Automatic Segmentation Method Research Articles

PDDS: A software for the early diagnosis of Parkinson’s disease from MRI and DaT scan images using detection and segmentation algorithms

Parkinson’s disease is a common neurodegenerative disorder that affects millions of people worldwide. Medical imaging techniques such as MRI and DaTScan can help diagnose PD by showing the changes in the brain structures related to the disease, such as the substantia nigra and the striatum. In this paper, we propose a software called PDDS (Parkinson’s Disease Diagnosis Software) that can automatically detect and segment the deep brain regions from MRI and DaTScan images using advanced deep learning models. Our software uses YOLO and an ensemble of UNETs to accurately locate the regions of interest (ROIs) from T2-weighted MRI and DaTScan images respectively and use them for quantitative assessment and decision support. The ensemble approach uses a weighted average ensemble which achieves the highest mean IOU after a grid search technique was implemented to get the appropriate weights. We used mosaic data augmentation to improve the generalization ability of our models by exposing them to objects in different contexts. The proposed architecture was trained and validated using the PPMI and IXI datasets and the detection results show that the YOLOv7x model achieves a mAP_0.5:0.95 of 70.39 % for DaTScan images and a mAP_0.5:0.95 of 64.16 % for MRI images, outperforming previous methods. For the segmentation results, our ensemble UNet model with different backbones achieves a mean IOU of 70.02 % for DaTScan images and 54.31 % for MRI images. According to our findings, our approach is a competitive automatic detection and segmentation method and can be applied to clinically challenging medical imaging problems.

Automated Whole Cochlear T2 Signal Demonstrates Weak Correlation with Hearing Loss in Observed Vestibular Schwannoma

Introduction: We sought to evaluate the correlation between whole cochlear T2 signal changes obtained with a novel automated segmentation method and hearing levels, both at diagnosis and over time, in patients with observed vestibular schwannoma. Methods: This retrospective correlation study within an academic medical center neurotology practice evaluated 127 patients with vestibular schwannoma observed over time, each with ≥2 MRI scans (367 total) and ≥2 audiograms (472 total). 86 patients had T2-weighted sequences with sufficient resolution for cochlear signal analysis, yielding 348 unique timepoint intervals. The main outcome measure was correlation of the ipsilateral-to-contralateral ratio of whole cochlear T2 signal with hearing outcomes as measured by pure tone average (PTA) and word recognition score (WRS). Results: Whole cochlear T2 signal ratios did not show a correlation with hearing levels at diagnosis. Change in signal ratio over time showed weak correlation with changes in PTA, but not WRS, over time. Cochlear signal ratio did not precede changes in hearing but did follow changes in both PTA and WRS. Conclusion: Whole cochlear T2 signal ratios were weakly correlated with changes in hearing in patients with observed vestibular schwannoma. The technology of automated segmentation and signal processing holds promise for future evaluation of clinical entities causing cochlear signal changes.

Automated deep learning auto-segmentation of air volumes for MRI-guided online adaptive radiation therapy of abdominal tumors

Objective. In the current MR-Linac online adaptive workflow, air regions on the MR images need to be manually delineated for abdominal targets, and then overridden by air density for dose calculation. Auto-delineation of these regions is desirable for speed purposes, but poses a challenge, since unlike computed tomography, they do not occupy all dark regions on the image. The purpose of this study is to develop an automated method to segment the air regions on MRI-guided adaptive radiation therapy (MRgART) of abdominal tumors. Approach. A modified ResUNet3D deep learning (DL)-based auto air delineation model was trained using 102 patients’ MR images. The MR images were acquired by a dedicated in-house sequence named ‘Air-Scan’, which is designed to generate air regions that are especially dark and accentuated. The air volumes generated by the newly developed DL model were compared with the manual air contours using geometric similarity (Dice Similarity Coefficient (DSC)), and dosimetric equivalence using Gamma index and dose-volume parameters. Main results. The average DSC agreement between the DL generated and manual air contours is 99% ± 1%. The gamma index between the dose calculations with overriding the DL versus manual air volumes with density of 0.01 is 97% ± 2% for a local gamma calculation with a tolerance of 2% and 2 mm. The dosimetric parameters from planning target volume—PTV and organs at risk—OARs were all within 1% between when DL versus manual contours were overridden by air density. The model runs in less than five seconds on a PC with 28 Core processor and NVIDIA Quadro® P2000 GPU. Significance: a DL based automated segmentation method was developed to generate air volumes on specialized abdominal MR images and generate results that are practically equivalent to the manual contouring of air volumes.

MEMbrain: an interactive deep learning MATLAB tool for connectomic segmentation on commodity desktops.

Connectomics is fundamental in propelling our understanding of the nervous system's organization, unearthing cells and wiring diagrams reconstructed from volume electron microscopy (EM) datasets. Such reconstructions, on the one hand, have benefited from ever more precise automatic segmentation methods, which leverage sophisticated deep learning architectures and advanced machine learning algorithms. On the other hand, the field of neuroscience at large, and of image processing in particular, has manifested a need for user-friendly and open source tools which enable the community to carry out advanced analyses. In line with this second vein, here we propose mEMbrain, an interactive MATLAB-based software which wraps algorithms and functions that enable labeling and segmentation of electron microscopy datasets in a user-friendly user interface compatible with Linux and Windows. Through its integration as an API to the volume annotation and segmentation tool VAST, mEMbrain encompasses functions for ground truth generation, image preprocessing, training of deep neural networks, and on-the-fly predictions for proofreading and evaluation. The final goals of our tool are to expedite manual labeling efforts and to harness MATLAB users with an array of semi-automatic approaches for instance segmentation. We tested our tool on a variety of datasets that span different species at various scales, regions of the nervous system and developmental stages. To further expedite research in connectomics, we provide an EM resource of ground truth annotation from four different animals and five datasets, amounting to around 180 h of expert annotations, yielding more than 1.2 GB of annotated EM images. In addition, we provide a set of four pre-trained networks for said datasets. All tools are available from https://lichtman.rc.fas.harvard.edu/mEMbrain/. With our software, our hope is to provide a solution for lab-based neural reconstructions which does not require coding by the user, thus paving the way to affordable connectomics.

#5276 DEVELOPMENT OF A MULTIMODAL “KIDNEY AGE” PREDICTION BASED ON AUTOMATIC SEGMENTATION CT IMAGE IN PATIENTS WITH NORMAL RENAL FUNCTION

Abstract Background and Aims Renal function, for decades, has been of interest to clinicians and researchers to describe. For example, serum creatinine (Scr) and estimated glomerulus filtration rate (eGFR) is familiar but also limited in many circumstances. Meanwhile, the physiological volumes of the kidney cortex and medulla are presumed to change with age and have been proven to change with decreasing kidney function. Method We recruited 182 patients with normal Scr levels and contrasted CT images between Oct. 2021 and Feb 2022 in Peking Union Medical College Hospital (PUMCH) with their demographic and clinical data. The automatic segmentation method was modified from U-NET and used for both cortex and medullary separation and their volume calculation, respectively. We combined the kidney volume and clinical data as multimodal features of the machine learning model. All the data were separated into a training dataset (PUMCH training set, 80%) and a test dataset (PUMCH test set, 20%). Besides, we included patients with the same inclusion criteria but with diabetes (PUMCH-DM test set) and diabetic nephropathy (PUMCH-DN test set) for internal comparison to verify the possible clinical value of “KIDNEY AGE” (K-AGE). Data from DongZhiMen Hospital (DZMH test set) was used as separate external validation sets to evaluate model generalizability. Results The PUMCH training set included 146 participants with a mean age of 47.5±7.4 years. 58.9% were female, and the mean Scr is 63.5±12.3 μmol/L. The PUMCH test set included 36 participants with a mean age of 47.1±7.9 years, 52.7% were female, and the mean Scr was 66.9±13.0 μmol/L. For segmented kidneys, volume differences between non-contrast-enhanced CT and non-contrast-enhanced CT in the left and right kidneys were not evident. The multimodal neural network predicted: K-AGE approximately close to the patient's actual physiological age, with 92% prediction within the 95% confidential interval (Figure 1). We also compared the K-AGE prediction in PUMCH, PUMCH-DM, and PUMCH-DN test sets by applying U-NET-nonCon segmentation algorithm in non-contrast CT images. The mean absolute error increases along with the disease process (control group 5.00, diabetes group 6.99, diabetic nephropathy group 9.32) (Figure 2). Conclusion We established a machine learning model for predicting the K-AGE of normal Scr patients.

Automatic lumen and anatomical layers segmentation in IVOCT images using meta learning.

Automated analysis of the vessel structure in intravascular optical coherence tomography (IVOCT) images is critical to assess the health status of vessels and monitor coronary artery disease progression. However, deep learning-based methods usually require well-annotated large datasets, which are difficult to obtain in the field of medical image analysis. Hence, an automatic layers segmentation method based on meta-learning was proposed, which can simultaneously extract the surfaces of the lumen, intima, media, and adventitia using a handful of annotated samples. Specifically, we leverage a bi-level gradient strategy to train a meta-learner for capturing the shared meta-knowledge among different anatomical layers and quickly adapting to unknown anatomical layers. Then, a Claw-type network and a contrast consistency loss were designed to better learn the meta-knowledge according to the characteristic of annotation of the lumen and anatomical layers. Experimental results on the two cardiovascular IVOCT datasets show that the proposed method achieved state-of-art performance.

A deep learning-based automatic segmentation of zygomatic bones from cone-beam computed tomography images: A proof of concept

ObjectivesTo investigate the efficiency and accuracy of a deep learning-based automatic segmentation method for zygomatic bones from cone-beam computed tomography (CBCT) images. MethodsOne hundred thirty CBCT scans were included and randomly divided into three subsets (training, validation, and test) in a 6:2:2 ratio. A deep learning-based model was developed, and it included a classification network and a segmentation network, where an edge supervision module was added to increase the attention of the edges of zygomatic bones. Attention maps were generated by the Grad-CAM and Guided Grad-CAM algorithms to improve the interpretability of the model. The performance of the model was then compared with that of four dentists on 10 CBCT scans from the test dataset. A p value <0.05 was considered statistically significant. ResultsThe accuracy of the classification network was 99.64%. The Dice coefficient (Dice) of the deep learning-based model for the test dataset was 92.34 ± 2.04%, the average surface distance (ASD) was 0.1 ± 0.15 mm, and the 95% Hausdorff distance (HD) was 0.98 ± 0.42 mm. The model required 17.03 s on average to segment zygomatic bones, whereas this task took 49.3 min for dentists to complete. The Dice score of the model for the 10 CBCT scans was 93.2 ± 1.3%, while that of the dentists was 90.37 ± 3.32%. ConclusionsThe proposed deep learning-based model could segment zygomatic bones with high accuracy and efficiency compared with those of dentists. Clinical significanceThe proposed automatic segmentation model for zygomatic bone could generate an accurate 3D model for the preoperative digital planning of zygoma reconstruction, orbital surgery, zygomatic implant surgery, and orthodontics.

IMG-05. A MULTI-INSTITUTIONAL AND MULTI-HISTOLOGY PEDIATRIC-SPECIFIC BRAIN TUMOR SUBREGION SEGMENTATION TOOL: FACILITATING RAPNO-BASED ASSESSMENT OF TREATMENT RESPONSE

Abstract Current response assessment in pediatric brain tumors (PBTs), as recommended by the Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group, relies on 2D measurements of changes in tumor size. However, there is growing evidence of underestimation of tumor size in PBTs using 2D compared to volumetric (3D) measurement approach. Accordingly, automated methods that reduce manual burden and intra- and inter-rater variability in segmenting tumor subregions and volumetric evaluations are warranted to facilitate tumor response assessment of PBTs. We have developed a fully automatic deep learning (DL) model using the nnUNet architecture on a large cohort of multi-institutional and multi-histology PBTs. The model was trained on widely available standard multiparametric MRI sequences (T1-pre, T1-post, T2, T2-FLAIR) for segmentation of the whole tumor and RAPNO-recommended subregions, including enhancing tumor (ET), non-enhancing tumor (NET), cystic components (CC), and peritumoral edema (ED). As a prerequisite step for accurate tumor segmentation, we also generated another DL model based on DeepMedic for brain extraction from mpMRIs. The models were trained on an institutional cohort of 151 subjects and independently tested on 64 subjects from the internal and 29 patients from external institutions. The trained models showed excellent performance with median Dice scores of 0.98±0.02/0.97±0.02 for brain tissue segmentation, 0.92±0.08/0.90±0.17 for whole tumor segmentation, 0.76±0.31/0.87±0.29 for ET subregion, and 0.82±0.15/0.80±0.28 for segmentation of non-enhancing components (combination of NET, CC, and ED) in internal/external test sets, respectively. The automated segmentation demonstrated strong agreement with expert segmentations in volumetric measurement of tumor components, with Pearson’s correlation coefficients of 0.97, 0.97, 0.99, and 0.79 (p&amp;lt;0.0001) for ET, NET, CC, and ED regions, respectively. Our proposed multi-institutional and multi-histology automated segmentation method has the potential to aid clinical neuro-oncology practice by providing reliable and reproducible volumetric measurements for treatment response assessment.

Novel Adaptive Histogram Binning-Based Lesion Segmentation for Discerning Severity in COVID-19 Chest CT Scan Images

Coronavirus sickness (COVID-19) recently adversely disrupted the medical care system and the entire economy. Doctors, researchers, and specialists are working on new-fangled methods to detect COVID-19 relatively efficiently, such as constructing computerized COVID-19 detection systems. Medical imaging, such as Computed Tomography (CT), has a lot of opportunity as a solution to RT-PCR approaches for quantitative assessment and disease monitoring. COVID-19 diagnosis based on CT images can provide speedy and accurate results. A quantitative criterion for diagnosis is provided by an automated segmentation method of infection areas in the lungs. As an outcome, automatic image segmentation is in high demand as a clinical decision aid tool. To detect COVID-19, Computed Tomography images might be employed instead of the time-consuming RT-PCR assay. In this research, a unique technique is provided for segmenting infection areas in the lungs using CT scan images from COVID-19 patients. “Ground Glass Opacity (GGO)” regions were detected using Novel Adaptive Histogram Binning Based Lesion Segmentation (NAHBLS) method. Many metrics were also employed to evaluate the proposed method, including “Sorensen–Dice similarity”, “Sensitivity”, “Specificity”, “Precision”, and “Accuracy” measures. Experiments have shown that the proposed method can effectively separate the lung infections with good accuracy. The results show that the proposed Novel Adaptive Histogram Binning Based Lesion Segmentation based on automatic approach is effective at segmenting the lesion region of the image and calculated the Infection Rate (IR) over the lung region in Computed Tomography scan.

Investigation on the multimodal failure characteristics of cement mortar under uniaxial compression loading

The physical condition and durability of cement-based structures can easily decrease after years of operation due to exposure to severe scenarios associated with internal defects, aggressive usage, and continuous load changes. Therefore, accurately assessing such infrastructures is essential for ensuring safety and serviceability and preventing hazards. In this study, an experimental investigation of the multimodal failure characteristics of cement mortar with various sand contents at different uniaxial compressive loading rates was conducted. Specifically, the multimodal failure characteristics include three main categories: mechanical properties (e.g., compressive strength), one-dimensional signals (e.g., micro-vibration and electromagnetic radiation), and two-dimensional videos/images (e.g., crack propagation trajectory). A geophysical acquisition and a high frame rate camera were employed to simultaneously record the micro-vibration, electromagnetic radiation and crack propagation videos of the cement specimens in a uniaxial compression test. Based on the computer vision technique and the feature pyramid network (FPN), an automatic pixel-level crack segmentation method was proposed to extract cracks of each critical moment in the fracture video. Then, the fractal dimension and crack area were calculated to quantitatively depict the crack propagation trajectory. Finally, the stress drop, micro-vibration, electromagnetic radiation, and crack propagation trajectory characteristics were analysed and discussed. The experimental results indicate the following. (1) The FPN offers a practical way to identify cracks in structures of cement-based materials at the pixel-level. (2) The micro-vibration, electromagnetic radiation, and crack propagation trajectory exhibit good consistency. In particular, the area and fractal dimension of cracks positively correlate with the stress drop of cement under compression loading. (3) The peak and cumulative energy values of micro-vibration and electromagnetic radiation tend to increase as the sand content increases when subjected to the same loading rate.

The effect of convolutional neural network architectures on phase segmentation of composite material X-ray micrographs

Porosity severely reduces the mechanical performance of composite laminates and methods for automatic segmentation of void phases are growing. This study investigates porosity in composite materials that take the form of interlaminar voids and dry tow areas. Deep Learning was used for the segmentation of X-ray micrographs via the implementation of eight state-of-the-art Convolutional Neural Network (CNN) architectures trained with data sets containing twenty-five, fifty, and one-hundred images. The combination of hyperparameters providing the highest accuracy for each architecture and training set size was achieved through the optimisation of six relevant hyperparameters, including the cut-off probability applied to output probability maps. Additionally, the properties of the CNN architectures ( e.g., layer typology, connections, density…) were found to play a determining role, not only in the segmentation results but also in the associated computing effort. U-Net and FCDenseNet outperformed the FCN-8s, FCN-16, SegNet, LinkNet, ResNet18 and Xception CNN architectures. However, the CNNs generally outperformed the standard thresholding approaches, especially in sub-volumes containing low porosity (1.07%) where the influence on strength is very sensitive in high-performance composites. In low porosity samples, U-Net and FCDenseNet consistently segmented voids to 85% + accuracy, whereas thresholding was only half as accurate, at around 40%. The results provide a strong motivation to replace thresholding as a segmentation method for composite X-ray micrographs. In terms of efficiency, the reduced complexity of the U-Net network allowed for an average reduction of the training time (−36%) and prediction time (−17%) when compared to FCDenseNet.

Automatic concrete infrastructure crack semantic segmentation using deep learning

To solve the privation of crack information during feature transmission, we propose an automatic concrete infrastructure crack semantic segmentation method using deep learning. Initially, based on the statistical analysis results of crack images, a multi-stage feature extraction network is created with multi-resolution parallel transmission to extract the crack features. Then, the extracted features are aggregated according to the correlation between segmentation classes and pixels to enhance the localization performance of the model for cracks. Moreover, using statistical analysis results as constraints construct the loss function to optimize the model and overcome the data imbalance issue. Experiments are conducted on a self-made manual annotation dataset, which contains 2000 images from the dam, the bridge, and the spillway tunnel, and our method reach 94.51% Precision, 86.39% Recall, 82.26% Intersection-over-Unions, and 90.27% F1_measure on the dataset. The experimental results show that the proposed method is optimal for the semantic segmentation of crack images.

Development and validation of a quality control procedure for automatic segmentation of hippocampal subfields.

Automatic segmentation methods for in vivo magnetic resonance imaging are increasing in popularity because of their high efficiency and reproducibility. However, automatic methods can be perfectly reliable and consistently wrong, and the validity of automatic segmentation methods cannot be taken for granted. Quality control (QC) by trained and reliable human raters is necessary to ensure the validity of automatic measurements. Yet QC practices for applied neuroimaging research are underdeveloped. We report a detailed QC and correction procedure to accompany our validated atlas for hippocampal subfield segmentation. We document a two-step QC procedure for identifying segmentation errors, along with a taxonomy of errors and an error severity rating scale. This detailed procedure has high between-rater reliability for error identification and manual correction. The latter introduces at maximum 3% error variance in volume measurement. All procedures were cross-validated on an independent sample collected at a second site with different imaging parameters. The analysis of error frequency revealed no evidence of bias. An independent rater with a third sample replicated procedures with high within-rater reliability for error identification and correction. We provide recommendations for implementing the described method along with hypothesis testing strategies. In sum, we present a detailed QC procedure that is optimized for efficiency while prioritizing measurement validity and suits any automatic atlas.

Systematic Review of Deep Learning Approaches for Automatic Segmentation of Abdominal Aortic Aneurysm and Thrombus on Computed Tomography Angiography Images

Abdominal Aortic Aneurysm (AAA) is a potentially life-threatening condition characterized by the enlargement of the abdominal aorta. Computed Tomography Angiography (CTA) is a widely used diagnostic tool for AAA, and accurate segmentation of the aneurysm and thrombus is critical for treatment planning. Deep learning approaches have shown promise in automating the segmentation process. We conducted a systematic review of the literature to evaluate the performance of deep learning methods for automatic segmentation of AAA and thrombus on CTA images. Six studies were identified that met our inclusion criteria. The studies utilized various deep learning architectures and loss functions to segment AAA and thrombus, and reported performance using metrics such as sensitivity, specificity, accuracy, and Dice coefficient. The results indicate that deep learning methods can achieve high accuracy and Dice coefficient values for segmentation of AAA and thrombus on CTA images. However, the performance of the methods varied depending on the specific architecture and loss function used. Further research is needed to determine the most effective deep learning approach for automatic segmentation of AAA and thrombus on CTA images.

Accurate segmentation algorithm of acoustic neuroma in the cerebellopontine angle based on ACP-TransUNet.

Acoustic neuroma is one of the most common tumors in the cerebellopontine angle area. Patients with acoustic neuroma have clinical manifestations of the cerebellopontine angle occupying syndrome, such as tinnitus, hearing impairment and even hearing loss. Acoustic neuromas often grow in the internal auditory canal. Neurosurgeons need to observe the lesion contour with the help of MRI images, which not only takes a lot of time, but also is easily affected by subjective factors. Therefore, the automatic and accurate segmentation of acoustic neuroma in cerebellopontine angle on MRI is of great significance for surgical treatment and expected rehabilitation. In this paper, an automatic segmentation method based on Transformer is proposed, using TransUNet as the core model. As some acoustic neuromas are irregular in shape and grow into the internal auditory canal, larger receptive fields are thus needed to synthesize the features. Therefore, we added Atrous Spatial Pyramid Pooling to CNN, which can obtain a larger receptive field without losing too much resolution. Since acoustic neuromas often occur in the cerebellopontine angle area with relatively fixed position, we combined channel attention with pixel attention in the up-sampling stage so as to make our model automatically learn different weights by adding the attention mechanism. In addition, we collected 300 MRI sequence nuclear resonance images of patients with acoustic neuromas in Tianjin Huanhu hospital for training and verification. The ablation experimental results show that the proposed method is reasonable and effective. The comparative experimental results show that the Dice and Hausdorff 95 metrics of the proposed method reach 95.74% and 1.9476 mm respectively, indicating that it is not only superior to the classical models such as UNet, PANet, PSPNet, UNet++, and DeepLabv3, but also show better performance than the newly-proposed SOTA (state-of-the-art) models such as CCNet, MANet, BiseNetv2, Swin-Unet, MedT, TransUNet, and UCTransNet.

Automatic segmentation of orbital wall from CT images via a thin wall region supervision-based multi-scale feature search network

Orbital wall segmentation is critical for orbital measurement and reconstruction. However, the orbital floor and medial wall are made up of thin walls (TW) with low gradient values, making it difficult to segment the blurred areas of the CT images. Clinically, doctors have to manually repair the missing parts of TW, which is time-consuming and laborious. To address these issues, this paper proposes an automatic orbital wall segmentation method based on TW region supervision using a multi-scale feature search network. First of all, in the encoding branch, the densely connected atrous spatial pyramid pooling based on the residual connection is adopted to achieve a multi-scale feature search. Then, for feature enhancement, multi-scale up-sampling and residual connection are applied to perform skip connection of features in multi-scale convolution. Finally, we explore a strategy for improving the loss function based on the TW region supervision, which effectively increases the TW region segmentation accuracy. The test results show that the proposed network performs well in terms of automatic segmentation. For the whole orbital wall region, the Dice coefficient (Dice) of segmentation accuracy reaches 96.086 ± 1.049%, the Intersection over Union (IOU) reaches 92.486 ± 1.924%, and the 95% Hausdorff distance (HD) reaches 0.509 ± 0.166mm. For the TW region, the Dice reaches 91.470 ± 1.739%, the IOU reaches 84.327 ± 2.938%, and the 95% HD reaches 0.481 ± 0.082mm. Compared with other segmentation networks, the proposed network improves the segmentation accuracy while filling the missing parts in the TW region. In the proposed network, the average segmentation time of each orbital wall is only 4.05s, obviously improving the segmentation efficiency of doctors. In the future, it may have a practical significance in clinical applications such as preoperative planning for orbital reconstruction, orbital modeling, orbital implant design, and so on.

Seg2Link: an efficient and versatile solution for semi-automatic cell segmentation in 3D image stacks

Recent advances in microscopy techniques, especially in electron microscopy, are transforming biomedical studies by acquiring large quantities of high-precision 3D cell image stacks. To examine cell morphology and connectivity in organs such as the brain, scientists need to conduct cell segmentation, which extracts individual cell regions of different shapes and sizes from a 3D image. This is challenging due to the indistinct images often encountered in real biomedical research: in many cases, automatic segmentation methods inevitably contain numerous mistakes in the segmentation results, even when using advanced deep learning methods. To analyze 3D cell images effectively, a semi-automated software solution is needed that combines powerful deep learning techniques with the ability to perform post-processing, generate accurate segmentations, and incorporate manual corrections. To address this gap, we developed Seg2Link, which takes deep learning predictions as inputs and use watershed 2D + cross-slice linking to generate more accurate automatic segmentations than previous methods. Additionally, it provides various manual correction tools essential for correcting mistakes in 3D segmentation results. Moreover, our software has been optimized for efficiently processing large 3D images in diverse organisms. Thus, Seg2Link offers an practical solution for scientists to study cell morphology and connectivity in 3D image stacks.

Predicting Breast Cancer Subtypes Using Magnetic Resonance Imaging Based Radiomics With Automatic Segmentation.

The aim of the study is to demonstrate whether radiomics based on an automatic segmentation method is feasible for predicting molecular subtypes. This retrospective study included 516 patients with confirmed breast cancer. An automatic segmentation-3-dimensional UNet-based Convolutional Neural Networks, trained on our in-house data set-was applied to segment the regions of interest. A set of 1316 radiomics features per region of interest was extracted. Eighteen cross-combination radiomics methods-with 6 feature selection methods and 3 classifiers-were used for model selection. Model classification performance was assessed using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity. The average dice similarity coefficient value of the automatic segmentation was 0.89. The radiomics models were predictive of 4 molecular subtypes with the best average: AUC = 0.8623, accuracy = 0.6596, sensitivity = 0.6383, and specificity = 0.8775. For luminal versus nonluminal subtypes, AUC = 0.8788 (95% confidence interval [CI], 0.8505-0.9071), accuracy = 0.7756, sensitivity = 0.7973, and specificity = 0.7466. For human epidermal growth factor receptor 2 (HER2)-enriched versus non-HER2-enriched subtypes, AUC = 0.8676 (95% CI, 0.8370-0.8982), accuracy = 0.7737, sensitivity = 0.8859, and specificity = 0.7283. For triple-negative breast cancer versus non-triple-negative breast cancer subtypes, AUC = 0.9335 (95% CI, 0.9027-0.9643), accuracy = 0.9110, sensitivity = 0.4444, and specificity = 0.9865. Radiomics based on automatic segmentation of magnetic resonance imaging can predict breast cancer of 4 molecular subtypes noninvasively and is potentially applicable in large samples.

Machine Learning Methods for Automatic Segmentation of Images of Field- and Glasshouse-Based Plants for High-Throughput Phenotyping.

Image segmentation is a fundamental but critical step for achieving automated high- throughput phenotyping. While conventional segmentation methods perform well in homogenous environments, the performance decreases when used in more complex environments. This study aimed to develop a fast and robust neural-network-based segmentation tool to phenotype plants in both field and glasshouse environments in a high-throughput manner. Digital images of cowpea (from glasshouse) and wheat (from field) with different nutrient supplies across their full growth cycle were acquired. Image patches from 20 randomly selected images from the acquired dataset were transformed from their original RGB format to multiple color spaces. The pixels in the patches were annotated as foreground and background with a pixel having a feature vector of 24 color properties. A feature selection technique was applied to choose the sensitive features, which were used to train a multilayer perceptron network (MLP) and two other traditional machine learning models: support vector machines (SVMs) and random forest (RF). The performance of these models, together with two standard color-index segmentation techniques (excess green (ExG) and excess green-red (ExGR)), was compared. The proposed method outperformed the other methods in producing quality segmented images with over 98%-pixel classification accuracy. Regression models developed from the different segmentation methods to predict Soil Plant Analysis Development (SPAD) values of cowpea and wheat showed that images from the proposed MLP method produced models with high predictive power and accuracy comparably. This method will be an essential tool for the development of a data analysis pipeline for high-throughput plant phenotyping. The proposed technique is capable of learning from different environmental conditions, with a high level of robustness.

CRV-NET: Robust Intensity Recognition of Coronavirus in Lung Computerized Tomography Scan Images.

The early diagnosis of infectious diseases is demanded by digital healthcare systems. Currently, the detection of the new coronavirus disease (COVID-19) is a major clinical requirement. For COVID-19 detection, deep learning models are used in various studies, but the robustness is still compromised. In recent years, deep learning models have increased in popularity in almost every area, particularly in medical image processing and analysis. The visualization of the human body's internal structure is critical in medical analysis; many imaging techniques are in use to perform this job. A computerized tomography (CT) scan is one of them, and it has been generally used for the non-invasive observation of the human body. The development of an automatic segmentation method for lung CT scans showing COVID-19 can save experts time and can reduce human error. In this article, the CRV-NET is proposed for the robust detection of COVID-19 in lung CT scan images. A public dataset (SARS-CoV-2 CT Scan dataset), is used for the experimental work and customized according to the scenario of the proposed model. The proposed modified deep-learning-based U-Net model is trained on a custom dataset with 221 training images and their ground truth, which was labeled by an expert. The proposed model is tested on 100 test images, and the results show that the model segments COVID-19 with a satisfactory level of accuracy. Moreover, the comparison of the proposed CRV-NET with different state-of-the-art convolutional neural network models (CNNs), including the U-Net Model, shows better results in terms of accuracy (96.67%) and robustness (low epoch value in detection and the smallest training data size).