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Automated detection of anatomical landmarks plays a crucial role in many diagnostic and surgical applications. Progresses in deep learning (DL) methods have resulted in significant performance enhancement in tasks related to anatomical landmark detection. While current research focuses on accurately localizing these landmarks in medical scans, the importance of inter-rater annotation variability in building DL models is often overlooked. Understanding how inter-rater variability impacts the performance and reliability of the resulting DL algorithms, which are crucial for clinical deployment, can inform the improvement of training data construction and boost DL models' outcomes. In this paper, we conducted a thorough study of different annotation-fusion strategies to preserve inter-rater variability in DL models for anatomical landmark detection, aiming to boost the performance and reliability of the resulting algorithms. Additionally, we explored the characteristics and reliability of four metrics, including a novel Weighted Coordinate Variance metric to quantify landmark detection uncertainty/inter-rater variability. Our research highlights the crucial connection between inter-rater variability, DL-models performances, and uncertainty, revealing how different approaches for multi-rater landmark annotation fusion can influence these factors., Comment: Accepted to SPIE Medical Imaging 2025

Anatomical landmark detection in medical images is essential for various clinical and research applications, including disease diagnosis and surgical planning. However, manual landmark annotation is time-consuming and requires significant expertise. Existing deep learning (DL) methods often require large amounts of well-annotated data, which are costly to acquire. In this paper, we introduce CAMLD, a novel self-supervised DL framework for anatomical landmark detection in unlabeled scans with varying contrasts by using only a single reference example. To achieve this, we employed an inter-subject landmark consistency loss with an image registration loss while introducing a 3D convolution-based contrast augmentation strategy to promote model generalization to new contrasts. Additionally, we utilize an adaptive mixed loss function to schedule the contributions of different sub-tasks for optimal outcomes. We demonstrate the proposed method with the intricate task of MRI-based 3D brain landmark detection. With comprehensive experiments on four diverse clinical and public datasets, including both T1w and T2w MRI scans at different MRI field strengths, we demonstrate that CAMLD outperforms the state-of-the-art methods in terms of mean radial errors (MREs) and success detection rates (SDRs). Our framework provides a robust and accurate solution for anatomical landmark detection, reducing the need for extensively annotated datasets and generalizing well across different imaging contrasts. Our code will be publicly available at: https://github.com/HealthX-Lab/CAMLD., Comment: 14 pages, 6 figures, 3 tables

Recent advancements in vision-language models (VLMs), such as CLIP, have demonstrated substantial success in self-supervised representation learning for vision tasks. However, effectively adapting VLMs to downstream applications remains challenging, as their accuracy often depends on time-intensive and expertise-demanding prompt engineering, while full model fine-tuning is costly. This is particularly true for biomedical images, which, unlike natural images, typically suffer from limited annotated datasets, unintuitive image contrasts, and nuanced visual features. Recent prompt learning techniques, such as Context Optimization (CoOp) intend to tackle these issues, but still fall short in generalizability. Meanwhile, explorations in prompt learning for biomedical image analysis are still highly limited. In this work, we propose BiomedCoOp, a novel prompt learning framework that enables efficient adaptation of BiomedCLIP for accurate and highly generalizable few-shot biomedical image classification. Our approach achieves effective prompt context learning by leveraging semantic consistency with average prompt ensembles from Large Language Models (LLMs) and knowledge distillation with a statistics-based prompt selection strategy. We conducted comprehensive validation of our proposed framework on 11 medical datasets across 9 modalities and 10 organs against existing state-of-the-art methods, demonstrating significant improvements in both accuracy and generalizability. The code will be publicly available at https://github.com/HealthX-Lab/BiomedCoOp., Comment: 18 pages, 5 figures, 10 tables

Carbon dots (CDs) shows great application potential with their unique and excellent performances. Coal and its derivatives are rich in aromatic ring structure, which is suitable for preparing CDs in microstructure. Coal burning dust from coal-fired power plants can be utilized as a rich resource to separate and extract CDs. It has been shown in our results that there have two main possible mechanisms for the formation of CDs in coal burning dust. One is the self-assembly of polycyclic aromatic hydrocarbons contained in coal or produced by incomplete combustion of coal. The other mechanism is that the bridge bonds linking different aromatic structures in coal are breaking which would form CDs with different functional groups when the coals are burning at high temperature. Under violet light excitation at 310-340 nm or red light at 610-640 nm, CDs extracted from coal burning dust can emit purple fluorescence around 410 nm. The mechanism of up-conversion fluorescence emission of CDs is due to a two-photon absorption process. The recycling of CDs from coal burning dust from coal-fired power plants are not only good to protect environment but also would be helpful for mass production of CDs.

Segmentation of anatomical structures and pathological regions in medical images is essential for modern clinical diagnosis, disease research, and treatment planning. While significant advancements have been made in deep learning-based segmentation techniques, many of these methods still suffer from limitations in data efficiency, generalizability, and interactivity. As a result, developing precise segmentation methods that require fewer labeled datasets remains a critical challenge in medical image analysis. Recently, the introduction of foundation models like CLIP and Segment-Anything-Model (SAM), with robust cross-domain representations, has paved the way for interactive and universal image segmentation. However, further exploration of these models for data-efficient segmentation in medical imaging is still needed and highly relevant. In this paper, we introduce MedCLIP-SAMv2, a novel framework that integrates the CLIP and SAM models to perform segmentation on clinical scans using text prompts, in both zero-shot and weakly supervised settings. Our approach includes fine-tuning the BiomedCLIP model with a new Decoupled Hard Negative Noise Contrastive Estimation (DHN-NCE) loss, and leveraging the Multi-modal Information Bottleneck (M2IB) to create visual prompts for generating segmentation masks from SAM in the zero-shot setting. We also investigate using zero-shot segmentation labels within a weakly supervised paradigm to enhance segmentation quality further. Extensive testing across four diverse segmentation tasks and medical imaging modalities (breast tumor ultrasound, brain tumor MRI, lung X-ray, and lung CT) demonstrates the high accuracy of our proposed framework. Our code is available at https://github.com/HealthX-Lab/MedCLIP-SAMv2., Comment: 10 pages, 2 figures, 6 tables

Video-assisted thoracic surgery (VATS) is a minimally invasive approach for treating early-stage non-small-cell lung cancer. Optimal trocar placement during VATS ensures comprehensive access to the thoracic cavity, provides a panoramic endoscopic view, and prevents instrument crowding. While established principles such as the Baseball Diamond Principle (BDP) and Triangle Target Principle (TTP) exist, surgeons mainly rely on experience and patient-specific anatomy for trocar placement, potentially leading to sub-optimal surgical plans that increase operative time and fatigue. To address this, we present the first virtual reality (VR)-based pre-operative planning tool with tailored data visualization and interaction designs for efficient and optimal VATS trocar placement, following the established surgical principles and consultation with an experienced surgeon. In our preliminary study, we demonstrate the system's application in right upper lung lobectomy, a common thoracic procedure typically using three trocars. A preliminary user study of our system indicates it is efficient, robust, and user-friendly for planning optimal trocar placement, with a great promise for clinical application while offering potentially valuable insights for the development of other surgical VR systems.

Parkinson's disease (PD) is a debilitating neurodegenerative disease that has severe impacts on an individual's quality of life. Compared with structural and functional MRI-based biomarkers for the disease, electroencephalography (EEG) can provide more accessible alternatives for clinical insights. While deep learning (DL) techniques have provided excellent outcomes, many techniques fail to model spatial information and dynamic brain connectivity, and face challenges in robust feature learning, limited data sizes, and poor explainability. To address these issues, we proposed a novel graph neural network (GNN) technique for explainable PD detection using resting state EEG. Specifically, we employ structured global convolutions with contrastive learning to better model complex features with limited data, a novel multi-head graph structure learner to capture the non-Euclidean structure of EEG data, and a head-wise gradient-weighted graph attention explainer to offer neural connectivity insights. We developed and evaluated our method using the UC San Diego Parkinson's disease EEG dataset, and achieved 69.40% detection accuracy in subject-wise leave-one-out cross-validation while generating intuitive explanations for the learnt graph topology., Comment: Accepted at MLCN 2024

Intracranial hemorrhage (ICH) is a life-threatening condition that requires rapid and accurate diagnosis to improve treatment outcomes and patient survival rates. Recent advancements in supervised deep learning have greatly improved the analysis of medical images, but often rely on extensive datasets with high-quality annotations, which are costly, time-consuming, and require medical expertise to prepare. To mitigate the need for large amounts of expert-prepared segmentation data, we have developed a novel weakly supervised ICH segmentation method that utilizes the YOLO object detection model and an uncertainty-rectified Segment Anything Model (SAM). In addition, we have proposed a novel point prompt generator for this model to further improve segmentation results with YOLO-predicted bounding box prompts. Our approach achieved a high accuracy of 0.933 and an AUC of 0.796 in ICH detection, along with a mean Dice score of 0.629 for ICH segmentation, outperforming existing weakly supervised and popular supervised (UNet and Swin-UNETR) approaches. Overall, the proposed method provides a robust and accurate alternative to the more commonly used supervised techniques for ICH quantification without requiring refined segmentation ground truths during model training., Comment: Manuscript was accepted at SWITCH2024. 10 pages, 2 figures

Efficient and accurate brain ventricle segmentation from clinical CT scans is critical for emergency surgeries like ventriculostomy. With the challenges in poor soft tissue contrast and a scarcity of well-annotated databases for clinical brain CTs, we introduce a novel uncertainty-aware ventricle segmentation technique without the need of CT segmentation ground truths by leveraging diffusion-model-based domain adaptation. Specifically, our method employs the diffusion Schr\"odinger Bridge and an attention recurrent residual U-Net to capitalize on unpaired CT and MRI scans to derive automatic CT segmentation from those of the MRIs, which are more accessible. Importantly, we propose an end-to-end, joint training framework of image translation and segmentation tasks, and demonstrate its benefit over training individual tasks separately. By comparing the proposed method against similar setups using two different GAN models for domain adaptation (CycleGAN and CUT), we also reveal the advantage of diffusion models towards improved segmentation and image translation quality. With a Dice score of 0.78$\pm$0.27, our proposed method outperformed the compared methods, including SynSeg-Net, while providing intuitive uncertainty measures to further facilitate quality control of the automatic segmentation outcomes. The implementation of our proposed method is available at: https://github.com/HealthX-Lab/DiffusionSynCTSeg., Comment: Early acceptance at MICCAI2024

Medical image segmentation of anatomical structures and pathology is crucial in modern clinical diagnosis, disease study, and treatment planning. To date, great progress has been made in deep learning-based segmentation techniques, but most methods still lack data efficiency, generalizability, and interactability. Consequently, the development of new, precise segmentation methods that demand fewer labeled datasets is of utmost importance in medical image analysis. Recently, the emergence of foundation models, such as CLIP and Segment-Anything-Model (SAM), with comprehensive cross-domain representation opened the door for interactive and universal image segmentation. However, exploration of these models for data-efficient medical image segmentation is still limited, but is highly necessary. In this paper, we propose a novel framework, called MedCLIP-SAM that combines CLIP and SAM models to generate segmentation of clinical scans using text prompts in both zero-shot and weakly supervised settings. To achieve this, we employed a new Decoupled Hard Negative Noise Contrastive Estimation (DHN-NCE) loss to fine-tune the BiomedCLIP model and the recent gScoreCAM to generate prompts to obtain segmentation masks from SAM in a zero-shot setting. Additionally, we explored the use of zero-shot segmentation labels in a weakly supervised paradigm to improve the segmentation quality further. By extensively testing three diverse segmentation tasks and medical image modalities (breast tumor ultrasound, brain tumor MRI, and lung X-ray), our proposed framework has demonstrated excellent accuracy. Code is available at https://github.com/HealthX-Lab/MedCLIP-SAM., Comment: 10 pages, 2 figures

Purpose: As visual inspection is an inherent process during radiological screening, the associated eye gaze data can provide valuable insights into relevant clinical decisions. As deep learning has become the state-of-the-art for computer-assisted diagnosis, integrating human behavior, such as eye gaze data, into these systems is instrumental to help align machine predictions with clinical diagnostic criteria, thus enhancing the quality of automatic radiological diagnosis. Methods: We propose a novel deep learning framework for joint disease diagnosis and prediction of corresponding clinical visual attention maps for chest X-ray scans. Specifically, we introduce a new dual-encoder multi-task UNet, which leverages both a DenseNet201 backbone and a Residual and Squeeze-and-Excitation block-based encoder to extract diverse features for visual attention map prediction, and a multi-scale feature-fusion classifier to perform disease classification. To tackle the issue of asynchronous training schedules of individual tasks in multi-task learning, we proposed a multi-stage cooperative learning strategy, with contrastive learning for feature encoder pretraining to boost performance. Results: Our proposed method is shown to significantly outperform existing techniques for chest X-ray diagnosis (AUC=0.93) and the quality of visual attention map prediction (Correlation coefficient=0.58). Conclusion: Benefiting from the proposed multi-task multi-stage cooperative learning, our technique demonstrates the benefit of integrating clinicians' eye gaze into clinical AI systems to boost performance and potentially explainability.

Recent rising interests in patient-specific thoracic surgical planning and simulation require efficient and robust creation of digital anatomical models from automatic medical image segmentation algorithms. Deep learning (DL) is now state-of-the-art in various radiological tasks, and U-shaped DL models have particularly excelled in medical image segmentation since the inception of the 2D UNet. To date, many variants of U-shaped models have been proposed by the integration of different attention mechanisms and network configurations. Systematic benchmark studies which analyze the architecture of these models by leveraging the recent development of the multi-label databases, can provide valuable insights for clinical deployment and future model designs, but such studies are still rare. We conduct the first systematic benchmark study for variants of 3D U-shaped models (3DUNet, STUNet, AttentionUNet, SwinUNETR, FocalSegNet, and a novel 3D SwinUnet with four variants) with a focus on CT-based anatomical segmentation for thoracic surgery. Our study systematically examines the impact of different attention mechanisms, the number of resolution stages, and network configurations on segmentation accuracy and computational complexity. To allow cross-reference with other recent benchmarking studies, we also included a performance assessment of the BTCV abdominal structural segmentation. With the STUNet ranking at the top, our study demonstrated the value of CNN-based U-shaped models for the investigated tasks and the benefit of residual blocks in network configuration designs to boost segmentation performance.

While deep learning techniques have provided the state-of-the-art performance in various clinical tasks, explainability regarding their decision-making process can greatly enhance the credence of these methods for safer and quicker clinical adoption. With high flexibility, Gradient-weighted Class Activation Mapping (Grad-CAM) has been widely adopted to offer intuitive visual interpretation of various deep learning models' reasoning processes in computer-assisted diagnosis. However, despite the popularity of the technique, there is still a lack of systematic study on Grad-CAM's performance on different deep learning architectures. In this study, we investigate its robustness and effectiveness across different popular deep learning models, with a focus on the impact of the networks' depths and architecture types, by using a case study of automatic pneumothorax diagnosis in X-ray scans. Our results show that deeper neural networks do not necessarily contribute to a strong improvement of pneumothorax diagnosis accuracy, and the effectiveness of GradCAM also varies among different network architectures.

Angiography is widely used to detect, diagnose, and treat cerebrovascular diseases. While numerous techniques have been proposed to segment the vascular network from different imaging modalities, deep learning (DL) has emerged as a promising approach. However, existing DL methods often depend on proprietary datasets and extensive manual annotation. Moreover, the availability of pre-trained networks specifically for medical domains and 3D volumes is limited. To overcome these challenges, we propose a few-shot learning approach called VesselShot for cerebrovascular segmentation. VesselShot leverages knowledge from a few annotated support images and mitigates the scarcity of labeled data and the need for extensive annotation in cerebral blood vessel segmentation. We evaluated the performance of VesselShot using the publicly available TubeTK dataset for the segmentation task, achieving a mean Dice coefficient (DC) of 0.62(0.03).

Early surgical treatment of brain tumors is crucial in reducing patient mortality rates. However, brain tissue deformation (called brain shift) occurs during the surgery, rendering pre-operative images invalid. As a cost-effective and portable tool, intra-operative ultrasound (iUS) can track brain shift, and accurate MRI-iUS registration techniques can update pre-surgical plans and facilitate the interpretation of iUS. This can boost surgical safety and outcomes by maximizing tumor removal while avoiding eloquent regions. However, manual assessment of MRI-iUS registration results in real-time is difficult and prone to errors due to the 3D nature of the data. Automatic algorithms that can quantify the quality of inter-modal medical image registration outcomes can be highly beneficial. Therefore, we propose a novel deep-learning (DL) based framework with the Swin UNETR to automatically assess 3D-patch-wise dense error maps for MRI-iUS registration in iUS-guided brain tumor resection and show its performance with real clinical data for the first time., Comment: Accepted in IEEE IUS 2023

Recent developments in deep learning (DL) techniques have led to great performance improvement in medical image segmentation tasks, especially with the latest Transformer model and its variants. While labels from fusing multi-rater manual segmentations are often employed as ideal ground truths in DL model training, inter-rater variability due to factors such as training bias, image noise, and extreme anatomical variability can still affect the performance and uncertainty of the resulting algorithms. Knowledge regarding how inter-rater variability affects the reliability of the resulting DL algorithms, a key element in clinical deployment, can help inform better training data construction and DL models, but has not been explored extensively. In this paper, we measure aleatoric and epistemic uncertainties using test-time augmentation (TTA), test-time dropout (TTD), and deep ensemble to explore their relationship with inter-rater variability. Furthermore, we compare UNet and TransUNet to study the impacts of Transformers on model uncertainty with two label fusion strategies. We conduct a case study using multi-class paraspinal muscle segmentation from T2w MRIs. Our study reveals the interplay between inter-rater variability and uncertainties, affected by choices of label fusion strategies and DL models., Comment: Accepted in UNSURE MICCAI 2023

Accurate identification and quantification of unruptured intracranial aneurysms (UIAs) is crucial for the risk assessment and treatment of this cerebrovascular disorder. Current 2D manual assessment on 3D magnetic resonance angiography (MRA) is suboptimal and time-consuming. In addition, one major issue in medical image segmentation is the need for large well-annotated data, which can be expensive to obtain. Techniques that mitigate this requirement, such as weakly supervised learning with coarse labels are highly desirable. In the paper, we propose FocalSegNet, a novel 3D focal modulation UNet, to detect an aneurysm and offer an initial, coarse segmentation of it from time-of-flight MRA image patches, which is further refined with a dense conditional random field (CRF) post-processing layer to produce a final segmentation map. We trained and evaluated our model on a public dataset, and in terms of UIA detection, our model showed a low false-positive rate of 0.21 and a high sensitivity of 0.80. For voxel-wise aneurysm segmentation, we achieved a Dice score of 0.68 and a 95% Hausdorff distance of ~0.95 mm, demonstrating its strong performance. We evaluated our algorithms against the state-of-the-art 3D Residual-UNet and Swin-UNETR, and illustrated the superior performance of our proposed FocalSegNet, highlighting the advantages of employing focal modulation for this task.

Homologous anatomical landmarks between medical scans are instrumental in quantitative assessment of image registration quality in various clinical applications, such as MRI-ultrasound registration for tissue shift correction in ultrasound-guided brain tumor resection. While manually identified landmark pairs between MRI and ultrasound (US) have greatly facilitated the validation of different registration algorithms for the task, the procedure requires significant expertise, labor, and time, and can be prone to inter- and intra-rater inconsistency. So far, many traditional and machine learning approaches have been presented for anatomical landmark detection, but they primarily focus on mono-modal applications. Unfortunately, despite the clinical needs, inter-modal/contrast landmark detection has very rarely been attempted. Therefore, we propose a novel contrastive learning framework to detect corresponding landmarks between MRI and intra-operative US scans in neurosurgery. Specifically, two convolutional neural networks were trained jointly to encode image features in MRI and US scans to help match the US image patch that contain the corresponding landmarks in the MRI. We developed and validated the technique using the public RESECT database. With a mean landmark detection accuracy of 5.88+-4.79 mm against 18.78+-4.77 mm with SIFT features, the proposed method offers promising results for MRI-US landmark detection in neurosurgical applications for the first time., Comment: Accepted in MICCAI 2023

In brain tumor resection, accurate removal of cancerous tissues while preserving eloquent regions is crucial to the safety and outcomes of the treatment. However, intra-operative tissue deformation (called brain shift) can move the surgical target and render the pre-surgical plan invalid. Intra-operative ultrasound (iUS) has been adopted to provide real-time images to track brain shift, and inter-modal (i.e., MRI-iUS) registration is often required to update the pre-surgical plan. Quality control for the registration results during surgery is important to avoid adverse outcomes, but manual verification faces great challenges due to difficult 3D visualization and the low contrast of iUS. Automatic algorithms are urgently needed to address this issue, but the problem was rarely attempted. Therefore, we propose a novel deep learning technique based on 3D focal modulation in conjunction with uncertainty estimation to accurately assess MRI-iUS registration errors for brain tumor surgery. Developed and validated with the public RESECT clinical database, the resulting algorithm can achieve an estimation error of 0.59+-0.57 mm., Comment: Accepted in MICCAI 2023

Intracranial hemorrhage (ICH) is a life-threatening medical emergency that requires timely and accurate diagnosis for effective treatment and improved patient survival rates. While deep learning techniques have emerged as the leading approach for medical image analysis and processing, the most commonly employed supervised learning often requires large, high-quality annotated datasets that can be costly to obtain, particularly for pixel/voxel-wise image segmentation. To address this challenge and facilitate ICH treatment decisions, we introduce a novel weakly supervised method for ICH segmentation, utilizing a Swin transformer trained on an ICH classification task with categorical labels. Our approach leverages a hierarchical combination of head-wise gradient-infused self-attention maps to generate accurate image segmentation. Additionally, we conducted an exploratory study on different learning strategies and showed that binary ICH classification has a more positive impact on self-attention maps compared to full ICH subtyping. With a mean Dice score of 0.44, our technique achieved similar ICH segmentation performance as the popular U-Net and Swin-UNETR models with full supervision and outperformed a similar weakly supervised approach using GradCAM, demonstrating the excellent potential of the proposed framework in challenging medical image segmentation tasks. Our code is available at https://github.com/HealthX-Lab/HGI-SAM., Comment: Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) https://melba-journal.org/2023:012

While mastery of neuroanatomy is important for the investigation of the brain, there is an increasing interest in exploring the neural pathways to better understand the roles of neural circuitry in brain functions. To tackle the limitations of traditional 2D-display-based neuronavigation software in intuitively visualizing complex 3D anatomies, several virtual reality (VR) and augmented reality (AR) solutions have been proposed to facilitate neuroanatomical education. However, with the increasing knowledge on brain connectivity and the functioning of the sub-systems, there is still a lack of similar software solutions for the education and exploration of these topics, which demand more elaborate visualization and interaction strategies. To address this gap, we designed the immerSive custOmizable Neuro learnIng plAform (SONIA), a novel user-friendly VR software system with a multi-scale interaction paradigm that allows flexible customization of learning materials. With both quantitative and qualitative evaluations through user studies, the proposed system is shown to have high usability, attractive visual design, and good educational value. As the first immersive system that integrates customizable design and detailed narratives of the brain sub-systems for the education of neuroanatomy and brain connectivity, SONIA showcases new potential directions and provides valuable insights regarding medical learning and exploration in VR.

While virtual-reality (VR) has shown great promise in radiological tasks, effective user-interaction strategies that can improve efficiency and ergonomics are still under-explored and systematic evaluations of VR interaction techniques in the context of complex anatomical models are rare. Therefore, our study aims to identify the most effective interaction techniques for two common neurosurgical planning tasks in VR (point annotation and note-taking) from the state-of-the-arts, and propose a novel technique for efficient sub-volume selection necessary in neuroanatomical navigation. We assessed seven user-interaction methods with multiple input modalities (gaze, head motion, controller, and voice) for point placement and note-taking in the context of annotating brain aneurysms for cerebrovascular surgery. Furthermore, we proposed and evaluated a novel technique, called magnified selection diorama (Maserama) for easy navigation and selection of complex 3D anatomies in VR. Both quantitative and semi-quantitative (i.e., NASA Task Load Index) metrics were employed through user studies to reveal the performance of each interaction scheme in terms of accuracy, efficiency, and usability. Our evaluations demonstrated that controller-based interaction is preferred over eye-tracking-based methods for point placement while voice recording and virtual keyboard typing are better than freehand writing for note-taking. Furthermore, our new Maserama sub-volume selection technique was proven to be highly efficient and easy-to-use. Our study is the first to provide a systematic assessment of existing and new VR interaction schemes for neurosurgical data navigation and annotation. It offers valuable insights and tools to guide the design of future VR systems for radiological and surgical applications.

Cigarette smoke is one of the six major pollution sources in the room air. It contains large number of particles with size less than 10 nm. There exist carbon dots (CDs) in cigarette smoke which have strong fluorescence and with good bio-compatibility and low toxicity. CDs in cigarette smoke can be applied in bio-imaging which has great potential applications in the integration of cancer diagnosis and treatment. In this paper, CDs were extracted from cigarette smoke. Then, sodium borohydride was added to CDs aqueous solution for reduction and the reduced CDs (R-CDs) were used for biological cell imaging. The results indicate that the CDs with the particle size $<$10 nm in cigarette smoke are self-assembled by the polymerizated polycyclic aromatic hydrocarbons (PAHs) and ammonium nitrite which are disk nano-structure composed of $sp^2$/$sp^3$ carbon and oxygen/nitrogen groups or polymers. Sodium borohydride can reduce the carbonyl group on the surface of CDs to hydroxyl group and increase the ratio of the Na 1s ratio of the CDs from 1.86 to 7.42. The CDs can emit blue fluorescence under ultraviolet irradiation. After reduction, the R-CDS have the intensity of fluorescence 7.2 times than before and the fluorescence quantum yield increase from 6.13\% to 8.86\%. The photoluminescence (PL) wavelength of R-CDS have red-shift of 7 nm which was due to the increasing of Na element ratio. The onion epidermal cells labeled with R-CDs show that the CDs could pass through the cell wall into the cell and reach the nucleus. The cell wall and the nucleus could be clearly visualized. CDs also shows low toxicity to human bronchial epithelial cells (BEAS-2B) with good biological activity. The obtained results indicate that the CDs and R-CDs have good fluorescent property which could be used as bio-imaging agent., Comment: 12 pages, 9 figures

Purpose: Diffeomorphic image registration is essential in many medical imaging applications. Several registration algorithms of such type have been proposed, but primarily for intra-contrast alignment. Currently, efficient inter-modal/contrast diffeomorphic registration, which is vital in numerous applications, remains a challenging task. Methods: We proposed a novel inter-modal/contrast registration algorithm that leverages Robust PaTch-based cOrrelation Ratio (RaPTOR) metric to allow inter-modal/contrast image alignment and bandlimited geodesic shooting demonstrated in Fourier Approximated Lie Algebras (FLASH) algorithm for fast diffeomorphic registration. Results: The proposed algorithm, named DiffeoRaptor, was validated with three public databases for the tasks of brain and abdominal image registration while comparing the results against three state-of-the-art techniques, including FLASH, NiftyReg, and Symmetric image normalization (SyN). Conclusions: Our results demonstrated that DiffeoRaptor offered comparable or better registration performance in terms of registration accuracy. Moreover, DiffeoRaptor produces smoother deformations than SyN in inter-modal and contrast registration. The code for DiffeoRaptor is publicly available at https://github.com/nimamasoumi/DiffeoRaptor.

Purpose: Registration and segmentation of magnetic resonance (MR) and ultrasound (US) images play an essential role in surgical planning and resection of brain tumors. However, validating these techniques is challenging due to the scarcity of publicly accessible sources with high-quality ground truth information. To this end, we propose a unique annotation dataset of tumor tissues and resection cavities from the previously published RESECT dataset (Xiao et al. 2017) to encourage a more rigorous assessments of image processing techniques. Acquisition and validation methods: The RESECT database consists of MR and intraoperative US (iUS) images of 23 patients who underwent resection surgeries. The proposed dataset contains tumor tissues and resection cavity annotations of the iUS images. The quality of annotations were validated by two highly experienced neurosurgeons through several assessment criteria. Data format and availability: Annotations of tumor tissues and resection cavities are provided in 3D NIFTI formats. Both sets of annotations are accessible online in the \url{https://osf.io/6y4db}. Discussion and potential applications: The proposed database includes tumor tissue and resection cavity annotations from real-world clinical ultrasound brain images to evaluate segmentation and registration methods. These labels could also be used to train deep learning approaches. Eventually, this dataset should further improve the quality of image guidance in neurosurgery., Comment: Bahareh Behboodi and Francois-Xavier Carton share the first authorship

With the advances in speech communication systems such as online conferencing applications, we can seamlessly work with people regardless of where they are. However, during online meetings, speech quality can be significantly affected by background noise, reverberation, packet loss, network jitter, etc. Because of its nature, speech quality is traditionally assessed in subjective tests in laboratories and lately also in crowdsourcing following the international standards from ITU-T Rec. P.800 series. However, those approaches are costly and cannot be applied to customer data. Therefore, an effective objective assessment approach is needed to evaluate or monitor the speech quality of the ongoing conversation. The ConferencingSpeech 2022 challenge targets the non-intrusive deep neural network models for the speech quality assessment task. We open-sourced a training corpus with more than 86K speech clips in different languages, with a wide range of synthesized and live degradations and their corresponding subjective quality scores through crowdsourcing. 18 teams submitted their models for evaluation in this challenge. The blind test sets included about 4300 clips from wide ranges of degradations. This paper describes the challenge, the datasets, and the evaluation methods and reports the final results.

Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration data set for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https://learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, as well as results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias. While no single approach worked best across all tasks, many methodological aspects could be identified that push the performance of medical image registration to new state-of-the-art performance. Furthermore, we demystified the common belief that conventional registration methods have to be much slower than deep-learning-based methods.