Segmentation Of Anatomical Structures Research Articles

Exploring Inherent Consistency for Semi-Supervised Anatomical Structure Segmentation in Medical Imaging.

Due to the exorbitant expense of obtaining labeled data in the field of medical image analysis, semi-supervised learning has emerged as a favorable method for the segmentation of anatomical structures. Although semi-supervised learning techniques have shown great potential in this field, existing methods only utilize image-level spatial consistency to impose unsupervised regularization on data in label space. Considering that anatomical structures often possess inherent anatomical properties that have not been focused on in previous works, this study introduces the inherent consistency into semi-supervised anatomical structure segmentation. First, the prediction and the ground-truth are projected into an embedding space to obtain latent representations that encapsulate the inherent anatomical properties of the structures. Then, two inherent consistency constraints are designed to leverage these inherent properties by aligning these latent representations. The proposed method is plug-and-play and can be seamlessly integrated with existing methods, thereby collaborating to improve segmentation performance and enhance the anatomical plausibility of the results. To evaluate the effectiveness of the proposed method, experiments are conducted on three public datasets (ACDC, LA, and Pancreas). Extensive experimental results demonstrate that the proposed method exhibits good generalizability and outperforms several state-of-the-art methods.

Necessity and impact of specialization of large foundation model for medical segmentation tasks.

Large foundation models, such as the Segment Anything Model (SAM), have shown remarkable performance in image segmentation tasks. However, the optimal approach to achieve true utility of these models for domain-specific applications, such as medical image segmentation, remains an open question. Recent studies have released a medical version of the foundation model MedSAM by training on vast medical data, who promised SOTA medical segmentation. Independent community inspection and dissection is needed. Foundation models are developed for general purposes. On the other hand, stable delivery of reliable performance is key to clinical utility. This study aims at elucidating the potential advantage and limitations of landing the foundation models in clinical use by assessing the performance of off-the-shelf medical foundation model MedSAM for the segmentation of anatomical structures in pelvic MR images. We also explore the simple remedies by evaluating the dependency on prompting scheme. Finally, we demonstrate the need and performance gain of further specialized fine-tuning. MedSAM and its lightweight version LiteMedSAM were evaluated out-of-the-box on a public MR dataset consisting of 589 pelvic images split 80:20 for training and testing. An nnU-Net model was trained from scratch to serve as a benchmark and to provide bounding box prompts for MedSAM. MedSAM was evaluated using different quality bounding boxes, those derived from ground truth labels, those derived from nnU-Net, and those derived from the former two but with 5-pixel isometric expansion. Lastly, LiteMedSAM was refined on the training set and reevaluated on this task. Out-of-the-box MedSAM and LiteMedSAM both performed poorly across the structure set, especially for disjoint or non-convex structures. Varying prompt with different bounding box inputs had minimal effect. For example, the mean Dice score and mean Hausdorff distances (in mm) for obturator internus using MedSAM and LiteMedSAM were {0.251±0.110, 0.101±0.079} and {34.142±5.196, 33.688±5.306}, respectively. Fine-tuning of LiteMedSAM led to significant performance gain, improving Dice score and Hausdorff distance for the obturator internus to 0.864±0.123 and 5.022±10.684, on par with nnU-Net with no significant difference in evaluation of most structures. All segmentation structures benefited significantly from specialized refinement, at varying improvement margin. While our study alludes to the potential of deep learning models like MedSAM and LiteMedSAM for medical segmentation, it highlights the need for specialized refinement and adjudication. Off-the-shelf use of such large foundation models is highly likely to be suboptimal, and specialized fine-tuning is often necessary to achieve clinical desired accuracy and stability.

Topology‐aware anatomical segmentation of the Circle of Willis: HUNet unveils the vascular network

AbstractThis research investigates the Circle of Willis, a critical vascular structure vital for cerebral blood supply. A modified novel dual‐pathway multi‐scale hierarchical upsampling network (HUNet) is presented, tailored explicitly for accurate segmentation of Circle of Willis anatomical components from medical imaging data. Evaluating both the multi‐label magnetic resonance angiography region of interest and the multi‐label magnetic resonance angiography whole brain‐case datasets, HUNet consistently outperforms the convolutional U‐net model, demonstrating superior capabilities and achieving higher accuracy across various classes. Additionally, the HUNet model achieves an exceptional dice similarity coefficient of 98.61 and 97.95, along with intersection over union scores of 73.32 and 85.76 in both the multi‐label magnetic resonance angiography region of interest and the multi‐label magnetic resonance angiography whole brain‐case datasets, respectively. These metrics highlight HUNet's exceptional performance in achieving precise and accurate segmentation of anatomical structures within the Circle of Willis, underscoring its robustness in medical image segmentation tasks. Visual representations substantiate HUNet's efficacy in delineating Circle of Willis structures, offering comprehensive insights into its superior performance.

Automatic segmentation and implicit surface representation of dynamic cardiac data

Segmentation of anatomical structures on 2D images of cardiac exams is necessary for performing 3D volumetric analysis, enabling the computation of parameters for diagnosing cardiovascular disease. In this work, we present robust algorithms to automatically segment cardiac imaging data and generate a volumetric anatomical reconstruction of a patient-specific heart model by propagating active contour output within a patient stack through a self-supervised learning model. Contour initializations are automatically generated, then output segmentations on sparse image slices are transferred and merged across a stack of images within the same heart data set during the segmentation process. We demonstrate whole-heart segmentation and compare the results with ground truth manual annotations. Additionally, we provide a framework to represent segmented heart data in the form of implicit surfaces, allowing interpolation operations to generate intermediary models of heart sections and volumes throughout the cardiac cycle and to estimate ejection fraction.

Automatic segmentation of 15 critical anatomical labels and measurements of cardiac axis and cardiothoracic ratio in fetal four chambers using nnU-NetV2

BackgroundAccurate segmentation of critical anatomical structures in fetal four-chamber view images is essential for the early detection of congenital heart defects. Current prenatal screening methods rely on manual measurements, which are time-consuming and prone to inter-observer variability. This study develops an AI-based model using the state-of-the-art nnU-NetV2 architecture for automatic segmentation and measurement of key anatomical structures in fetal four-chamber view images.MethodsA dataset, consisting of 1,083 high-quality fetal four-chamber view images, was annotated with 15 critical anatomical labels and divided into training/validation (867 images) and test (216 images) sets. An AI-based model using the nnU-NetV2 architecture was trained on the annotated images and evaluated using the mean Dice coefficient (mDice) and mean intersection over union (mIoU) metrics. The model’s performance in automatically computing the cardiac axis (CAx) and cardiothoracic ratio (CTR) was compared with measurements from sonographers with varying levels of experience.ResultsThe AI-based model achieved a mDice coefficient of 87.11% and an mIoU of 77.68% for the segmentation of critical anatomical structures. The model’s automated CAx and CTR measurements showed strong agreement with those of experienced sonographers, with respective intraclass correlation coefficients (ICCs) of 0.83 and 0.81. Bland–Altman analysis further confirmed the high agreement between the model and experienced sonographers.ConclusionWe developed an AI-based model using the nnU-NetV2 architecture for accurate segmentation and automated measurement of critical anatomical structures in fetal four-chamber view images. Our model demonstrated high segmentation accuracy and strong agreement with experienced sonographers in computing clinically relevant parameters. This approach has the potential to improve the efficiency and reliability of prenatal cardiac screening, ultimately contributing to the early detection of congenital heart defects.

Transfer learning for anatomical structure segmentation in otorhinolaryngology microsurgery.

Reducing the annotation burden is an active and meaningful area of artificial intelligence (AI) research. Multiple datasets for the segmentation of two landmarks were constructed based on 41257 labelled images and 6 different microsurgical scenarios. These datasets were trained using the multi-stage transfer learning (TL) methodology. The multi-stage TL enhanced segmentation performance over baseline (mIOU 0.6892 vs. 0.8869). Besides, Convolutional Neural Networks (CNNs) achieved a robust performance (mIOU 0.8917 vs. 0.8603) even when the training dataset size was reduced from 90% (30078 images) to 10% (3342 images). When directly applying the weight from one certain surgical scenario to recognise the same target in images of other scenarios without training, CNNs still obtained an optimal mIOU of 0.6190±0.0789. Model performance can be improved with TL in datasets with reduced size and increased complexity. It is feasible for data-based domain adaptation among different microsurgical fields.

An overview of artificial intelligence based applications for assisting digital data acquisition and implant planning procedures.

To provide an overview of the current artificial intelligence (AI) based applications for assisting digital data acquisition and implant planning procedures. A review of the main AI-based applications integrated into digital data acquisitions technologies (facial scanners (FS), intraoral scanners (IOSs), cone beam computed tomography (CBCT) devices, and jaw trackers) and computer-aided static implant planning programs are provided. The main AI-based application integrated in some FS's programs involves the automatic alignment of facial and intraoral scans for virtual patient integration. The AI-based applications integrated into IOSs programs include scan cleaning, assist scanning, and automatic alignment between the implant scan body with its corresponding CAD object while scanning. The more frequently AI-based applications integrated into the programs of CBCT units involve positioning assistant, noise and artifacts reduction, structures identification and segmentation, airway analysis, and alignment of facial, intraoral, and CBCT scans. Some computer-aided static implant planning programs include patient's digital files, identification, labeling, and segmentation of anatomical structures, mandibular nerve tracing, automatic implant placement, and surgical implant guide design.

Wallerian Degeneration Assessed by Multi-Modal Magnetic Resonance Imaging of Cervical Spinal Cord Is Associated With Neurological Impairment After Spinal Cord Injury.

While Wallerian degeneration (WD) is a crucial pathological process induced with spinal cord injury (SCI), its underlying mechanisms is still understudied. In this study, we aim to assess structural alterations and clinical significance of WD in the cervical cord following SCI using multi-modal magnetic resonance imaging (MRI), which combines T2*-weighted imaging and diffusion tensor imaging (DTI). T2*-weighted images allow segmentation of anatomical structures and the detection of WD on macrostructural level. DTI, on the other hand, can identify the reduction in neuroaxonal integrity by measuring the diffusion of water molecules on the microstructural level. In this prospective study, 35 SCI patients (19 paraplegic and 16 tetraplegic patients) and 12 healthy controls were recruited between July 2020 and May 2022. The hyperintensity voxels in the dorsal column was manually labeled as WD on T2*-weighted images. The mean cross-sectional area (CSA) and mean DTI indexes of WD at the C2 level were calculated and compared between groups. Correlation analysis was used to determine the associations of the magnitude of WD with lesion characteristics and clinical outcomes. Compared with controls, SCI patients showed evident hyperintensity (35/35) and decreased neuroaxonal integrity (p < 0.05) within the dorsal column at the C2 level. A higher neurological level of injury was associated with a larger mean CSA and reduction in neuroaxonal integrity within WD (p < 0.05). Smaller total and dorsal tissue bridges were related to greater mean CSA and lower fractional anisotropy values in WD (p < 0.05), respectively. Moreover, SCI participants with significantly larger CSAs and significantly lower microstructural integrity had worse sensory outcomes (p < 0.05). This comprehensive evaluation of WD can help us better understand the mechanisms of WD, monitor progression, and assess the effectiveness of therapeutic interventions after SCI.

Data-driven normative values based on generative manifold learning for quantitative MRI

In medicine, abnormalities in quantitative metrics such as the volume reduction of one brain region of an individual versus a control group are often provided as deviations from so-called normal values. These normative reference values are traditionally calculated based on the quantitative values from a control group, which can be adjusted for relevant clinical co-variables, such as age or sex. However, these average normative values do not take into account the globality of the available quantitative information. For example, quantitative analysis of T1-weighted magnetic resonance images based on anatomical structure segmentation frequently includes over 100 cerebral structures in the quantitative reports, and these tend to be analyzed separately. In this study, we propose a global approach to personalized normative values for each brain structure using an unsupervised Artificial Intelligence technique known as generative manifold learning. We test the potential benefit of these personalized normative values in comparison with the more traditional average normative values on a population of patients with drug-resistant epilepsy operated for focal cortical dysplasia, as well as on a supplementary healthy group and on patients with Alzheimer’s disease.

Shape-constrained deformable brain segmentation: Methods and quantitative validation

MRI-guided neuro interventions require rapid, accurate, and reproducible segmentation of anatomical brain structures for identification of targets during surgical procedures and post-surgical evaluation of intervention efficiency. Segmentation algorithms must be validated and cleared for clinical use. This work introduces a methodology for shape-constrained deformable brain segmentation, describes the quantitative validation used for its clinical clearance, and presents a comparison with manual expert segmentation and FreeSurfer, an open source software for neuroimaging data analysis. ClearPoint Maestro is software for fully-automatic brain segmentation from T1-weighted MRI that combines a shape-constrained deformable brain model with voxel-wise tissue segmentation within the cerebral hemispheres and the cerebellum. The performance of the segmentation was validated in terms of accuracy and reproducibility. Segmentation accuracy was evaluated with respect to training data and independently traced ground truth. Segmentation reproducibility was quantified and compared with manual expert segmentation and FreeSurfer. Quantitative reproducibility analysis indicates superior performance compared to both manual expert segmentation and FreeSurfer. The shape-constrained methodology results in accurate and highly reproducible segmentation. Inherent point based-correspondence provides consistent target identification ideal for MRI-guided neuro interventions.

Variability in Manual Segmentation of Temporal Bone Structures in Cone Beam CT Images.

Manual segmentation of anatomical structures is the accepted "gold standard" for labeling structures in clinical images. However, the variability in manual segmentation of temporal bone structures in CBCT images of the temporal bone has not been systematically evaluated using multiple reviewers. Therefore, we evaluated the intravariability and intervariability of manual segmentation of inner ear structures in CBCT images of the temporal bone. Preoperative CBCTs scans of the inner ear were obtained from 10 patients who had undergone cochlear implant surgery. The cochlea, facial nerve, chorda tympani, mid-modiolar (MM) axis, and round window (RW) were manually segmented by five reviewers in two separate sessions that were at least 1 month apart. Interreviewer and intrareviewer variabilities were assessed using the Dice coefficient (DICE), volume similarity, mean Hausdorff Distance metrics, and visual review. Manual segmentation of the cochlea was the most consistent within and across reviewers with a mean DICE of 0.91 (SD = 0.02) and 0.89 (SD = 0.01) respectively, followed by the facial nerve with a mean DICE of 0.83 (SD = 0.02) and 0.80 (SD = 0.03), respectively. The chorda tympani had the greatest amount of reviewer variability due to its thin size, and the location of the centroid of the RW and the MM axis were also quite variable between and within reviewers. We observed significant variability in manual segmentation of some of the temporal bone structures across reviewers. This variability needs to be considered when interpreting the results in studies using one manual reviewer.

CMF defects database: A craniomaxillofacial defects dataset and a data-driven repair method

Due to the large number of medical images generated each year, data-driven machine learning methods hold great promise in the field of medical image diagnosis and analysis. In recent years, the application of deep neural networks in oral and cranio-maxillofacial surgery has gradually increased, helping surgeons to obtain more comprehensive information and develop more accurate treatment planning, including segmentation and recognition of anatomical structures, disease diagnosis, and automatic surgical planning. This paper presents a new dataset of maxillofacial defect images, containing computed tomography (CT) data of 125 normal human cranial skeletal 3D reconstructions and 2625 corresponding craniomaxillofacial bone defects. The data are classified according to seven different types of defects which are anterior skull and forehead, zygomatic arch, zygomatic bone, Naso-orbital-ethmoidal (NOE), wall of the maxillary sinus, mandibular body, mandibular ramus, and condylar respectively. Each kind of defect is further divided into three categories according to the different locations, including left side, right side, and bilateral sides (or defect passes through the midline of the face). There are three main contributions: first, a dataset is publicly available to assist researchers in the development of data-based methods for generating missing portions of the skull; second, a repair method is proposed to evaluate the dataset; third, a review of various related datasets. The release of this dataset aims to advance artificial intelligence methods in the field of oral and cranio-maxillofacial surgery and plastic surgery helping physicians to reduce the difficulty and time consumption while improving the efficiency and accuracy of prosthesis design.

A YOLOX-Based Deep Instance Segmentation Neural Network for Cardiac Anatomical Structures in Fetal Ultrasound Images.

Echocardiography is an essential procedure for the prenatal examination of the fetus for congenital heart disease (CHD). Accurate segmentation of key anatomical structures in a four-chamber view is an essential step in measuring fetal growth parameters and diagnosing CHD. Currently, most obstetricians perform segmentation tasks manually, but the pixel-level operation is labor-intensive and requires extensive anatomical knowledge and clinical experience. As such, efficiently and accurately detecting structures from real-world fetal ultrasound images is a key challenge. In this paper, we propose a YOLOX-based deep instance segmentation neural network (i.e., IS-YOLOX) for cardiac anatomical structure location and segmentation in fetal ultrasound images. Specifically, we reconstruct a new instance segmentation branch based on a multi-task deep learning framework. We then design a new multi-level non-maximum suppression (NMS) mechanism to further improve the segmentation performance that consists of three levels of selection. Moreover, unlike two-stage instance segmentation approaches, our method does not rely on object detection results. To the best of our knowledge, this is the first study regarding instance segmentation on 13 types of anatomical structures in the fetal four-chamber view. Extensive experiments were carried out on clinical datasets, and the experimental results show that our method outperforms nine competitive baselines.

Validation of a Finite Element Simulation for Predicting Individual Knee Joint Kinematics.

Goal: We introduce an in-vivo validated finite element (FE) simulation approach for predicting individual knee joint kinematics. Our vision is to improve clinicians' understanding of the complex individual anatomy and potential pathologies to improve treatment and restore physiological joint kinematics. Methods: Our 3D FE modeling approach for individual human knee joints is based on segmentation of anatomical structures extracted from routine static magnetic resonance (MR) images. We validate the predictive abilities of our model using static MR images of the knees of eleven healthy volunteers in dedicated knee poses, which are achieved using a customized MR-compatible pneumatic loading device. Results: Our FE simulations reach an average translational accuracy of 2 mm and an average angular accuracy of 1[Formula: see text] compared to the reference knee pose. Conclusions: Reaching high accuracy, our individual FE model can be used in the decision-making process to restore knee joint stability and functionality after various knee injuries.

PCNet: Prior Category Network for CT Universal Segmentation Model.

Accurate segmentation of anatomical structures in Computed Tomography (CT) images is crucial for clinical diagnosis, treatment planning, and disease monitoring. The present deep learning segmentation methods are hindered by factors such as data scale and model size. Inspired by how doctors identify tissues, we propose a novel approach, the Prior Category Network (PCNet), that boosts segmentation performance by leveraging prior knowledge between different categories of anatomical structures. Our PCNet comprises three key components: prior category prompt (PCP), hierarchy category system (HCS), and hierarchy category loss (HCL). PCP utilizes Contrastive Language-Image Pretraining (CLIP), along with attention modules, to systematically define the relationships between anatomical categories as identified by clinicians. HCS guides the segmentation model in distinguishing between specific organs, anatomical structures, and functional systems through hierarchical relationships. HCL serves as a consistency constraint, fortifying the directional guidance provided by HCS to enhance the segmentation model's accuracy and robustness. We conducted extensive experiments to validate the effectiveness of our approach, and the results indicate that PCNet can generate a high-performance, universal model for CT segmentation. The PCNet framework also demonstrates a significant transferability on multiple downstream tasks. The ablation experiments show that the methodology employed in constructing the HCS is of critical importance. The prompt and HCS can be accessed at https://github.com/YixinChen-AI/PCNet.

Improved segmentation of basal ganglia from MR images using convolutional neural network with crossover-typed skip connection.

Accurate and automatic segmentation of basal ganglia from magnetic resonance (MR) images is important for diagnosis and treatment of various brain disorders. However, the basal ganglia segmentation is a challenging task because of the class imbalance and the unclear boundaries among basal ganglia anatomical structures. Thus, we aim to present an encoder-decoder convolutional neural network (CNN)-based method for improved segmentation of basal ganglia by focusing on skip connections that determine the segmentation performance of encoder-decoder CNNs. We also aim to reveal the effect of skip connections on the segmentation of basal ganglia with unclear boundaries. We used the encoder-decoder CNNs with the following five patterns of skip connections: without skip connection, with full-resolution horizontal skip connection, with horizontal skip connections, with vertical skip connections, and with crossover-typed skip connections (the proposed method). We compared and evaluated the performance of the CNNs in the experiment of basal ganglia segmentation using T1-weighted MR brain images of 79 patients. The experimental results showed that the skip connections at each scale level help CNNs to acquire multi-scale image features, the vertical skip connections contribute on acquiring finer image features for segmentation of smaller anatomical structures with more blurred boundaries, and the crossover-typed skip connections, a combination of horizontal and vertical skip connections, provided better segmentation accuracy. This paper investigated the effect of skip connections on the basal ganglia segmentation and revealed the crossover-typed skip connections might be effective for improving the segmentation of basal ganglia with the class imbalance and the unclear boundaries.

Coarse-to-fine prior-guided attention network for multi-structure segmentation on dental panoramic radiographs

Objective. Accurate segmentation of various anatomical structures from dental panoramic radiographs is essential for the diagnosis and treatment planning of various diseases in digital dentistry. In this paper, we propose a novel deep learning-based method for accurate and fully automatic segmentation of the maxillary sinus, mandibular condyle, mandibular nerve, alveolar bone and teeth on panoramic radiographs. Approach. A two-stage coarse-to-fine prior-guided segmentation framework is proposed to segment multiple structures on dental panoramic radiographs. In the coarse stage, a multi-label segmentation network is used to generate the coarse segmentation mask, and in the fine-tuning stage, a prior-guided attention network with an encoder-decoder architecture is proposed to precisely predict the mask of each anatomical structure. First, a prior-guided edge fusion module is incorporated into the network at the input of each convolution level of the encode path to generate edge-enhanced image feature maps. Second, a prior-guided spatial attention module is proposed to guide the network to extract relevant spatial features from foreground regions based on the combination of the prior information and the spatial attention mechanism. Finally, a prior-guided hybrid attention module is integrated at the bottleneck of the network to explore global context from both spatial and category perspectives. Main results. We evaluated the segmentation performance of our method on a testing dataset that contains 150 panoramic radiographs collected from real-world clinical scenarios. The segmentation results indicate that our proposed method achieves more accurate segmentation performance compared with state-of-the-art methods. The average Jaccard scores are 87.91%, 85.25%, 63.94%, 93.46% and 88.96% for the maxillary sinus, mandibular condyle, mandibular nerve, alveolar bone and teeth, respectively. Significance. The proposed method was able to accurately segment multiple structures on panoramic radiographs. This method has the potential to be part of the process of automatic pathology diagnosis from dental panoramic radiographs.

Machine Learning Empowering Personalized Medicine: A Comprehensive Review of Medical Image Analysis Methods

Artificial intelligence (AI) advancements, especially deep learning, have significantly improved medical image processing and analysis in various tasks such as disease detection, classification, and anatomical structure segmentation. This work overviews fundamental concepts, state-of-the-art models, and publicly available datasets in the field of medical imaging. First, we introduce the types of learning problems commonly employed in medical image processing and then proceed to present an overview of commonly used deep learning methods, including convolutional neural networks (CNNs), recurrent neural networks (RNNs), and generative adversarial networks (GANs), with a focus on the image analysis task they are solving, including image classification, object detection/localization, segmentation, generation, and registration. Further, we highlight studies conducted in various application areas, encompassing neurology, brain imaging, retinal analysis, pulmonary imaging, digital pathology, breast imaging, cardiac imaging, bone analysis, abdominal imaging, and musculoskeletal imaging. The strengths and limitations of each method are carefully examined, and the paper identifies pertinent challenges that still require attention, such as the limited availability of annotated data, variability in medical images, and the interpretability issues. Finally, we discuss future research directions with a particular focus on developing explainable deep learning methods and integrating multi-modal data.

EU-Net: Automatic U-Net neural architecture search with differential evolutionary algorithm for medical image segmentation

Medical images are crucial in clinical practice, providing essential information for patient assessment and treatment planning. However, manual extraction of information from images is both time-consuming and prone to errors. The emergence of U-Net addresses this challenge by automating the segmentation of anatomical structures and pathological lesions in medical images, thereby significantly enhancing the accuracy of image interpretation and diagnosis. However, the performance of U-Net largely depends on its encoder–decoder structure, which requires researchers with knowledge of neural network architecture design and an in-depth understanding of medical images. In this paper, we propose an automatic U-Net Neural Architecture Search (NAS) algorithm using the differential evolutionary (DE) algorithm, named EU-Net, to segment critical information in medical images to assist physicians in diagnosis. Specifically, by presenting the variable-length strategy, the proposed EU-Net algorithm can sufficiently and automatically search for the neural network architecture without expertise. Moreover, the utilization of crossover, mutation, and selection strategies of DE takes account of the trade-off between exploration and exploitation in the search space. Finally, in the encoding and decoding phases of the proposed algorithm, different block-based and layer-based structures are introduced for architectural optimization. The proposed EU-Net algorithm is validated on two widely used medical datasets, i.e., CHAOS and BUSI, for image segmentation tasks. Extensive experimental results show that the proposed EU-Net algorithm outperforms the chosen peer competitors in both two datasets. In particular, compared to the original U-Net, our proposed method improves the metric mIou by at least 6%.

Automated segmentation of insect anatomy from micro‐CT images using deep learning

AbstractThree‐dimensional (3D) imaging, such as microcomputed tomography (micro‐CT), is increasingly being used by organismal biologists for precise and comprehensive anatomical characterization. However, the segmentation of anatomical structures remains a bottleneck in research, often requiring tedious manual work. Here, we propose a pipeline for the fully automated segmentation of anatomical structures in micro‐CT images utilizing state‐of‐the‐art deep learning methods, selecting the ant brain as a test case. We implemented the U‐Net architecture for two‐dimensional (2D) image segmentation for our convolutional neural network (CNN), combined with pixel‐island detection. For training and validation of the network, we assembled a data set of semimanually segmented brain images of 76 ant species. The trained network predicted the brain area in ant images fast and accurately; its performance tested on validation sets showed good agreement between the prediction and the target, scoring 80% Intersection over Union (IoU) and 90% Dice Coefficient (F1) accuracy. While manual segmentation usually takes many hours for each brain, the trained network takes only a few minutes. Furthermore, our network is generalizable for segmenting the whole neural system in full‐body scans, and works in tests on distantly related and morphologically divergent insects (e.g., fruit flies). The latter suggests that methods like the one presented here generally apply across diverse taxa. Our method makes the construction of segmented maps and the morphological quantification of different species more efficient and scalable to large data sets, a step toward a big data approach to organismal anatomy.Key points Development of a deep learning‐based pipeline for the fully automated segmentation of micro‐CT images of insects, using ant brains as a starting point. Creation of an open access data set of micro‐CT images of ant heads for training and testing. Generalizable computer vision methodology, extendable across diverse taxa and anatomical features.