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1.
J Biomed Opt ; 30(Suppl 1): S13703, 2025 Jan.
Article in English | MEDLINE | ID: mdl-39034959

ABSTRACT

Significance: Standardization of fluorescence molecular imaging (FMI) is critical for ensuring quality control in guiding surgical procedures. To accurately evaluate system performance, two metrics, the signal-to-noise ratio (SNR) and contrast, are widely employed. However, there is currently no consensus on how these metrics can be computed. Aim: We aim to examine the impact of SNR and contrast definitions on the performance assessment of FMI systems. Approach: We quantified the SNR and contrast of six near-infrared FMI systems by imaging a multi-parametric phantom. Based on approaches commonly used in the literature, we quantified seven SNRs and four contrast values considering different background regions and/or formulas. Then, we calculated benchmarking (BM) scores and respective rank values for each system. Results: We show that the performance assessment of an FMI system changes depending on the background locations and the applied quantification method. For a single system, the different metrics can vary up to ∼ 35 dB (SNR), ∼ 8.65 a . u . (contrast), and ∼ 0.67 a . u . (BM score). Conclusions: The definition of precise guidelines for FMI performance assessment is imperative to ensure successful clinical translation of the technology. Such guidelines can also enable quality control for the already clinically approved indocyanine green-based fluorescence image-guided surgery.


Subject(s)
Benchmarking , Molecular Imaging , Optical Imaging , Phantoms, Imaging , Signal-To-Noise Ratio , Molecular Imaging/methods , Molecular Imaging/standards , Optical Imaging/methods , Optical Imaging/standards , Image Processing, Computer-Assisted/methods
2.
IEEE Trans Med Imaging ; 43(8): 3013-3026, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39088484

ABSTRACT

Accurate motion estimation at high acceleration factors enables rapid motion-compensated reconstruction in Magnetic Resonance Imaging (MRI) without compromising the diagnostic image quality. In this work, we introduce an attention-aware deep learning-based framework that can perform non-rigid pairwise registration for fully sampled and accelerated MRI. We extract local visual representations to build similarity maps between the registered image pairs at multiple resolution levels and additionally leverage long-range contextual information using a transformer-based module to alleviate ambiguities in the presence of artifacts caused by undersampling. We combine local and global dependencies to perform simultaneous coarse and fine motion estimation. The proposed method was evaluated on in-house acquired fully sampled and accelerated data of 101 patients and 62 healthy subjects undergoing cardiac and thoracic MRI. The impact of motion estimation accuracy on the downstream task of motion-compensated reconstruction was analyzed. We demonstrate that our model derives reliable and consistent motion fields across different sampling trajectories (Cartesian and radial) and acceleration factors of up to 16x for cardiac motion and 30x for respiratory motion and achieves superior image quality in motion-compensated reconstruction qualitatively and quantitatively compared to conventional and recent deep learning-based approaches. The code is publicly available at https://github.com/lab-midas/GMARAFT.


Subject(s)
Deep Learning , Heart , Image Processing, Computer-Assisted , Magnetic Resonance Imaging , Humans , Magnetic Resonance Imaging/methods , Image Processing, Computer-Assisted/methods , Heart/diagnostic imaging , Algorithms , Artifacts , Movement/physiology , Thorax/diagnostic imaging , Adult
3.
J Biomed Opt ; 29(8): 080501, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39119134

ABSTRACT

Significance: The technique of remote focusing (RF) has attracted considerable attention among microscopists due to its ability to quickly adjust focus across different planes, thus facilitating quicker volumetric imaging. However, the difficulty in changing objectives to align with a matching objective in a remote setting while upholding key requirements remains a challenge. Aim: We aim to propose a customized yet straightforward technique to align multiple objectives with a remote objective, employing an identical set of optical elements to ensure meeting the criteria of remote focusing. Approach: We propose a simple optical approach for aligning multiple objectives with a singular remote objective to achieve a perfect imaging system. This method utilizes readily accessible, commercial optical components to meet the fundamental requirements of remote focusing. Results: Our experimental observations indicate that the proposed RF technique offers at least comparable, if not superior, performance over a significant axial depth compared with the conventional RF technique based on commercial lenses while offering the flexibility to switch the objective for multi-scale imaging. Conclusions: The proposed technique addresses various microscopy challenges, particularly in the realm of multi-resolution imaging. We have experimentally demonstrated the efficacy of this technique by capturing images of focal volumes generated by two distinct objectives in a water medium.


Subject(s)
Equipment Design , Image Processing, Computer-Assisted/methods , Microscopy/methods , Lenses
4.
Nat Commun ; 15(1): 6708, 2024 Aug 07.
Article in English | MEDLINE | ID: mdl-39112455

ABSTRACT

Functional magnetic resonance imaging in rodents holds great potential for advancing our understanding of brain networks. Unlike the human community, there remains no standardized resource in rodents for image processing, analysis and quality control, posing significant reproducibility limitations. Our software platform, Rodent Automated Bold Improvement of EPI Sequences, is a pipeline designed to address these limitations for preprocessing, quality control, and confound correction, along with best practices for reproducibility and transparency. We demonstrate the robustness of the preprocessing workflow by validating performance across multiple acquisition sites and both mouse and rat data. Building upon a thorough investigation into data quality metrics across acquisition sites, we introduce guidelines for the quality control of network analysis and offer recommendations for addressing issues. Taken together, this software platform will allow the emerging community to adopt reproducible practices and foster progress in translational neuroscience.


Subject(s)
Brain , Image Processing, Computer-Assisted , Magnetic Resonance Imaging , Software , Animals , Magnetic Resonance Imaging/methods , Rats , Mice , Image Processing, Computer-Assisted/methods , Brain/diagnostic imaging , Brain/physiology , Reproducibility of Results , Data Accuracy , Brain Mapping/methods , Male , Quality Control
5.
Radiat Oncol ; 19(1): 106, 2024 Aug 07.
Article in English | MEDLINE | ID: mdl-39113123

ABSTRACT

PURPOSE: Convolutional Neural Networks (CNNs) have emerged as transformative tools in the field of radiation oncology, significantly advancing the precision of contouring practices. However, the adaptability of these algorithms across diverse scanners, institutions, and imaging protocols remains a considerable obstacle. This study aims to investigate the effects of incorporating institution-specific datasets into the training regimen of CNNs to assess their generalization ability in real-world clinical environments. Focusing on a data-centric analysis, the influence of varying multi- and single center training approaches on algorithm performance is conducted. METHODS: nnU-Net is trained using a dataset comprising 161 18F-PSMA-1007 PET images collected from four distinct institutions (Freiburg: n = 96, Munich: n = 19, Cyprus: n = 32, Dresden: n = 14). The dataset is partitioned such that data from each center are systematically excluded from training and used solely for testing to assess the model's generalizability and adaptability to data from unfamiliar sources. Performance is compared through a 5-Fold Cross-Validation, providing a detailed comparison between models trained on datasets from single centers to those trained on aggregated multi-center datasets. Dice Similarity Score, Hausdorff distance and volumetric analysis are used as primary evaluation metrics. RESULTS: The mixed training approach yielded a median DSC of 0.76 (IQR: 0.64-0.84) in a five-fold cross-validation, showing no significant differences (p = 0.18) compared to models trained with data exclusion from each center, which performed with a median DSC of 0.74 (IQR: 0.56-0.86). Significant performance improvements regarding multi-center training were observed for the Dresden cohort (multi-center median DSC 0.71, IQR: 0.58-0.80 vs. single-center 0.68, IQR: 0.50-0.80, p < 0.001) and Cyprus cohort (multi-center 0.74, IQR: 0.62-0.83 vs. single-center 0.72, IQR: 0.54-0.82, p < 0.01). While Munich and Freiburg also showed performance improvements with multi-center training, results showed no statistical significance (Munich: multi-center DSC 0.74, IQR: 0.60-0.80 vs. single-center 0.72, IQR: 0.59-0.82, p > 0.05; Freiburg: multi-center 0.78, IQR: 0.53-0.87 vs. single-center 0.71, IQR: 0.53-0.83, p = 0.23). CONCLUSION: CNNs trained for auto contouring intraprostatic GTV in 18F-PSMA-1007 PET on a diverse dataset from multiple centers mostly generalize well to unseen data from other centers. Training on a multicentric dataset can improve performance compared to training exclusively with a single-center dataset regarding intraprostatic 18F-PSMA-1007 PET GTV segmentation. The segmentation performance of the same CNN can vary depending on the dataset employed for training and testing.


Subject(s)
Neural Networks, Computer , Prostatic Neoplasms , Humans , Male , Prostatic Neoplasms/diagnostic imaging , Prostatic Neoplasms/radiotherapy , Prostatic Neoplasms/pathology , Positron-Emission Tomography/methods , Niacinamide/analogs & derivatives , Oligopeptides , Radiopharmaceuticals , Fluorine Radioisotopes , Image Processing, Computer-Assisted/methods , Datasets as Topic , Algorithms
6.
Skin Res Technol ; 30(8): e13783, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39113617

ABSTRACT

BACKGROUND: In recent years, the increasing prevalence of skin cancers, particularly malignant melanoma, has become a major concern for public health. The development of accurate automated segmentation techniques for skin lesions holds immense potential in alleviating the burden on medical professionals. It is of substantial clinical importance for the early identification and intervention of skin cancer. Nevertheless, the irregular shape, uneven color, and noise interference of the skin lesions have presented significant challenges to the precise segmentation. Therefore, it is crucial to develop a high-precision and intelligent skin lesion segmentation framework for clinical treatment. METHODS: A precision-driven segmentation model for skin cancer images is proposed based on the Transformer U-Net, called BiADATU-Net, which integrates the deformable attention Transformer and bidirectional attention blocks into the U-Net. The encoder part utilizes deformable attention Transformer with dual attention block, allowing adaptive learning of global and local features. The decoder part incorporates specifically tailored scSE attention modules within skip connection layers to capture image-specific context information for strong feature fusion. Additionally, deformable convolution is aggregated into two different attention blocks to learn irregular lesion features for high-precision prediction. RESULTS: A series of experiments are conducted on four skin cancer image datasets (i.e., ISIC2016, ISIC2017, ISIC2018, and PH2). The findings show that our model exhibits satisfactory segmentation performance, all achieving an accuracy rate of over 96%. CONCLUSION: Our experiment results validate the proposed BiADATU-Net achieves competitive performance supremacy compared to some state-of-the-art methods. It is potential and valuable in the field of skin lesion segmentation.


Subject(s)
Melanoma , Skin Neoplasms , Humans , Skin Neoplasms/diagnostic imaging , Skin Neoplasms/pathology , Melanoma/diagnostic imaging , Melanoma/pathology , Algorithms , Neural Networks, Computer , Image Processing, Computer-Assisted/methods , Image Interpretation, Computer-Assisted/methods , Dermoscopy/methods , Deep Learning
7.
PLoS One ; 19(8): e0304827, 2024.
Article in English | MEDLINE | ID: mdl-39116043

ABSTRACT

The zebrafish Danio rerio has become a popular model host to explore disease pathology caused by infectious agents. A main advantage is its transparency at an early age, which enables live imaging of infection dynamics. While multispecies infections are common in patients, the zebrafish model is rarely used to study them, although the model would be ideal for investigating pathogen-pathogen and pathogen-host interactions. This may be due to the absence of an established multispecies infection protocol for a defined organ and the lack of suitable image analysis pipelines for automated image processing. To address these issues, we developed a protocol for establishing and tracking single and multispecies bacterial infections in the inner ear structure (otic vesicle) of the zebrafish by imaging. Subsequently, we generated an image analysis pipeline that involved deep learning for the automated segmentation of the otic vesicle, and scripts for quantifying pathogen frequencies through fluorescence intensity measures. We used Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae, three of the difficult-to-treat ESKAPE pathogens, to show that our infection protocol and image analysis pipeline work both for single pathogens and pairwise pathogen combinations. Thus, our protocols provide a comprehensive toolbox for studying single and multispecies infections in real-time in zebrafish.


Subject(s)
Image Processing, Computer-Assisted , Pseudomonas aeruginosa , Zebrafish , Zebrafish/microbiology , Animals , Image Processing, Computer-Assisted/methods , Bacterial Infections/microbiology , Bacterial Infections/diagnostic imaging , Acinetobacter baumannii/pathogenicity , Disease Models, Animal , Host-Pathogen Interactions , Klebsiella pneumoniae/pathogenicity , Ear, Inner/microbiology , Ear, Inner/diagnostic imaging , Deep Learning
8.
Sci Rep ; 14(1): 17854, 2024 08 01.
Article in English | MEDLINE | ID: mdl-39090141

ABSTRACT

Analyses of complex behaviors of Cerebrospinal Fluid (CSF) have become increasingly important in diseases diagnosis. The changes of the phase-contrast magnetic resonance imaging (PC-MRI) signal formed by the velocity of flowing CSF are represented as a set of velocity-encoded images or maps, which can be thought of as signal data in the context of medical imaging, enabling the evaluation of pulsatile patterns throughout a cardiac cycle. However, automatic segmentation of the CSF region in a PC-MRI image is challenging, and implementing an explained ML method using pulsatile data as a feature remains unexplored. This paper presents lightweight machine learning (ML) algorithms to perform CSF lumen segmentation in spinal, utilizing sets of velocity-encoded images or maps as a feature. The Dataset contains 57 PC-MRI slabs by 3T MRI scanner from control and idiopathic scoliosis participants are involved to collect data. The ML models are trained with 2176 time series images. Different cardiac periods image (frame) numbers of PC-MRIs are interpolated in the preprocessing step to align to features of equal size. The fivefold cross-validation procedure is used to estimate the success of the ML models. Additionally, the study focusses on enhancing the interpretability of the highest-accuracy eXtreme gradient boosting (XGB) model by applying the shapley additive explanations (SHAP) technique. The XGB algorithm presented its highest accuracy, with an average fivefold accuracy of 0.99% precision, 0.95% recall, and 0.97% F1 score. We evaluated the significance of each pulsatile feature's contribution to predictions, offering a more profound understanding of the model's behavior in distinguishing CSF lumen pixels with SHAP. Introducing a novel approach in the field, develop ML models offer comprehension into feature extraction and selection from PC-MRI pulsatile data. Moreover, the explained ML model offers novel and valuable insights to domain experts, contributing to an enhanced scholarly understanding of CSF dynamics.


Subject(s)
Cerebrospinal Fluid , Machine Learning , Magnetic Resonance Imaging , Pulsatile Flow , Humans , Magnetic Resonance Imaging/methods , Algorithms , Scoliosis/diagnostic imaging , Image Processing, Computer-Assisted/methods , Female , Male
9.
Sci Rep ; 14(1): 17779, 2024 08 01.
Article in English | MEDLINE | ID: mdl-39090237

ABSTRACT

Video-based monitoring is essential nowadays in cattle farm management systems for automated evaluation of cow health, encompassing body condition scores, lameness detection, calving events, and other factors. In order to efficiently monitor the well-being of each individual animal, it is vital to automatically identify them in real time. Although there are various techniques available for cattle identification, a significant number of them depend on radio frequency or visible ear tags, which are prone to being lost or damaged. This can result in financial difficulties for farmers. Therefore, this paper presents a novel method for tracking and identifying the cattle with an RGB image-based camera. As a first step, to detect the cattle in the video, we employ the YOLOv8 (You Only Look Once) model. The sample data contains the raw video that was recorded with the cameras that were installed at above from the designated lane used by cattle after the milk production process and above from the rotating milking parlor. As a second step, the detected cattle are continuously tracked and assigned unique local IDs. The tracked images of each individual cattle are then stored in individual folders according to their respective IDs, facilitating the identification process. The images of each folder will be the features which are extracted using a feature extractor called VGG (Visual Geometry Group). After feature extraction task, as a final step, the SVM (Support Vector Machine) identifier for cattle identification will be used to get the identified ID of the cattle. The final ID of a cattle is determined based on the maximum identified output ID from the tracked images of that particular animal. The outcomes of this paper will act as proof of the concept for the use of combining VGG features with SVM is an effective and promising approach for an automatic cattle identification system.


Subject(s)
Video Recording , Animals , Cattle , Video Recording/methods , Artificial Intelligence , Animal Identification Systems/methods , Animal Identification Systems/instrumentation , Support Vector Machine , Dairying/methods , Female , Image Processing, Computer-Assisted/methods
10.
Sci Rep ; 14(1): 17785, 2024 08 01.
Article in English | MEDLINE | ID: mdl-39090261

ABSTRACT

Skin cancer is a lethal disease, and its early detection plays a pivotal role in preventing its spread to other body organs and tissues. Artificial Intelligence (AI)-based automated methods can play a significant role in its early detection. This study presents an AI-based novel approach, termed 'DualAutoELM' for the effective identification of various types of skin cancers. The proposed method leverages a network of autoencoders, comprising two distinct autoencoders: the spatial autoencoder and the FFT (Fast Fourier Transform)-autoencoder. The spatial-autoencoder specializes in learning spatial features within input lesion images whereas the FFT-autoencoder learns to capture textural and distinguishing frequency patterns within transformed input skin lesion images through the reconstruction process. The use of attention modules at various levels within the encoder part of these autoencoders significantly improves their discriminative feature learning capabilities. An Extreme Learning Machine (ELM) with a single layer of feedforward is trained to classify skin malignancies using the characteristics that were recovered from the bottleneck layers of these autoencoders. The 'HAM10000' and 'ISIC-2017' are two publicly available datasets used to thoroughly assess the suggested approach. The experimental findings demonstrate the accuracy and robustness of the proposed technique, with AUC, precision, and accuracy values for the 'HAM10000' dataset being 0.98, 97.68% and 97.66%, and for the 'ISIC-2017' dataset being 0.95, 86.75% and 86.68%, respectively. This study highlights the possibility of the suggested approach for accurate detection of skin cancer.


Subject(s)
Machine Learning , Skin Neoplasms , Humans , Skin Neoplasms/diagnosis , Skin Neoplasms/diagnostic imaging , Early Detection of Cancer/methods , Algorithms , Artificial Intelligence , Image Processing, Computer-Assisted/methods
11.
Sci Rep ; 14(1): 17847, 2024 08 01.
Article in English | MEDLINE | ID: mdl-39090284

ABSTRACT

The problem of artifacts in whole slide image acquisition, prevalent in both clinical workflows and research-oriented settings, necessitates human intervention and re-scanning. Overcoming this challenge requires developing quality control algorithms, that are hindered by the limited availability of relevant annotated data in histopathology. The manual annotation of ground-truth for artifact detection methods is expensive and time-consuming. This work addresses the issue by proposing a method dedicated to augmenting whole slide images with artifacts. The tool seamlessly generates and blends artifacts from an external library to a given histopathology dataset. The augmented datasets are then utilized to train artifact classification methods. The evaluation shows their usefulness in classification of the artifacts, where they show an improvement from 0.10 to 0.01 AUROC depending on the artifact type. The framework, model, weights, and ground-truth annotations are freely released to facilitate open science and reproducible research.


Subject(s)
Algorithms , Artifacts , Image Processing, Computer-Assisted , Quality Control , Humans , Image Processing, Computer-Assisted/methods
12.
Sci Rep ; 14(1): 17809, 2024 08 01.
Article in English | MEDLINE | ID: mdl-39090263

ABSTRACT

Skin microvasculature is vital for human cardiovascular health and thermoregulation, but its imaging and analysis presents significant challenges. Statistical methods such as speckle decorrelation in optical coherence tomography angiography (OCTA) often require multiple co-located B-scans, leading to lengthy acquisitions prone to motion artefacts. Deep learning has shown promise in enhancing accuracy and reducing measurement time by leveraging local information. However, both statistical and deep learning methods typically focus solely on processing individual 2D B-scans, neglecting contextual information from neighbouring B-scans. This limitation compromises spatial context and disregards the 3D features within tissue, potentially affecting OCTA image accuracy. In this study, we propose a novel approach utilising 3D convolutional neural networks (CNNs) to address this limitation. By considering the 3D spatial context, these 3D CNNs mitigate information loss, preserving fine details and boundaries in OCTA images. Our method reduces the required number of B-scans while enhancing accuracy, thereby increasing clinical applicability. This advancement holds promise for improving clinical practices and understanding skin microvascular dynamics crucial for cardiovascular health and thermoregulation.


Subject(s)
Imaging, Three-Dimensional , Microvessels , Neural Networks, Computer , Skin , Tomography, Optical Coherence , Tomography, Optical Coherence/methods , Humans , Microvessels/diagnostic imaging , Microvessels/physiology , Skin/diagnostic imaging , Skin/blood supply , Imaging, Three-Dimensional/methods , Image Processing, Computer-Assisted/methods , Deep Learning
13.
Biomed Phys Eng Express ; 10(5)2024 Aug 08.
Article in English | MEDLINE | ID: mdl-39094603

ABSTRACT

Objective. Auto-segmentation in mouse micro-CT enhances the efficiency and consistency of preclinical experiments but often struggles with low-native-contrast and morphologically complex organs, such as the spleen, resulting in poor segmentation performance. While CT contrast agents can improve organ conspicuity, their use complicates experimental protocols and reduces feasibility. We developed a 3D Cycle Generative Adversarial Network (CycleGAN) incorporating anatomy-constrained U-Net models to leverage contrast-enhanced CT (CECT) insights to improve unenhanced native CT (NACT) segmentation.Approach.We employed a standard CycleGAN with an anatomical loss function to synthesize virtual CECT images from unpaired NACT scans at two different resolutions. Prior to training, two U-Nets were trained to automatically segment six major organs in NACT and CECT datasets, respectively. These pretrained 3D U-Nets were integrated during the CycleGAN training, segmenting synthetic images, and comparing them against ground truth annotations. The compound loss within the CycleGAN maintained anatomical fidelity. Full image processing was achieved for low-resolution datasets, while high-resolution datasets employed a patch-based method due to GPU memory constraints. Automated segmentation was applied to original NACT and synthetic CECT scans to evaluate CycleGAN performance using the Dice Similarity Coefficient (DSC) and the 95th percentile Hausdorff Distance (HD95p).Main results.High-resolution scans showed improved auto-segmentation, with an average DSC increase from 0.728 to 0.773 and a reduced HD95p from 1.19 mm to 0.94 mm. Low-resolution scans benefited more from synthetic contrast, showing a DSC increase from 0.586 to 0.682 and an HD95preduction from 3.46 mm to 1.24 mm.Significance.Implementing CycleGAN to synthesize CECT scans substantially improved the visibility of the mouse spleen, leading to more precise auto-segmentation. This approach shows the potential in preclinical imaging studies where contrast agent use is impractical.


Subject(s)
Contrast Media , Imaging, Three-Dimensional , Spleen , X-Ray Microtomography , Animals , Mice , Spleen/diagnostic imaging , X-Ray Microtomography/methods , Imaging, Three-Dimensional/methods , Algorithms , Image Processing, Computer-Assisted/methods , Neural Networks, Computer
14.
Sci Rep ; 14(1): 17954, 2024 08 02.
Article in English | MEDLINE | ID: mdl-39095416

ABSTRACT

The pharynx is one of the few areas in the body where blood vessels and immune tissues can readily be observed from outside the body non-invasively. Although prior studies have found that sex could be identified from retinal images using artificial intelligence, it remains unknown as to whether individuals' sex could also be identified using pharyngeal images. Demographic information and pharyngeal images were collected from patients who visited 64 primary care clinics in Japan for influenza-like symptoms. We trained a deep learning-based classification model to predict reported sex, which incorporated a multiple instance convolutional neural network, on 20,319 images from 51 clinics. Validation was performed using 4869 images from the remaining 13 clinics not used for the training. The performance of the classification model was assessed using the area under the receiver operating characteristic curve. To interpret the model, we proposed a framework that combines a saliency map and organ segmentation map to quantitatively evaluate salient regions. The model achieved the area under the receiver operating characteristic curve of 0.883 (95% CI 0.866-0.900). In subgroup analyses, a substantial improvement in classification performance was observed for individuals aged 20 and older, indicating that sex-specific patterns between women and men may manifest as humans age (e.g., may manifest after puberty). The saliency map suggested the model primarily focused on the posterior pharyngeal wall and the uvula. Our study revealed the potential utility of pharyngeal images by accurately identifying individuals' reported sex using deep learning algorithm.


Subject(s)
Deep Learning , Pharynx , Humans , Female , Male , Pharynx/diagnostic imaging , Adult , Middle Aged , Aged , Algorithms , Young Adult , ROC Curve , Neural Networks, Computer , Image Processing, Computer-Assisted/methods , Japan , Adolescent
15.
Sci Rep ; 14(1): 18007, 2024 08 03.
Article in English | MEDLINE | ID: mdl-39097627

ABSTRACT

Within the scope of this investigation, we carried out experiments to investigate the potential of the Vision Transformer (ViT) in the field of medical image analysis. The diagnosis of osteoporosis through inspection of X-ray radio-images is a substantial classification problem that we were able to address with the assistance of Vision Transformer models. In order to provide a basis for comparison, we conducted a parallel analysis in which we sought to solve the same problem by employing traditional convolutional neural networks (CNNs), which are well-known and commonly used techniques for the solution of image categorization issues. The findings of our research led us to conclude that ViT is capable of achieving superior outcomes compared to CNN. Furthermore, provided that methods have access to a sufficient quantity of training data, the probability increases that both methods arrive at more appropriate solutions to critical issues.


Subject(s)
Neural Networks, Computer , Osteoporosis , Osteoporosis/diagnostic imaging , Humans , X-Rays , Image Processing, Computer-Assisted/methods , Algorithms
16.
Sci Rep ; 14(1): 17995, 2024 08 03.
Article in English | MEDLINE | ID: mdl-39097661

ABSTRACT

Diffusion tensor magnetic resonance electrical impedance tomography (DT-MREIT) and electrodeless conductivity tensor imaging (CTI) are two emerging modalities that can quantify low-frequency tissue anisotropic conductivity properties by assuming similar properties underlie ionic mobility and water diffusion. While both methods have potential applications to estimating neuro-modulation fields or formulating forward models used for electrical source imaging, a direct comparison of the two modalities has not yet been performed in-vitro or in-vivo. Therefore, the aim of this study was to test the equivalence of these two modalities. We scanned a tissue phantom and the head of human subject using DT-MREIT and CTI protocols and reconstructed conductivity tensor and effective low frequency conductivities. We found both gray and white matter conductivities recovered by each technique were equivalent within 0.05 S/m. Both DT-MREIT and CTI require multiple processing steps, and we further assess the effects of each factor on reconstructions and evaluate the extent to which different measurement mechanisms potentially cause discrepancies between the two methods. Finally, we discuss the implications for spectral models of measuring conductivity using these techniques. The study further establishes the credibility of CTI as an electrodeless non-invasive method of measuring low frequency conductivity properties.


Subject(s)
Diffusion Tensor Imaging , Electric Conductivity , Electric Impedance , Phantoms, Imaging , Humans , Diffusion Tensor Imaging/methods , Tomography/methods , Brain/physiology , Brain/diagnostic imaging , Image Processing, Computer-Assisted/methods , Adult
17.
PLoS One ; 19(8): e0306530, 2024.
Article in English | MEDLINE | ID: mdl-39110679

ABSTRACT

Heatmap-based cattle pose estimation methods suffer from high network complexity and low detection speed. Addressing the issue of cattle pose estimation for complex scenarios without heatmaps, an end-to-end, lightweight cattle pose estimation network utilizing a reparameterized network and an attention mechanism is proposed to improve the overall network performance. The EfficientRepBiPAN (Efficient Representation Bi-Directional Progressive Attention Network) module, incorporated into the neck network, adeptly captures target features across various scales while also mitigating model redundancy. Moreover, a 3D parameterless SimAM (Similarity-based Attention Mechanism) attention mechanism is introduced into the backbone to capture richer directional and positional feature information. We constructed 6846 images to evaluate the performance of the model. The experimental results demonstrate that the proposed network outperforms the baseline method with a 4.3% increase in average accuracy at OKS = 0.5 on the test set. The proposed network reduces the number of floating-point computations by 1.0 G and the number of parameters by 0.16 M. Through comparative evaluations with heatmap and regression-based models such as HRNet, HigherHRNet, DEKR, DEKRv2, and YOLOv5-pose, our method improves AP0.5 by at least 0.4%, reduces the number of parameters by at least 0.4%, and decreases the amount of computation by at least 1.0 GFLOPs, achieving a harmonious balance between accuracy and efficiency. This method can serve as a theoretical reference for estimating cattle poses in various livestock industries.


Subject(s)
Algorithms , Cattle , Animals , Image Processing, Computer-Assisted/methods , Neural Networks, Computer
18.
PLoS One ; 19(8): e0306794, 2024.
Article in English | MEDLINE | ID: mdl-39110715

ABSTRACT

BACKGROUND AND OBJECTIVES: To develop and test VMseg, a new image processing algorithm performing automatic segmentation of retinal non-perfusion in widefield OCT-Angiography images, in order to estimate the non-perfusion index in diabetic patients. METHODS: We included diabetic patients with severe non-proliferative or proliferative diabetic retinopathy. We acquired images using the PlexElite 9000 OCT-A device with a photomontage of 5 images of size 12 x 12 mm. We then developed VMseg, a Python algorithm for non-perfusion detection, which binarizes a variance map calculated through convolution and morphological operations. We used 70% of our data set (development set) to fine-tune the algorithm parameters (convolution and morphological parameters, binarization thresholds) and evaluated the algorithm performance on the remaining 30% (test set). The obtained automatic segmentations were compared to a ground truth corresponding to manual segmentation from a retina expert and the inference processing time was estimated. RESULTS: We included 51 eyes of 30 patients (27 severe non-proliferative, 24 proliferative diabetic retinopathy). Using the optimal parameters found on the development set to tune the algorithm, the mean dice for the test set was 0.683 (sd = 0.175). We found a higher dice coefficient for images with a higher area of retinal non-perfusion (rs = 0.722, p < 10-4). There was a strong correlation (rs = 0.877, p < 10-4) between VMseg estimated non-perfusion indexes and indexes estimated using the ground truth segmentation. The Bland-Altman plot revealed that 3 eyes (5.9%) were significantly under-segmented by VMseg. CONCLUSION: We developed VMseg, an automatic algorithm for retinal non-perfusion segmentation on 12 x 12 mm OCT-A widefield photomontages. This simple algorithm was fast at inference time, segmented images in full-resolution and for the OCT-A format, was accurate enough for automatic estimation of retinal non-perfusion index in diabetic patients with diabetic retinopathy.


Subject(s)
Algorithms , Diabetic Retinopathy , Tomography, Optical Coherence , Humans , Diabetic Retinopathy/diagnostic imaging , Tomography, Optical Coherence/methods , Female , Male , Middle Aged , Aged , Image Processing, Computer-Assisted/methods , Retinal Vessels/diagnostic imaging , Retina/diagnostic imaging , Retina/pathology , Angiography/methods , Fluorescein Angiography/methods
19.
PLoS One ; 19(8): e0308236, 2024.
Article in English | MEDLINE | ID: mdl-39106259

ABSTRACT

A fundamental computer vision task called semantic segmentation has significant uses in the understanding of medical pictures, including the segmentation of tumors in the brain. The G-Shaped Net architecture appears in this context as an innovative and promising design that combines components from many models to attain improved accuracy and efficiency. In order to improve efficiency, the G-Shaped Net architecture synergistically incorporates four fundamental components: the Self-Attention, Squeeze Excitation, Fusion, and Spatial Pyramid Pooling block structures. These factors work together to improve the precision and effectiveness of brain tumor segmentation. Self-Attention, a crucial component of G-Shaped architecture, gives the model the ability to concentrate on the image's most informative areas, enabling accurate localization of tumor boundaries. By adjusting channel-wise feature maps, Squeeze Excitation completes this by improving the model's capacity to capture fine-grained information in the medical pictures. Since the G-Shaped model's Spatial Pyramid Pooling component provides multi-scale contextual information, the model is capable of handling tumors of various sizes and complexity levels. Additionally, the Fusion block architectures combine characteristics from many sources, enabling a thorough comprehension of the image and improving the segmentation outcomes. The G-Shaped Net architecture is an asset for medical imaging and diagnostics and represents a substantial development in semantic segmentation, which is needed more and more for accurate brain tumor segmentation.


Subject(s)
Brain Neoplasms , Semantics , Humans , Brain Neoplasms/diagnostic imaging , Brain Neoplasms/pathology , Image Processing, Computer-Assisted/methods , Algorithms , Magnetic Resonance Imaging/methods , Neural Networks, Computer
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