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At least 73 records · Page 4

Batch Active Learning for Multispectral and Hyperspectral Image Segmentation Using Similarity Graphs

Abstract Graph learning, when used as a semi-supervised learning (SSL) method, performs well for classification tasks with a low label rate. We provide a graph-based batch active learning pipeline for pixel/patch neighborhood multi- or hyperspectral image segmentation. Our batch active learning approach selects a collection of unlabeled pixels that satisfy a graph local maximum constraint for the active learning acquisition function that determines the relative importance of each pixel to the classification. This work builds on recent advances in the design of novel active learning acquisition functions (e.g., the Model Change approach in arXiv:2110.07739) while adding important further developments including patch-neighborhood image analysis and batch active learning methods to further increase the accuracy and greatly increase the computational efficiency of these methods. In addition to improvements in the accuracy, our approach can greatly reduce the number of labeled pixels needed to achieve the same level of the accuracy based on randomly selected labeled pixels.

97 MATHEMATICS AND COMPUTING↗

Nested-hierarchical scene models and image segmentation

An improved model of scenes for image analysis purposes, a nested-hierarchical approach which explicitly acknowledges multiple scales of objects or categories of objects, is presented. A multiple-pass, region-based segmentation algorithm improves the segmentation of images from scenes better modeled as a nested hierarchy. A multiple-pass approach allows slow and careful growth of regions while interregion distances are below a global threshold. Past the global threshold, a minimum region size parameter forces development of regions in areas of high local variance. Maximum and viable region size parameters limit the development of undesirably large regions. Application of the segmentation algorithm for forest stand delineation in TM imagery yields regions corresponding to identifiable features in the landscape. The use of a local variance, adaptive-window texture channel in conjunction with spectral bands improves the ability to define regions corresponding to sparsely stocked forest stands which have high internal variance.

Woodcock, C.↗

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determination. However, existing methods trained on a limited amount of cryo-EM data still cannot accurately pick protein particles from noisy cryo-EM images. The general foundational artificial intelligence–based image segmentation model such as Meta’s Segment Anything Model (SAM) cannot segment protein particles well because their training data do not include cryo-EM images. Here, we present a novel approach (CryoSegNet) of integrating an attention-gated U-shape network (U-Net) specially designed and trained for cryo-EM particle picking and the SAM. The U-Net is first trained on a large cryo-EM image dataset and then used to generate input from original cryo-EM images for SAM to make particle pickings. CryoSegNet shows both high precision and recall in segmenting protein particles from cryo-EM micrographs, irrespective of protein type, shape and size. On several independent datasets of various protein types, CryoSegNet outperforms two top machine learning particle pickers crYOLO and Topaz as well as SAM itself. The average resolution of density maps reconstructed from the particles picked by CryoSegNet is 3.33 Å, 7% better than 3.58 Å of Topaz and 14% better than 3.87 Å of crYOLO. It is publicly available at https://github.com/jianlin-cheng/CryoSegNet

59 BASIC BIOLOGICAL SCIENCES↗

ExtremeMETA: High-speed Lightweight Image Segmentation Model by Remodeling Multi-channel Metamaterial Imagers

Deep neural networks (DNNs) have heavily relied on traditional computational units, such as CPUs and GPUs. However, this conventional approach brings significant computational burden, latency issues, and high power consumption, limiting their effectiveness. This has sparked the need for lightweight networks such as ExtremeC3Net. Meanwhile, there have been notable advancements in optical computational units, particularly with metamaterials, offering the exciting prospect of energy-efficient neural networks operating at the speed of light. Yet, the digital design of metamaterial neural networks (MNNs) faces precision, noise, and bandwidth challenges, limiting their application to intuitive tasks and low-resolution images. In this study, we proposed a large kernel lightweight segmentation model, ExtremeMETA. Based on ExtremeC3Net, our proposed model, ExtremeMETA maximized the ability of the first convolution layer by exploring a larger convolution kernel and multiple processing paths. With the large kernel convolution model, we extended the optic neural network application boundary to the segmentation task. To further lighten the computation burden of the digital processing part, a set of model compression methods was applied to improve model efficiency in the inference stage. The experimental results on three publicly available datasets demonstrated that the optimized efficient design improved segmentation performance from 92.45 to 95.97 on mIoU while reducing computational FLOPs from 461.07 MMacs to 166.03 MMacs. The large kernel lightweight model ExtremeMETA showcased the hybrid design’s ability on complex tasks.

large convolution kernel↗

Parallel Markov Random Fields for Image Segmentation (PMRF-IS) v1.0

This software performs multi-label segmentation of 2D/3D images. It is highly accurate, results rely on use of an Markov random field (MRF) formulation. It runs in both shared and distributed memory parallel modes. MRF algorithms are powerful tools in image analysis to explore contextual information of data.

Heinemann, Colleen↗

SU-E-I-71: Quality Assessment of Surrogate Metrics in Multi-Atlas-Based Image Segmentation

Purpose: With the ever-growing data of heterogeneous quality, relevance assessment of atlases becomes increasingly critical for multi-atlas-based image segmentation. However, there is no universally recognized best relevance metric and even a standard to compare amongst candidates remains elusive. This study, for the first time, designs a quantification to assess relevance metrics’ quality, based on a novel perspective of the metric as surrogate for inferring the inaccessible oracle geometric agreement. Methods: We first develop an inference model to relate surrogate metrics in image space to the underlying oracle relevance metric in segmentation label space, with a monotonically non-decreasing function subject to random perturbations. Subsequently, we investigate model parameters to reveal key contributing factors to surrogates’ ability in prognosticating the oracle relevance value, for the specific task of atlas selection. Finally, we design an effective contract-to-noise ratio (eCNR) to quantify surrogates’ quality based on insights from these analyses and empirical observations. Results: The inference model was specialized to a linear function with normally distributed perturbations, with surrogate metric exemplified by several widely-used image similarity metrics, i.e., MSD/NCC/(N)MI. Surrogates’ behaviors in selecting the most relevant atlases were assessed under varying eCNR, showing that surrogates with high eCNR dominated those with low eCNR in retaining the most relevant atlases. In an end-to-end validation, NCC/(N)MI with eCNR of 0.12 compared to MSD with eCNR of 0.10 resulted in statistically better segmentation with mean DSC of about 0.85 and the first and third quartiles of (0.83, 0.89), compared to MSD with mean DSC of 0.84 and the first and third quartiles of (0.81, 0.89). Conclusion: The designed eCNR is capable of characterizing surrogate metrics’ quality in prognosticating the oracle relevance value. It has been demonstrated to be correlated with the performance of relevant atlas selection and ultimate label fusion.

60 APPLIED LIFE SCIENCES↗

The Analysis of the Patterns of Radiation-Induced DNA Damage Foci by a Stochastic Monte Carlo Model of DNA Double Strand Breaks Induction by Heavy Ions and Image Segmentation Software

To create a generalized mechanistic model of DNA damage in human cells that will generate analytical and image data corresponding to experimentally observed DNA damage foci and will help to improve the experimental foci yields by simulating spatial foci patterns and resolving problems with quantitative image analysis. Material and Methods: The analysis of patterns of RIFs (radiation-induced foci) produced by low- and high-LET (linear energy transfer) radiation was conducted by using a Monte Carlo model that combines the heavy ion track structure with characteristics of the human genome on the level of chromosomes. The foci patterns were also simulated in the maximum projection plane for flat nuclei. Some data analysis was done with the help of image segmentation software that identifies individual classes of RIFs and colocolized RIFs, which is of importance to some experimental assays that assign DNA damage a dual phosphorescent signal. Results: The model predicts the spatial and genomic distributions of DNA DSBs (double strand breaks) and associated RIFs in a human cell nucleus for a particular dose of either low- or high-LET radiation. We used the model to do analyses for different irradiation scenarios. In the beam-parallel-to-the-disk-of-a-flattened-nucleus scenario we found that the foci appeared to be merged due to their high density, while, in the perpendicular-beam scenario, the foci appeared as one bright spot per hit. The statistics and spatial distribution of regions of densely arranged foci, termed DNA foci chains, were predicted numerically using this model. Another analysis was done to evaluate the number of ion hits per nucleus, which were visible from streaks of closely located foci. In another analysis, our image segmentaiton software determined foci yields directly from images with single-class or colocolized foci. Conclusions: We showed that DSB clustering needs to be taken into account to determine the true DNA damage foci yield, which helps to determine the DSB yield. Using the model analysis, a researcher can refine the DSB yield per nucleus per particle. We showed that purely geometric artifacts, present in the experimental images, can be analytically resolved with the model, and that the quantization of track hits and DSB yields can be provided to the experimentalists who use enumeration of radiation-induced foci in immunofluorescence experiments using proteins that detect DNA damage. An automated image segmentaiton software can prove useful in a faster and more precise object counting for colocolized foci images.

Ponomarev, Artem↗

Reinforcement Learning as a Parsimonious Alternative to Prediction Cascades: A Case Study on Image Segmentation

Deep learning architectures have achieved state-of-the-art (SOTA) performance on computer vision tasks such as object detection and image segmentation. This may be attributed to the use of over-parameterized, monolithic deep learning architectures executed on large datasets. Although such large architectures lead to increased accuracy, this is usually accompanied by a larger increase in computation and memory requirements during inference. While this is a non-issue in traditional machine learning (ML) pipelines, the recent confluence of machine learning and fields like the Internet of Things (IoT) has rendered such large architectures infeasible for execution in low-resource settings. For some datasets, large monolithic pipelines may be overkill for simpler inputs. To address this problem, previous efforts have proposed decision cascades where inputs are passed through models of increasing complexity until the desired performance is achieved. However, we argue that cascaded prediction leads to sub-optimal throughput and increased computational cost due to wasteful intermediate computations. To address this, we propose PaSeR (Parsimonious Segmentation with Reinforcement Learning) a non-cascading, cost-aware learning pipeline as an efficient alternative to cascaded decision architectures. Through experimental evaluation on both real-world and standard datasets, we demonstrate that PaSeR achieves better accuracy while minimizing computational cost relative to cascaded models. Further, we introduce a new metric IoU/GigaFlop to evaluate the balance between cost and performance. On the real-world task of battery material phase segmentation, PaSeR yields 179% improvement over SOTA MatPhase model and a 196% improvement over IDK Cascades under the IoU/GigaFlop metric. We also demonstrate PaSeR’s adaptability to complementary models trained on a noisy MNIST dataset, where it outperforms all baselines on IoU/GigaFlop by an average of 44%.

Srikshan, Bharat↗

Image segmentation for analyzing galaxy-galaxy strong lensing systems

The goal of this Letter is to develop a machine learning model to analyze the main gravitational lens and detect dark substructure (subhalos) within simulated images of strongly lensed galaxies. Using the technique of image segmentation, we turn the task of identifying subhalos into a classification problem, where we label each pixel in an image as coming from the main lens, a subhalo within a binned mass range, or neither. Our network is only trained on images with a single smooth lens and either zero or one subhalo near the Einstein ring. On an independent test set with lenses with large ellipticities, quadrupole and octopole moments, and for source apparent magnitudes between 17–25, the area of the main lens is recovered accurately. On average, only 1.3% of the true area is missed and 1.2% of the true area is added to another part of the lens. In addition, subhalos as light as 10 8.5 M ⊙ can be detected if they lie in bright pixels along the Einstein ring. Furthermore, the model is able to generalize to new contexts it has not been trained on, such as locating multiple subhalos with varying masses or more than one large smooth lens.

79 ASTRONOMY AND ASTROPHYSICS↗

SU-E-J-142: Performance Study of Automatic Image-Segmentation Algorithms in Motion Tracking Via MR-IGRT

Purpose: Evaluate commonly used segmentation algorithms on a commercially available real-time MR image guided radiotherapy (MR-IGRT) system (ViewRay), compare the strengths and weaknesses of each method, with the purpose of improving motion tracking for more accurate radiotherapy. Methods: MR motion images of bladder, kidney, duodenum, and liver tumor were acquired for three patients using a commercial on-board MR imaging system and an imaging protocol used during MR-IGRT. A series of 40 frames were selected for each case to cover at least 3 respiratory cycles. Thresholding, Canny edge detection, fuzzy k-means (FKM), k-harmonic means (KHM), and reaction-diffusion level set evolution (RD-LSE), along with the ViewRay treatment planning and delivery system (TPDS) were included in the comparisons. To evaluate the segmentation results, an expert manual contouring of the organs or tumor from a physician was used as a ground-truth. Metrics value of sensitivity, specificity, Jaccard similarity, and Dice coefficient were computed for comparison. Results: In the segmentation of single image frame, all methods successfully segmented the bladder and kidney, but only FKM, KHM and TPDS were able to segment the liver tumor and the duodenum. For segmenting motion image series, the TPDS method had the highest sensitivity, Jarccard, and Dice coefficients in segmenting bladder and kidney, while FKM and KHM had a slightly higher specificity. A similar pattern was observed when segmenting the liver tumor and the duodenum. The Canny method is not suitable for consistently segmenting motion frames in an automated process, while thresholding and RD-LSE cannot consistently segment a liver tumor and the duodenum. Conclusion: The study compared six different segmentation methods and showed the effectiveness of the ViewRay TPDS algorithm in segmenting motion images during MR-IGRT. Future studies include a selection of conformal segmentation methods based on image/organ-specific information, different filtering methods and their influences on the segmentation results. Parag Parikh receives research grant from ViewRay. Sasa Mutic has consulting and research agreements with ViewRay. Yanle Hu receives travel reimbursement from ViewRay. Iwan Kawrakow and James Dempsey are ViewRay employees.

60 APPLIED LIFE SCIENCES↗

Volume of Lytic Vertebral Body Metastatic Disease Quantified Using Computed Tomography–Based Image Segmentation Predicts Fracture Risk After Spine Stereotactic Body Radiation Therapy

Purpose: To determine a threshold of vertebral body (VB) osteolytic or osteoblastic tumor involvement that would predict vertebral compression fracture (VCF) risk after stereotactic body radiation therapy (SBRT), using volumetric image-segmentation software. Methods and Materials: A computational semiautomated skeletal metastasis segmentation process refined in our laboratory was applied to the pretreatment planning CT scan of 100 vertebral segments in 55 patients treated with spine SBRT. Each VB was segmented and the percentage of lytic and/or blastic disease by volume determined. Results: The cumulative incidence of VCF at 3 and 12 months was 14.1% and 17.3%, respectively. The median follow-up was 7.3 months (range, 0.6-67.6 months). In all, 56% of segments were determined lytic, 23% blastic, and 21% mixed, according to clinical radiologic determination. Within these 3 clinical cohorts, the segmentation-determined mean percentages of lytic and blastic tumor were 8.9% and 6.0%, 0.2% and 26.9%, and 3.4% and 15.8% by volume, respectively. On the basis of the entire cohort (n=100), a significant association was observed for the osteolytic percentage measures and the occurrence of VCF (P<.001) but not for the osteoblastic measures. The most significant lytic disease threshold was observed at ≥11.6% (odds ratio 37.4, 95% confidence interval 9.4-148.9). On multivariable analysis, ≥11.6% lytic disease (P<.001), baseline VCF (P<.001), and SBRT with ≥20 Gy per fraction (P=.014) were predictive. Conclusions: Pretreatment lytic VB disease volumetric measures, independent of the blastic component, predict for SBRT-induced VCF. Larger-scale trials evaluating our software are planned to validate the results.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

A geometric deformable model for echocardiographic image segmentation

Gradient vector flow (GVF), an elegant external force for parametric deformable models, can capture object boundaries from both sides. A new geometric deformable model is proposed that combines GVF and the geodesic active contour model. The level set method is used as the numerical method of this model. The model is applied for echocardiographic image segmentation.

NASA Program Biomedical Research and Countermeasur↗

Machine learning-based multidomain processing for texture-based image segmentation and analysis

Atomic and molecular resolved atomic force microscopy (AFM) images offer unique insights into materials' properties such as local ordering, molecular orientation, and topological defects, which can be used to pinpoint physical and chemical interactions occurring at the surface. Utilizing machine learning for extracting underlying physical parameters increases the throughput of AFM data processing and eliminates inconsistencies intrinsic to manual image analysis, thus enabling the creation of reliable frameworks for qualitative and quantitative evaluation of experimental data. Here, we present a robust and scalable approach to the segmentation of AFM images based on flexible pre-selected classification criteria. The usage of supervised learning and feature extraction allows us to retain the consideration of specific problem-dependent features (such as types of periodical structures observed in the images and the associated numerical parameters: spacing, orientation, etc.). We highlight the applicability of this approach for the segmentation of molecular resolved AFM images based on the crystal orientation of the observed domains, automated selection of boundaries, and collection of relevant statistics. Finally, we outline a general strategy for machine learning-enabled analysis of nanoscale systems exhibiting periodic order that could be applied to any analytical imaging technique

36 MATERIALS SCIENCE↗

Deep Learning Image Segmentation for Atmospheric Rivers

Abstract The identification of atmospheric rivers (ARs) is crucial for weather and climate predictions as they are often associated with severe storm systems and extreme precipitation, which can cause large impacts on society. This study presents a deep learning model, termed ARDetect, for image segmentation of ARs using ERA5 data from 1960 to 2020 with labels obtained from the TempestExtremes tracking algorithm. ARDetect is a convolutional neural network (CNN)-based U-Net model, with its structure having been optimized using automatic hyperparameter tuning. Inputs to ARDetect were selected to be the integrated water vapor transport (IVT) and total column water (TCW) fields, as well as the AR mask from TempestExtremes from the previous time step to the one being considered. ARDetect achieved a mean intersection-over-union (mIoU) rate of 89.04% for ARs, indicating its high accuracy in identifying these weather patterns and a superior performance than most deep learning–based models for AR detection. In addition, ARDetect can be executed faster than the TempestExtremes method (seconds vs minutes) for the same period. This provides a significant benefit for online AR detection, especially for high-resolution global models. An ensemble of 10 models, each trained on the same dataset but having different starting weights, was used to further improve on the performance produced by ARDetect, thus demonstrating the importance of model diversity in improving performance. ARDetect provides an effective and fast deep learning–based model for researchers and weather forecasters to better detect and understand ARs, which have significant impacts on weather-related events such as floods and droughts.

Galea, Daniel↗

3D-SIFT-Flow for atlas-based CT liver image segmentation

Purpose: In this paper, the authors proposed a new 3D registration algorithm, 3D-scale invariant feature transform (SIFT)-Flow, for multiatlas-based liver segmentation in computed tomography (CT) images. Methods: In the registration work, the authors developed a new registration method that takes advantage of dense correspondence using the informative and robust SIFT feature. The authors computed the dense SIFT features for the source image and the target image and designed an objective function to obtain the correspondence between these two images. Labeling of the source image was then mapped to the target image according to the former correspondence, resulting in accurate segmentation. In the fusion work, the 2D-based nonparametric label transfer method was extended to 3D for fusing the registered 3D atlases. Results: Compared with existing registration algorithms, 3D-SIFT-Flow has its particular advantage in matching anatomical structures (such as the liver) that observe large variation/deformation. The authors observed consistent improvement over widely adopted state-of-the-art registration methods such as ELASTIX, ANTS, and multiatlas fusion methods such as joint label fusion. Experimental results of liver segmentation on the MICCAI 2007 Grand Challenge are encouraging, e.g., Dice overlap ratio 96.27% ± 0.96% by our method compared with the previous state-of-the-art result of 94.90% ± 2.86%. Conclusions: Experimental results show that 3D-SIFT-Flow is robust for segmenting the liver from CT images, which has large tissue deformation and blurry boundary, and 3D label transfer is effective and efficient for improving the registration accuracy.

60 APPLIED LIFE SCIENCES↗

Range image segmentation using Zernike moment-based generalized edge detector

The authors proposed a novel Zernike moment-based generalized step edge detection method which can be used for segmenting range and intensity images. A generalized step edge detector is developed to identify different kinds of edges in range images. These edge maps are thinned and linked to provide final segmentation. A generalized edge is modeled in terms of five parameters: orientation, two slopes, one step jump at the location of the edge, and the background gray level. Two complex and two real Zernike moment-based masks are required to determine all these parameters of the edge model. Theoretical noise analysis is performed to show that these operators are quite noise tolerant. Experimental results are included to demonstrate edge-based segmentation technique.

Ghosal, S.↗

Enhancement of the MODIS Snow and Ice Product Suite Utilizing Image Segmentation

A problem has been noticed with the current NODIS Snow and Ice Product in that fringes of certain snow fields are labeled as "cloud" whereas close inspection of the data indicates that the correct labeling is a non-cloud category such as snow or land. This occurs because the current MODIS Snow and Ice Product generation algorithm relies solely on the MODIS Cloud Mask Product for the labeling of image pixels as cloud. It is proposed here that information obtained from image segmentation can be used to determine when it is appropriate to override the cloud indication from the cloud mask product. Initial tests show that this approach can significantly reduce the cloud "fringing" in modified snow cover labeling. More comprehensive testing is required to determine whether or not this approach consistently improves the accuracy of the snow and ice product.

Tilton, James C.↗

Segmenting Images for a Better Diagnosis

NASA's Hierarchical Segmentation (HSEG) software has been adapted by Bartron Medical Imaging, LLC, for use in segmentation feature extraction, pattern recognition, and classification of medical images. Bartron acquired licenses from NASA Goddard Space Flight Center for application of the HSEG concept to medical imaging, from the California Institute of Technology/Jet Propulsion Laboratory to incorporate pattern-matching software, and from Kennedy Space Center for data-mining and edge-detection programs. The Med-Seg[TM] united developed by Bartron provides improved diagnoses for a wide range of medical images, including computed tomography scans, positron emission tomography scans, magnetic resonance imaging, ultrasound, digitized Z-ray, digitized mammography, dental X-ray, soft tissue analysis, and moving object analysis. It also can be used in analysis of soft-tissue slides. Bartron's future plans include the application of HSEG technology to drug development. NASA is advancing it's HSEG software to learn more about the Earth's magnetosphere.

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