Deep Learning-based Segmentation Methods Research Articles

Automatic Time-Resolved Cardiovascular Segmentation of 4D Flow MRI Using Deep Learning.

Segmenting the whole heart over the cardiac cycle in 4D flow MRI is a challenging and time-consuming process, as there is considerable motion and limited contrast between blood and tissue. To develop and evaluate a deep learning-based segmentation method to automatically segment the cardiac chambers and great thoracic vessels from 4D flow MRI. Retrospective. A total of 205 subjects, including 40 healthy volunteers and 165 patients with a variety of cardiac disorders were included. Data were randomly divided into training (n = 144), validation (n = 20), and testing (n = 41) sets. A 3 T/time-resolved velocity encoded 3D gradient echo sequence (4D flow MRI). A 3D neural network based on the U-net architecture was trained to segment the four cardiac chambers, aorta, and pulmonary artery. The segmentations generated were compared to manually corrected atlas-based segmentations. End-diastolic (ED) and end-systolic (ES) volumes of the four cardiac chambers were calculated for both segmentations. Dice score, Hausdorff distance, average surface distance, sensitivity, precision, and miss rate were used to measure segmentation accuracy. Bland-Altman analysis was used to evaluate agreement between volumetric parameters. The following evaluation metrics were computed: mean Dice score (0.908 ± 0.023) (mean ± SD), Hausdorff distance (1.253 ± 0.293 mm), average surface distance (0.466 ± 0.136 mm), sensitivity (0.907 ± 0.032), precision (0.913 ± 0.028), and miss rate (0.093 ± 0.032). Bland-Altman analyses showed good agreement between volumetric parameters for all chambers. Limits of agreement as percentage of mean chamber volume (LoA%), left ventricular: 9.3%, 13.5%, left atrial: 12.4%, 16.9%, right ventricular: 9.9%, 15.6%, and right atrial: 18.7%, 14.4%; for ED and ES, respectively. The addition of this technique to the 4D flow MRI assessment pipeline could expedite and improve the utility of this type of acquisition in the clinical setting. 4 TECHNICAL EFFICACY: Stage 1.

A deep learning-based method for segmentation and quantitative characterization of microstructures in weathering steel from sequential scanning electron microscope images

A deep learning-based method for segmentation and quantitative characterization of microstructures in weathering steel from sequential scanning electron microscope images

Deep learning-based automatic segmentation of meningioma from multiparametric MRI for preoperative meningioma differentiation using radiomic features: a multicentre study.

Develop and evaluate a deep learning-based automatic meningioma segmentation method for preoperative meningioma differentiation using radiomic features. A retrospective multicentre inclusion of MR examinations (T1/T2-weighted and contrast-enhanced T1-weighted imaging) was conducted. Data from centre 1 were allocated to training (n = 307, age = 50.94 ± 11.51) and internal testing (n = 238, age = 50.70 ± 12.72) cohorts, and data from centre 2 external testing cohort (n = 64, age = 48.45 ± 13.59). A modified attention U-Net was trained for meningioma segmentation. Segmentation accuracy was evaluated by five quantitative metrics. The agreement between radiomic features from manual and automatic segmentations was assessed using intra class correlation coefficient (ICC). After univariate and minimum-redundancy-maximum-relevance feature selection, L1-regularized logistic regression models for differentiating between low-grade (I) and high-grade (II and III) meningiomas were separately constructed using manual and automatic segmentations; their performances were evaluated using ROC analysis. Dice of meningioma segmentation for the internal testing cohort were 0.94 ± 0.04 and 0.91 ± 0.05 for tumour volumes in contrast-enhanced T1-weighted and T2-weighted images, respectively; those for the external testing cohort were 0.90 ± 0.07 and 0.88 ± 0.07. Features extracted using manual and automatic segmentations agreed well, for both the internal (ICC = 0.94, interquartile range: 0.88-0.97) and external (ICC = 0.90, interquartile range: 0.78-70.96) testing cohorts. AUC of radiomic model with automatic segmentation was comparable with that of the model with manual segmentation for both the internal (0.95 vs. 0.93, p = 0.176) and external (0.88 vs. 0.91, p = 0.419) testing cohorts. The developed deep learning-based segmentation method enables automatic and accurate extraction of meningioma from multiparametric MR images and can help deploy radiomics for preoperative meningioma differentiation in clinical practice. • A deep learning-based method was developed for automatic segmentation of meningioma from multiparametric MR images. • The automatic segmentation method enabled accurate extraction of meningiomas and yielded radiomic features that were highly consistent with those that were obtained using manual segmentation. • High-grade meningiomas were preoperatively differentiated from low-grade meningiomas using a radiomic model constructed on features from automatic segmentation.

Image Segmentation Techniques for Intelligent Monitoring of Putonghua Examinations

Image recognition and image processing usually contain the technique of image segmentation. Excellent segmentation results can directly affect the accuracy of image recognition and processing. The essence of image segmentation is to segment each frame of a certain image or a video into multiple specific objects or regions and represent them with different labels. This paper focuses on the segmentation results obtained in image segmentation of images used for intelligent monitoring of Mandarin exams are usually visualized for image analysis. In this paper, we first investigate the performance improvement techniques for semantic segmentation in the image segmentation task for intelligent monitoring of Mandarin exams, improve the pixel classification capability by performing semantic migration, and, for the first time, extend the dataset substantially by style transformation to improve the model’s recognition of advanced features. In addition, to further address the shortcomings of the dataset, this paper improves the performance of image segmentation using synthetic datasets by investigating synthetic dataset image segmentation improvement techniques that reduce the reliance on manually annotated datasets. Image segmentation techniques continue to advance, and there are even thousands of commonly used segmentation methods for image segmentation development to date. Among them, they can be broadly classified as region-based segmentation methods, threshold-based segmentation methods, edge-based segmentation methods, specific theory-based segmentation methods, and deep learning-based segmentation methods. However, the methods used in this paper have all been experimentally demonstrated to improve the effectiveness of the techniques and proved to outperform other existing methods in the same field in the publicly available datasets LSUN, Cityscapes, and GTA5 datasets, respectively.

Superpixel-Oriented Label Distribution Learning for Skin Lesion Segmentation.

Lesion segmentation is a critical task in skin cancer analysis and detection. When developing deep learning-based segmentation methods, we need a large number of human-annotated labels to serve as ground truth for model-supervised learning. Due to the complexity of dermatological images and the subjective differences of different dermatologists in decision-making, the labels in the segmentation target boundary region are prone to produce uncertain labels or error labels. These labels may lead to unsatisfactory performance of dermoscopy segmentation. In addition, the model trained by the errored one-hot label may be overconfident, which can lead to arbitrary prediction and model overfitting. In this paper, a superpixel-oriented label distribution learning method is proposed. The superpixels formed by the simple linear iterative cluster (SLIC) algorithm combine one-hot labels constraint and define a distance function to convert it into a soft probability distribution. Referring to the model structure of knowledge distillation, after Superpixel-oriented label distribution learning, we get soft labels with structural prior information. Then the soft labels are transferred as new knowledge to the lesion segmentation network for training. Ours method on ISIC 2018 datasets achieves an Dice coefficient reaching 84%, sensitivity 79.6%, precision 80.4%, improved by 19.3%, 8.6% and 2.5% respectively in comparison with the results of U-Net. We also evaluate our method on the tasks of skin lesion segmentation via several general neural network architectures. The experiments show that ours method improves the performance of network image segmentation and can be easily integrated into most existing deep learning architectures.

Automatic zonal segmentation of the prostate from 2D and 3D T2-weighted MRI and evaluation for clinical use.

Purpose: An accurate zonal segmentation of the prostate is required for prostate cancer (PCa) management with MRI. Approach: The aim of this work is to present UFNet, a deep learning-based method for automatic zonal segmentation of the prostate from T2-weighted (T2w) MRI. It takes into account the image anisotropy, includes both spatial and channelwise attention mechanisms and uses loss functions to enforce prostate partition. The method was applied on a private multicentric three-dimensional T2w MRI dataset and on the public two-dimensional T2w MRI dataset ProstateX. To assess the model performance, the structures segmented by the algorithm on the private dataset were compared with those obtained by seven radiologists of various experience levels. Results: On the private dataset, we obtained a Dice score (DSC) of for the whole gland (WG), for the transition zone (TZ), and for the peripheral zone (PZ). Results were significantly better than other compared networks' ( ). On ProstateX, we obtained a DSC of for WG, for TZ, and for PZ. These results are similar to state-of-the art results and, on the private dataset, are coherent with those obtained by radiologists. Zonal locations and sectorial positions of lesions annotated by radiologists were also preserved. Conclusions: Deep learning-based methods can provide an accurate zonal segmentation of the prostate leading to a consistent zonal location and sectorial position of lesions, and therefore can be used as a helping tool for PCa diagnosis.

Optimization of deep learning based segmentation method

Optimization of deep learning based segmentation method

Learning a Discriminative Feature Attention Network for pancreas CT segmentation

Accurate pancreas segmentation is critical for the diagnosis and management of diseases of the pancreas. It is challenging to precisely delineate pancreas due to the highly variations in volume, shape and location. In recent years, coarse-to-fine methods have been widely used to alleviate class imbalance issue and improve pancreas segmentation accuracy. However, cascaded methods could be computationally intensive and the refined results are significantly dependent on the performance of its coarse segmentation results. To balance the segmentation accuracy and computational efficiency, we propose a Discriminative Feature Attention Network for pancreas segmentation, to effectively highlight pancreas features and improve segmentation accuracy without explicit pancreas location. The final segmentation is obtained by applying a simple yet effective post-processing step. Two experiments on both public NIH pancreas CT dataset and abdominal BTCV multi-organ dataset are individually conducted to show the effectiveness of our method for 2D pancreas segmentation. We obtained average Dice Similarity Coefficient (DSC) of 82.82±6.09%, average Jaccard Index (JI) of 71.13± 8.30% and average Symmetric Average Surface Distance (ASD) of 1.69 ± 0.83 mm on the NIH dataset. Compared to the existing deep learning-based pancreas segmentation methods, our experimental results achieve the best average DSC and JI value.

One-Shot Learning with Pseudo-Labeling for Cattle Video Segmentation in Smart Livestock Farming.

Simple SummaryDeep learning-based segmentation methods rely on large-scale pixel-labeled datasets to achieve good performance. However, it is resource-costly to label animal images due to their irregular contours and changing postures. To keep a balance between segmentation accuracy and speed using limited label data, we propose a one-shot learning-based approach with pseudo-labeling to segment animals in videos, relying on only one labeled frame. Experiments were conducted on a challenging feedlot cattle video dataset acquired by the authors, and the results show that the proposed method outperformed state-of-the-art methods such as one-shot video object segmentation (OSVOS) and one-shot modulation network (OSMN). Our proposed one-shot learning with pseudo-labeling reduces the reliance on labeled data and could serve as an enabling component for smart farming-related applications.Computer vision-based technologies play a key role in precision livestock farming, and video-based analysis approaches have been advocated as useful tools for automatic animal monitoring, behavior analysis, and efficient welfare measurement management. Accurately and efficiently segmenting animals’ contours from their backgrounds is a prerequisite for vision-based technologies. Deep learning-based segmentation methods have shown good performance through training models on a large amount of pixel-labeled images. However, it is challenging and time-consuming to label animal images due to their irregular contours and changing postures. In order to reduce the reliance on the number of labeled images, one-shot learning with a pseudo-labeling approach is proposed using only one labeled image frame to segment animals in videos. The proposed approach is mainly comprised of an Xception-based Fully Convolutional Neural Network (Xception-FCN) module and a pseudo-labeling (PL) module. Xception-FCN utilizes depth-wise separable convolutions to learn different-level visual features and localize dense prediction based on the one single labeled frame. Then, PL leverages the segmentation results of the Xception-FCN model to fine-tune the model, leading to performance boosts in cattle video segmentation. Systematic experiments were conducted on a challenging feedlot cattle video dataset acquired by the authors, and the proposed approach achieved a mean intersection-over-union score of 88.7% and a contour accuracy of 80.8%, outperforming state-of-the-art methods (OSVOS and OSMN). Our proposed one-shot learning approach could serve as an enabling component for livestock farming-related segmentation and detection applications.

Convolutional Blur Attention Network for Cell Nuclei Segmentation.

Accurately segmented nuclei are important, not only for cancer classification, but also for predicting treatment effectiveness and other biomedical applications. However, the diversity of cell types, various external factors, and illumination conditions make nucleus segmentation a challenging task. In this work, we present a new deep learning-based method for cell nucleus segmentation. The proposed convolutional blur attention (CBA) network consists of downsampling and upsampling procedures. A blur attention module and a blur pooling operation are used to retain the feature salience and avoid noise generation in the downsampling procedure. A pyramid blur pooling (PBP) module is proposed to capture the multi-scale information in the upsampling procedure. The superiority of the proposed method has been compared with a few prior segmentation models, namely U-Net, ENet, SegNet, LinkNet, and Mask RCNN on the 2018 Data Science Bowl (DSB) challenge dataset and the multi-organ nucleus segmentation (MoNuSeg) at MICCAI 2018. The Dice similarity coefficient and some evaluation matrices, such as F1 score, recall, precision, and average Jaccard index (AJI) were used to evaluate the segmentation efficiency of these models. Overall, the proposal method in this paper has the best performance, the AJI indicator on the DSB dataset and MoNuSeg is 0.8429, 0.7985, respectively.

A Quantitative Imaging Biomarker Supporting Radiological Assessment of Hippocampal Sclerosis Derived From Deep Learning-Based Segmentation of T1w-MRI.

PurposeHippocampal volumetry is an important biomarker to quantify atrophy in patients with mesial temporal lobe epilepsy. We investigate the sensitivity of automated segmentation methods to support radiological assessments of hippocampal sclerosis (HS). Results from FreeSurfer and FSL-FIRST are contrasted to a deep learning (DL)-based segmentation method.Materials and MethodsWe used T1-weighted MRI scans from 105 patients with epilepsy and 354 healthy controls. FreeSurfer, FSL, and a DL-based method were applied for brain anatomy segmentation. We calculated effect sizes (Cohen's d) between left/right HS and healthy controls based on the asymmetry of hippocampal volumes. Additionally, we derived 14 shape features from the segmentations and determined the most discriminating feature to identify patients with hippocampal sclerosis by a support vector machine (SVM).ResultsDeep learning-based segmentation of the hippocampus was the most sensitive to detecting HS. The effect sizes of the volume asymmetries were larger with the DL-based segmentations (HS left d= −4.2, right = 4.2) than with FreeSurfer (left= −3.1, right = 3.7) and FSL (left= −2.3, right = 2.5). For the classification based on the shape features, the surface-to-volume ratio was identified as the most important feature. Its absolute asymmetry yielded a higher area under the curve (AUC) for the deep learning-based segmentation (AUC = 0.87) than for FreeSurfer (0.85) and FSL (0.78) to dichotomize HS from other epilepsy cases. The robustness estimated from repeated scans was statistically significantly higher with DL than all other methods.ConclusionOur findings suggest that deep learning-based segmentation methods yield a higher sensitivity to quantify hippocampal sclerosis than atlas-based methods and derived shape features are more robust. We propose an increased asymmetry in the surface-to-volume ratio of the hippocampus as an easy-to-interpret quantitative imaging biomarker for HS.

Structure attention co-training neural network for neovascularization segmentation in intravascular optical coherence tomography.

To development and validate a neovascularization (NV) segmentation model in intravascular optical coherence tomography (IVOCT) through deep learning methods. A total of 1950 2D slices of 70 IVOCT pullbacks were used in our study. We randomly selected 1273 2D slices from 44 patients as the training set, 379 2D slices from 11 patients as the validation set, and 298 2D slices from the last 15 patients as the testing set. Automatic NV segmentation is quite challenging, as it must address issues of speckle noise, shadow artifacts, high distribution variation, etc. To meet these challenges, a new deep learning-based segmentation method is developed based on a co-training architecture with an integrated structural attention mechanism. Co-training is developed to exploit the features of three consecutive slices. The structural attention mechanism comprises spatial and channel attention modules and is integrated into the co-training architecture at each up-sampling step. A cascaded fixed network is further incorporated to achieve segmentation at the image level in a coarse-to-fine manner. Extensive experiments were performed involving a comparison with several state-of-the-art deep learning-based segmentation methods. Moreover, the consistency of the results with those of manual segmentation was also investigated. Our proposed NV automatic segmentation method achieved the highest correlation with the manual delineation by interventional cardiologists (the Pearson correlation coefficient is 0.825). In this work, we proposed a co-training architecture with an integrated structural attention mechanism to segment NV in IVOCT images. The good agreement between our segmentation results and manual segmentation indicates that the proposed method has great potential for application in the clinical investigation of NV-related plaque diagnosis and treatment.

A novel level set model initialized with guided filter for automated PET-CT image segmentation

Positron emission tomography (PET) and computed tomography (CT) scanner image analysis plays an important role in clinical radiotherapy treatment. PET and CT images provide complementary cues for identifying tumor tissues. In specific, PET images can clearly denote the tumor tissue, whereas this source suffers from the problem of low spatial resolution. On the contrary, CT images have a high resolution, but they can not recognize the tumor from normal tissues. In this work, we firstly fuse PET and CT images by using the guided filter. Then, a region and edge-based level set model is proposed to segment PET-CT fusion images. At last, a normalization term is designed by combining length, distance and H 1 terms with the aim to improve segmentation accuracy. The proposed method was validated in the robust delineation of lung tumor tissues on 20 PET-CT samples. Both qualitative and quantitative results demonstrate significant improvement compared to both the data-independent and deep learning based segmentation methods.

Review of Nodule Mineral Image Segmentation Algorithms for Deep-Sea Mineral Resource Assessment

A large number of nodule minerals exist in the deep sea. Based on the factors of difficulty in shooting, high economic cost and high accuracy of resource assessment, large-scale planned commercial mining has not yet been conducted. Only experimental mining has been carried out in areas with high mineral density and obvious benefits after mineral resource assessment. As an efficient method for deep-sea mineral resource assessment, the deep towing system is equipped with a visual system for mineral resource analysis using collected images and videos, which has become a key component of resource assessment. Therefore, high accuracy in deep-sea mineral image segmentation is the primary goal of the segmentation algorithm. In this paper, the existing deep-sea nodule mineral image segmentation algorithms are studied in depth and divided into traditional and deep learning-based segmentation methods, and the advantages and disadvantages of each are compared and summarized. The deep learning methods show great advantages in deep-sea mineral image segmentation, and there is a great improvement in segmentation accuracy and efficiency compared with the traditional methods. Then, the mineral image dataset and segmentation evaluation metrics are listed. Finally, possible future research topics and improvement measures are discussed for the reference of other researchers.

Multi-Spectral Imaging for Weed Identification in Herbicides Testing

A new methodology to help to improve the efficiency of herbicide assessment is explained. It consists of an automatic tool to quantify the percentage of weeds and plants of interest (sunflowers) that are present in a given area. Images of the crop field taken from Sequoia camera were used. Firstly, the quality of the images of each band is improved. Later, the resulting multi-spectral images are classified into several classes (soil, sunflower and weed) through a novel algorithm implemented in e-Cognition software. Obtained results of the proposed classifications have been compared with two deep learning-based segmentation methods (U-Net and FPN).

Remote-Sensing Image Segmentation Based on Implicit 3-D Scene Representation

Remote sensing image segmentation, as a challenging but fundamental task, has drawn increasing attention in the remote sensing field. Recent advances in deep learning have greatly boosted research on this task. However, the existing deep learning-based segmentation methods heavily rely on a large amount of pixel-wise labeled training data, and the labeling process is time-consuming and labor-intensive. In this paper, we focus on the scenario that leverages the 3D structure of multi-view images and a limited number of annotations to generate accurate novel view segmentation. Under this scenario, we propose a novel method for remote sensing image segmentation based on implicit 3D scene representation, which generates arbitrary-view segmentation output from limited segmentation annotations. The proposed method employs a two-stage training strategy. In the first stage, we optimize the implicit neural representations of a 3D scene and encode their multi-view images into a neural radiance field. In the second stage, we transform the scene color attribute into semantic labels and propose a ray-convolution network to aggregate local 3D consistency cues across different locations. We also design a color-radiance network to help our method generalize to unseen views. Experiments on both synthetic and real-world data suggest that our method significantly outperforms deep convolutional networks (CNN)-based methods and other view synthesis-based methods. We also show that the proposed method can be applied as a novel data augmentation approach that benefits CNN-based segmentation methods.

Real-Time Cerebral Vessel Segmentation in Laser Speckle Contrast Image Based on Unsupervised Domain Adaptation.

Laser speckle contrast imaging (LSCI) is a full-field, high spatiotemporal resolution and low-cost optical technique for measuring blood flow, which has been successfully used for neurovascular imaging. However, due to the low signal–noise ratio and the relatively small sizes, segmenting the cerebral vessels in LSCI has always been a technical challenge. Recently, deep learning has shown its advantages in vascular segmentation. Nonetheless, ground truth by manual labeling is usually required for training the network, which makes it difficult to implement in practice. In this manuscript, we proposed a deep learning-based method for real-time cerebral vessel segmentation of LSCI without ground truth labels, which could be further integrated into intraoperative blood vessel imaging system. Synthetic LSCI images were obtained with a synthesis network from LSCI images and public labeled dataset of Digital Retinal Images for Vessel Extraction, which were then used to train the segmentation network. Using matching strategies to reduce the size discrepancy between retinal images and laser speckle contrast images, we could further significantly improve image synthesis and segmentation performance. In the testing LSCI images of rodent cerebral vessels, the proposed method resulted in a dice similarity coefficient of over 75%.

Deep-Learning-Based Multi-Organ Auto-Segmentation on 3D Transrectal Ultrasound for Ultrasound-Guided Prostate Brachytherapy

Ultrasound (US) imaging has been widely used in image-guided prostate brachytherapy. Current prostate brachytherapy uses transrectal US (TRUS) images for implant guidance, where contours of prostate and organs-at risk are necessary for treatment planning and dose evaluation. This work aims to develop a deep learning-based method for pelvic multi-organ TRUS segmentation to improve TRUS-guided prostate brachytherapy.We developed an anchor-free mask convolutional neural network (CNN) that consist of three subnetworks, i.e., a backbone, a fully convolutional one-state object detector (FCOS) head, and a mask head. The backbone extracts multi-level and multi-scale features from US image. The FOCS head utilizes these features to detect the location of volume-of-interest (VOI) of each organ. In contrast to previous mask regional CNN (Mask R-CNN) method, which perform detection and segmentation within several pre-defined potential VOIs (called as anchors), FCOS head is anchor-free, which can capture spatial correlation of multi-organs due to whole image input. Mask head performs segmentation on each detected VOI, where a spatial attention strategy is integrated into mask head that helps to focus on informative features that can well-represent the organ boundary and suppress noise introduced by previous subnetwork and by arrival TRUS image itself. For evaluation, we retrospectively investigated 80 prostate cancer patients by a five-fold cross-validation. Prostate, bladder, rectum and urethra were segmented and compared with manual contours using Dice similarity coefficient (DSC), 95% Hausdorff distance (HD95), and mean surface distance (MSD).For all patients, the DSC, HD95 and MSD were 0.93 ± 0.03, 2.28 ± 0.64 mm and 0.57 ± 0.20 mm for prostate; 0.75 ± 0.12, 2.58 ± 0.7 mm and 1.26 ± 0.23 mm for bladder; 0.90 ± 0.07, 1.65 ± 0.52 mm and 0.34 ± 0.16 mm for rectum; and 0.86 ± 0.07, 1.85 ± 1.71 mm and 0.44 ± 0.32mm for urethra. The proposed method outperforms two state-of-art methods (U-Net and Mask R-CNN) with better agreement with physicians' manual contours and less mis-identified speckles.We proposed an automatic deep learning-based pelvic multi-organ segmentation on 3D TRUS images for TRUS-guided prostate brachytherapy. The proposed method could provide fast and accurate multi-organ segmentations for prostate, bladder, rectum and urethra, and outperformed two competing methods. This deep-learning-based multi-organ auto-segmentation may play an important role in future clinical practice to improve auto-planning and auto-evaluation during TRUS-guided prostate brachytherapy.

Deep learning-based segmentation of the placenta and uterus on MR images.

Purpose: Magnetic resonance imaging has been recently used to examine the abnormalities of the placenta during pregnancy. Segmentation of the placenta and uterine cavity allows quantitative measures and further analyses of the organs. The objective of this study is to develop a segmentation method with minimal user interaction. Approach: We developed a fully convolutional neural network (CNN) for simultaneous segmentation of the uterine cavity and placenta in three dimensions (3D) while a minimal operator interaction was incorporated for training and testing of the network. The user interaction guided the network to localize the placenta more accurately. In the experiments, we trained two CNNs, one using 70 normal training cases and the other using 129 training cases including normal cases as well as cases with suspected placenta accreta spectrum (PAS). We evaluated the performance of the segmentation algorithms on two test sets: one with 20 normal cases and the other with 50 images from both normal women and women with suspected PAS. Results: For the normal test data, the average Dice similarity coefficient (DSC) was 92% and 82% for the uterine cavity and placenta, respectively. For the combination of normal and abnormal cases, the DSC was 88% and 83% for the uterine cavity and placenta, respectively. The 3D segmentation algorithm estimated the volume of the normal and abnormal uterine cavity and placenta with average volume estimation errors of 4% and 9%, respectively. Conclusions: The deep learning-based segmentation method provides a useful tool for volume estimation and analysis of the placenta and uterus cavity in human placental imaging.

Misic, a general deep learning-based method for the high-throughput cell segmentation of complex bacterial communities.

Studies of bacterial communities, biofilms and microbiomes, are multiplying due to their impact on health and ecology. Live imaging of microbial communities requires new tools for the robust identification of bacterial cells in dense and often inter-species populations, sometimes over very large scales. Here, we developed MiSiC, a general deep-learning-based 2D segmentation method that automatically segments single bacteria in complex images of interacting bacterial communities with very little parameter adjustment, independent of the microscopy settings and imaging modality. Using a bacterial predator-prey interaction model, we demonstrate that MiSiC enables the analysis of interspecies interactions, resolving processes at subcellular scales and discriminating between species in millimeter size datasets. The simple implementation of MiSiC and the relatively low need in computing power make its use broadly accessible to fields interested in bacterial interactions and cell biology.