducer was driven with a 4 cycle burst at a power level that generated harmonics up to 30 MHz.All measurements were acquired using an automated scanning tank filled with degassed, deionised water. The transducers mounted in a fixed xyz position with automated tilt, rotate adjustment. Hydrophones were mounted on an automated xyz stage, with manual tilt, rotate adjustment. In total this study contains 12 datasets, the corresponding figure or table in the paper is given in brackets: 1-4: Repeatability and reproducibility - H151 x 4 hydrophones (Figs 1-4, Table 3) Each dataset contains axial and lateral line scans at 2 drive levels, with a 4 cycle and a 40 cycle burst, with 5 sets of scans at the high drive level and one set of scans at the low drive level 5-8: Reproducibility - H101 x 4 hydrophones (Figs 4-5, Table 3) Each dataset contains a single set of axial and lateral line scan at each of 2 drive levels, with a 4 cycle and a 120 cycle burst. 9-12: Reproducibility - L14-5 x 4 hydrophones (Fig 6, Table 3) Each dataset contains lateral scans at 1 power level. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Experimental measurements are critical for the development of medical ultrasound software and devices, including for validation of modelling tools and for comparison of measurement equipment and protocols. Data sharing encourages reproducibility and consistency across labs, and provides access to other researchers who may not have the equipment or expertise to conduct their own measurements. 
URL https://rdr.ucl.ac.uk/articles/dataset/Repeatability_and_reproducibility_of_hydrophone_measurements_...
 
Title Sensitivity of simulated transcranial ultrasound fields to acoustic medium property maps 
Description This data was collected in order to validate models of ultrasound propagation through skull bone phantoms. A single element spherically focusing ultrasound transducer (PA332 at 1 MHz, Precision Acoustics) was used to generate an acoustic field. Measurements were performed with a 0.2 mm PVDF needle hydrophone (Precision Acoustics) to characterise the source under short burst conditions (3 cycles). These measurements include planar scans in the prefocal region in free field for characterisation of the source, and planar scans further from the source after propagation through 3 different bone phantoms: a parametric araldite resin phantom, a mesh based skull bone phantom obtained from a T1 weighted MRI scan of the head, cast in araldite and printed in VeroBlack. Medium maps used in simulations, which match the experimental set up are included as a supplementary file, these include speed of sound, attenuation coefficient and density. The .stl file containing the mesh is also included as a supplementary file. All measurements were acquired using an automated scanning tank filled with degassed, deionised water. The transducer was mounted in a fixed xyz position. Hydrophones were mounted on an automated xyz stage, with manual tilt, rotate adjustment. In total this study contains 5 datasets contained 5 files, the corresponding figure or table in the paper is given in brackets: 1: Free field XY planar transverse scan at z = 45 mm, corresponds to dataset 2, which was performed in the same measurement session. 2. XY planar transverse scan at z = 58 mm after propagation through a parametric araldite 1302 resin phantom. (Fig 13) 3. Free field XY planar transverse scan at 45 mm, corresponds to datasets 4 and 5, which were performed in the same measurement session. 4. Planar transverse scan at z = 85 mm after propagation through a mesh based skull bone phantom cast in araldite 1302. (Fig 14) 5. Planar transverse scan at z = 85 mm after propagation though a mesh based skull bone phantom printed in VeroBlack. (Fig 14) Supplementary files: 6. *_supplementary_01.h5, h5 file containing fields medium1, medium2 and medium3, which contain grid based medium maps (sound speed, attenuation coefficient at 1 MHz, and density), with coordinates and description, for medium1: parametric resin phantom, medium2: mesh based resin phantom, medium3: mesh based VeroBlack phantom. 7. *_supplementary-02.stl, .stl file containing mesh used to construct the anatomical bone phantom 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Experimental measurements are critical for the development of medical ultrasound software and devices, including for validation of modelling tools and for comparison of measurement equipment and protocols. Data sharing encourages reproducibility and consistency across labs, and provides access to other researchers who may not have the equipment or expertise to conduct their own measurements. 
URL https://rdr.ucl.ac.uk/articles/dataset/Sensitivity_of_simulated_transcranial_ultrasound_fields_to_ac...
 
Title Sensitivity of simulated transcranial ultrasound fields to acoustic medium property maps 
Description This data was collected in order to validate models of ultrasound propagation through skull bone phantoms. A single element spherically focusing ultrasound transducer (PA332 at 1 MHz, Precision Acoustics) was used to generate an acoustic field. Measurements were performed with a 0.2 mm PVDF needle hydrophone (Precision Acoustics) to characterise the source under short burst conditions (3 cycles). These measurements include planar scans in the prefocal region in free field for characterisation of the source, and planar scans further from the source after propagation through 3 different bone phantoms: a parametric araldite resin phantom, a mesh based skull bone phantom obtained from a T1 weighted MRI scan of the head, cast in araldite and printed in VeroBlack. Medium maps used in simulations, which match the experimental set up are included as a supplementary file, these include speed of sound, attenuation coefficient and density. The .stl file containing the mesh is also included as a supplementary file. All measurements were acquired using an automated scanning tank filled with degassed, deionised water. The transducer was mounted in a fixed xyz position. Hydrophones were mounted on an automated xyz stage, with manual tilt, rotate adjustment. In total this study contains 5 datasets contained 5 files, the corresponding figure or table in the paper is given in brackets: 1: Free field XY planar transverse scan at z = 45 mm, corresponds to dataset 2, which was performed in the same measurement session. 2. XY planar transverse scan at z = 58 mm after propagation through a parametric araldite 1302 resin phantom. (Fig 13) 3. Free field XY planar transverse scan at 45 mm, corresponds to datasets 4 and 5, which were performed in the same measurement session. 4. Planar transverse scan at z = 85 mm after propagation through a mesh based skull bone phantom cast in araldite 1302. (Fig 14) 5. Planar transverse scan at z = 85 mm after propagation though a mesh based skull bone phantom printed in VeroBlack. (Fig 14) Supplementary files: 6. *_supplementary_01.h5, h5 file containing fields medium1, medium2 and medium3, which contain grid based medium maps (sound speed, attenuation coefficient at 1 MHz, and density), with coordinates and description, for medium1: parametric resin phantom, medium2: mesh based resin phantom, medium3: mesh based VeroBlack phantom. 7. *_supplementary-02.stl, .stl file containing mesh used to construct the anatomical bone phantom 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Experimental measurements are critical for the development of medical ultrasound software and devices, including for validation of modelling tools and for comparison of measurement equipment and protocols. Data sharing encourages reproducibility and consistency across labs, and provides access to other researchers who may not have the equipment or expertise to conduct their own measurements. 
URL https://rdr.ucl.ac.uk/articles/dataset/Sensitivity_of_simulated_transcranial_ultrasound_fields_to_ac...
 
Title Simulating Focused Ultrasound Transducers using Discrete Sources on Regular Cartesian Grids 
Description This data was collected in order to validate models of curved sources on cartesian grids. A single element spherically focusing ultrasound transducer (H101 at 1.1 MHz, Sonic Concepts) was used to generate an acoustic field. Measurements were performed with a 0.2 mm PVDF needle hydrophone (Precision Acoustics) to characterise the source under quasi continuous wave and short burst conditions. These measurements include planar scans in the prefocal region for the two driving regimes, and axial scans at the same drive level for both drive regimes. There are additional axial scans at one further higher drive level (very weakly nonlinear) for each of the driving regimes which were acquired for comparison with the model with scaled input source amplitude. All measurements were acquired using an automated scanning tank filled with degassed, deionised water. The transducers mounted in a fixed xyz position with automated tilt, rotate adjustment. Hydrophones were mounted on an automated xyz stage, with manual tilt, rotate adjustment. In total this study contains 6 datasets contained in one file, the corresponding figure or table in the paper is given in brackets: 1: Planar scan with 45 cycle burst (qCW) at z = 42.5 mm, linear field 2: Axial scan 45 cycle burst (qCW), linear field (conditions as in 1), Fig 8, 9. 3: Axial scan 45 cycle burst (qCW), weakly nonlinear field, Fig 8, 9. 4: Planar scan with 4 cycle burst at z = 42.5 mm, linear field 5: Axial scan 4 cycle burst, linear field (conditions as in 4), Fig 10, 11. 6. Axial scan 4 cycle burst, weakly nonlinear field, Fig 10, 11. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://rdr.ucl.ac.uk/articles/dataset/Simulating_Focused_Ultrasound_Transducers_using_Discrete_Sour...
 
Title Simulating Focused Ultrasound Transducers using Discrete Sources on Regular Cartesian Grids 
Description This data was collected in order to validate models of curved sources on cartesian grids. A single element spherically focusing ultrasound transducer (H101 at 1.1 MHz, Sonic Concepts) was used to generate an acoustic field. Measurements were performed with a 0.2 mm PVDF needle hydrophone (Precision Acoustics) to characterise the source under quasi continuous wave and short burst conditions. These measurements include planar scans in the prefocal region for the two driving regimes, and axial scans at the same drive level for both drive regimes. There are additional axial scans at one further higher drive level (very weakly nonlinear) for each of the driving regimes which were acquired for comparison with the model with scaled input source amplitude. All measurements were acquired using an automated scanning tank filled with degassed, deionised water. The transducers mounted in a fixed xyz position with automated tilt, rotate adjustment. Hydrophones were mounted on an automated xyz stage, with manual tilt, rotate adjustment. In total this study contains 6 datasets contained in one file, the corresponding figure or table in the paper is given in brackets: 1: Planar scan with 45 cycle burst (qCW) at z = 42.5 mm, linear field 2: Axial scan 45 cycle burst (qCW), linear field (conditions as in 1), Fig 8, 9. 3: Axial scan 45 cycle burst (qCW), weakly nonlinear field, Fig 8, 9. 4: Planar scan with 4 cycle burst at z = 42.5 mm, linear field 5: Axial scan 4 cycle burst, linear field (conditions as in 4), Fig 10, 11. 6. Axial scan 4 cycle burst, weakly nonlinear field, Fig 10, 11. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Experimental measurements are critical for the development of medical ultrasound software and devices, including for validation of modelling tools and for comparison of measurement equipment and protocols. Data sharing encourages reproducibility and consistency across labs, and provides access to other researchers who may not have the equipment or expertise to conduct their own measurements. 
URL https://rdr.ucl.ac.uk/articles/dataset/Simulating_Focused_Ultrasound_Transducers_using_Discrete_Sour...
 
Title k-Plan: Ultrasound Therapy Planning 
Description k-Plan is an advanced modelling tool for precision planning of transcranial ultrasound procedures. It uses a streamlined and intuitive workflow that allows users to select an ultrasound device, position the device using a template or medical image, and specify the sonication parameters. High-resolution calculations of the ultrasound field and temperature inside the skull and brain are then automatically calculated in the cloud with a single click. 
Type Of Technology Software 
Year Produced 2022 
Impact k-Plan is developed by researchers at University College London and the Brno University of Technology based on more than a decade of cutting-edge research into ultrasound modelling and planning for transcranial ultrasound therapy. It is the first software tool for model-based treatment planning for ultrasound therapy, and is being brought to market in collaboration with Brainbox, Ltd. 
URL https://k-plan.io/
 
Title k-Wave Acoustics Toolbox 
Description k-Wave is an open source MATLAB toolbox designed for the time-domain simulation of propagating acoustic waves in 1D, 2D, or 3D. The toolbox has a wide range of functionality, but at its heart is an advanced numerical model that can account for both linear and nonlinear wave propagation, an arbitrary distribution of heterogeneous material parameters, and power law acoustic absorption. The numerical model is based on the solution of three coupled first-order partial differential equations which are equivalent to a generalised form of the Westervelt equation. The equations are solved using a k-space pseudospectral method, where spatial gradients are calculated using a Fourier collocation scheme, and temporal gradients are calculated using a k-space corrected finite-difference scheme. The temporal scheme is exact in the limit of linear wave propagation in a homogeneous and lossless medium, and significantly reduces numerical dispersion in the more general case. Power law acoustic absorption is accounted for using a linear integro-differential operator based on the fractional Laplacian. A split-field perfectly matched layer (PML) is used to absorb the waves at the edges of the computational domain. The main advantage of the numerical model used in k-Wave compared to models based on finite-difference time domain (FDTD) schemes is that fewer spatial and temporal grid points are needed for accurate simulations. This means the models run faster and use less memory. Major k-Wave versions were released in 2014, 2017, and 2020. 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact The toolbox is widely used in academia and industry, and has been used for research into transcranial ultrasound, ultrasound therapy, the development of novel ultrasound sources, photoacoustic imaging, and many other applications. There have been ten releases of the toolbox. It currently has more than 16,000 registered users in 70 countries. A 2010 paper describing the first release of the toolbox has >1400 citations, and the active online user forum has >4500 posts.