Mengjie Shi

Ms. Mengjie Shi

orcid

Research Focus & Metrics

Academic Career Length

5Years (2022-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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7 April 2022 in Photoacoustics
Verified
Journal Article
Open access
MSMengjie Shi
Mengjie Shi
TZTianrui Zhao
Tianrui Zhao
SWSimeon J. West
Simeon J. West
ADAdrien E. Desjardins
Adrien E. Desjardins
TVTom Vercauteren
Tom Vercauteren
Wenfeng XiaWenfeng Xia
Wenfeng Xia
Photoacoustic imaging has shown great potential for guiding minimally invasive procedures by accurate identification of critical tissue targets and invasive medical devices (such as metallic needles). The use of light emitting diodes (LEDs) as the excitation light sources accelerates its clinical translation owing to its high affordability and portability. However, needle visibility in LED-based photoacoustic imaging is compromised primarily due to its low optical fluence. In this work, we propose a deep learning framework based on U-Net to improve the visibility of clinical metallic needles with a LED-based photoacoustic and ultrasound imaging system. To address the complexity of capturing ground truth for real data and the poor realism of purely simulated data, this framework included the generation of semi-synthetic training datasets combining both simulated data to represent features from the needles and in vivo measurements for tissue background. Evaluation of the trained neural network was performed with needle insertions into blood-vessel-mimicking phantoms, pork joint tissue ex vivo and measurements on human volunteers. This deep learning-based framework substantially improved the needle visibility in photoacoustic imaging in vivo compared to conventional reconstruction by suppressing background noise and image artefacts, achieving 5.8 and 4.5 times improvements in terms of signal-to-noise ratio and the modified Hausdorff distance, respectively. Thus, the proposed framework could be helpful for reducing complications during percutaneous needle insertions by accurate identification of clinical needles in photoacoustic imaging.

10 April 2023 in Remote Sensing
Verified
Journal Article
Open access
PDF file
Panagiotis BarmpoutisPanagiotis Barmpoutis
Panagiotis Barmpoutis
AKAristeidis Kastridis
Aristeidis Kastridis
Tania  StathakiTania Stathaki
Tania Stathaki
JYJing Yuan
Jing Yuan
MSMengjie Shi
Mengjie Shi
NGNikos GRAMMALIDIS
Nikos GRAMMALIDIS
In the current context of climate change and demographic expansion, one of the phenomena that humanity faces are the suburban wildfires. To prevent the occurrence of suburban forest fires, fire risk assessment and early fire detection approaches need to be applied. Forest fire risk mapping depends on various factors and contributes to the identification and monitoring of vulnerable zones where risk factors are most severe. Therefore, watchtowers, sensors, and base stations of autonomous unmanned aerial vehicles need to be placed carefully in order to ensure adequate visibility or battery autonomy. In this study, fire risk assessment of an urban forest was performed and the recently introduced 360-degree data were used for early fire detection. Furthermore, a single-step approach that integrates a multiscale vision transformer was introduced for accurate fire detection. The study area includes the suburban pine forest of Thessaloniki city (Greece) named Seich Sou, which is prone to wildfires. For the evaluation of the performance of the proposed workflow, real and synthetic 360-degree images were used. Experimental results demonstrate the great potential of the proposed system, which achieved an F-score for real fire event detection rate equal to 91.6%. This indicates that the proposed method could significantly contribute to the monitoring, protection, and early fire detection of the suburban forest of Thessaloniki.

28 May 2024 in Photoacoustics
Verified
Journal Article
Open access
MSMengjie Shi
Mengjie Shi
TVTom Vercauteren
Tom Vercauteren
Wenfeng XiaWenfeng Xia
Wenfeng Xia
Photoacoustic (PA) image reconstruction involves acoustic inversion that necessitates the specification of the speed of sound (SoS) within the medium of propagation. Due to the lack of information on the spatial distribution of the SoS within heterogeneous soft tissue, a homogeneous SoS distribution (such as 1540 m/s) is typically assumed in PA image reconstruction, similar to that of ultrasound (US) imaging. Failure to compensate for the SoS variations leads to aberration artefacts, deteriorating the image quality. Various methods have been proposed to address this issue, but they usually involve complex hardware and/or time-consuming algorithms, hindering clinical translation. In this work, we introduce a deep learning framework for SoS estimation and subsequent aberration correction in a dual-modal PA/US imaging system exploiting a clinical US probe. As the acquired PA and US images were inherently co-registered, the estimated SoS distribution from US channel data using a deep neural network was incorporated for accurate PA image reconstruction. The framework comprised an initial pre-training stage based on digital phantoms, which was further enhanced through transfer learning using physical phantom data and associated SoS maps obtained from measurements. This framework achieved a root mean square error of 10.2 m/s and 15.2 m/s for SoS estimation on digital and physical phantoms, respectively and structural similarity index measures of up to 0.88 for PA reconstructions compared to the conventional approach of 0.69. A maximum of 1.2 times improvement in the signal-to-noise ratio of PA images was further demonstrated with a human volunteer study. Our results show that the proposed framework could be valuable in various clinical and preclinical applications to enhance PA image reconstruction.

25 August 2022 in Sensors
Verified
Journal Article
Open access
PDF file
MSMengjie Shi
Mengjie Shi
SBSemyon Bodian
Semyon Bodian
SWSimeon J. West
Simeon J. West
SSSanjayan Sathasivam
Sanjayan Sathasivam
RGRoss J. Gordon
Ross J. Gordon
Wenfeng XiaWenfeng Xia
Wenfeng Xia
Ultrasound (US) image guidance is widely used for minimally invasive procedures, but the invasive medical devices (such as metallic needles), especially their tips, can be poorly visualised in US images, leading to significant complications. Photoacoustic (PA) imaging is promising for visualising invasive devices and peripheral tissue targets. Light-emitting diodes (LEDs) acting as PA excitation sources facilitate the clinical translation of PA imaging, but the image quality is degraded due to the low pulse energy leading to insufficient contrast with needles at deep locations. In this paper, photoacoustic visualisation of clinical needles was enhanced by elastomeric nanocomposite coatings with superficial and interstitial illumination. Candle soot nanoparticle-polydimethylsiloxane (CSNP-PDMS) composites with high optical absorption and large thermal expansion coefficients were applied onto the needle exterior and the end-face of an optical fibre placed in the needle lumen. The excitation light was delivered at the surface by LED arrays and through the embedded optical fibre by a pulsed diode laser to improve the visibility of the needle tip. The performance was validated using an ex-vivo tissue model. An LED-based PA/US imaging system was used for imaging the needle out-of-plane and in-plane insertions over approach angles of 20 deg to 55 deg. The CSNP-PDMS composite conferred substantial visual enhancements on both the needle shaft and the tip, with an average of 1.7- and 1.6-fold improvements in signal-to-noise ratios (SNRs), respectively. With the extended light field involving extracorporeal and interstitial illumination and the highly absorbing coatings, enhanced visualisation of the needle shaft and needle tip was achieved with PA imaging, which could be helpful in current US-guided minimally invasive surgeries.

4 September 2024
Verified
Book Chapter
Open access
PDF file
MSMengjie Shi
Mengjie Shi
SWSimeon J. West
Simeon J. West
TVTom Vercauteren
Tom Vercauteren
SNSacha Noimark
Sacha Noimark
ADAdrien Desjardins
Adrien Desjardins
Wenfeng XiaWenfeng Xia
Wenfeng Xia
Despite rapid advancements in medical technology, accurate identification and assessment of abnormalities and precise visualisation of interventional devices are imperative for successful outcomes in minimally invasive medical procedures. In the past few decades, photoacoustic (PA) imaging has emerged as a promising intraoperative imaging modality for surgical guidance, offering rich optical absorption contrast derived from intrinsic tissue chromophores, extrinsic contrast agents, and interventional devices. This chapter reviews recent developments in PA imaging for guiding minimally invasive medical procedures, with a particular focus on its capability of visualising interventional devices including clinical metallic needles, catheters, and metal implants, and signal and image processing methods for enhanced visualisation.

3 March 2022
Verified
Conference Paper
Closed access
TZTianrui Zhao
Tianrui Zhao
MSMengjie Shi
Mengjie Shi
SOSébastien Ourselin
Sébastien Ourselin
TVTom Vercauteren
Tom Vercauteren
Wenfeng XiaWenfeng Xia
Wenfeng Xia
Photoacoustic (PA) endoscopy promises to be useful in a variety of clinical contexts including intravascular imaging, gastrointestinal tracts imaging and surgical guidance. Recent advancements of optical wavefront shaping allow the development of ultrathin endoscopy probes based on multimode optical fibres, which can provide higher spatial resolution than previously reported fibre bundle-based endoscopes. In this work, we developed a forward-viewing PA endomicroscopy imaging system and further improved its performance with a deep image prior (DIP) neural network. Laser was focused and scanned through a multimode fibre via wavefront shaping, in which a real-valued intensity transmission matrix approach was used for fibre characterisation, and a digital micromirror device (DMD) was used for light modulation. The excited ultrasound waves at the distal fibre tip were detected by an ultrasound transducer. High fidelity images of ex vivo mouse red blood cells were acquired. A DIP neural network was then used to improve the spatial resolution with unsupervised learning. Convolutional filters were used to learn features of low-level images as priors and reconstruct high-resolution images accordingly. The performance of the DIP approach was evaluated using a structural similarity index measure (SSIM) at a level of 0.85 with 25% effective pixels, which outperformed the bicubic method. The use of DIP allows reducing scanning positions by several times, and thus improves the speed of pixel-wise PA microscopy imaging. With further miniaturisation of the ultrasound detector, we anticipate that this system could be used for real-time guidance of minimally invasive surgeries by providing micro-structural, molecular, and functional information of tissue.