High-throughput measurement of plant fitness traits with an object detection method using Faster R-CNN.
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ABSTRACT:
SUBMITTER: Wang P
PROVIDER: S-EPMC9310946 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Deep learning based models have had great success in object detection, but the state of the art models have not yet been widely applied to biological image data. We apply for the first time an object detection model previously used on natural images to identify cells and recognize their stages in brightfield microscopy images of malaria-infected blood. Many micro-organisms like malaria parasites are still studied by expert manual inspection and hand counting. This type of object detection task is challenging due to factors like variations in cell shape, density, and color, and uncertainty of some cell classes. In addition, annotated data useful for training is scarce, and the class distribution is inherently highly imbalanced due to the dominance of uninfected red blood cells. We use Faster Region-based Convolutional Neural Network (Faster R-CNN), one of the top performing object detection models in recent years, pre-trained on ImageNet but fine tuned with our data, and compare it to a baseline, which is based on a traditional approach consisting of cell segmentation, extraction of several single-cell features, and classification using random forests. To conduct our initial study, we collect and label a dataset of 1300 fields of view consisting of around 100,000 individual cells. We demonstrate that Faster R-CNN outperforms our baseline and put the results in context of human performance.
| S-EPMC8691760 | biostudies-literature
Project description:ObjectiveTo propose a method for mitigate the impact of anomaly points (such as dust, bubbles, scratches on the chip surface, and minor indentations) in images on the results of digital droplet PCR (ddPCR) detection to achieve high-throughput, stable, and accurate detection.MethodsWe propose a Filter Faster R-CNN ddPCR detection model, which employs Faster R-CNN to generate droplet prediction boxes followed by removing the anomalies within the positive droplet prediction boxes using an outlier filtering module (Filter). Using a plasmid carrying a norovirus fragment as the template, we established a ddPCR dataset for model training (2462 instances, 78.56%) and testing (672 instances, 21.44%). Ablation experiments were performed to test the effectiveness of 3 filtering branches of the Filter for anomaly removal on the validation dataset. Comparative experiments with other ddPCR droplet detection models and absolute quantification experiments of ddPCR were conducted to assess the performance of the Filter Faster R-CNN model.ResultsIn low-dust and dusty environments, the Filter Faster R-CNN model achieved detection accuracies of 98.23% and 88.35% for positive droplets, respectively, with composite F1 scores reaching 99.15% and 99.14%, obviously superior to the other models. The introduction of the filtering module significantly enhanced the positive accuracy of the model in dusty environments. In the absolute quantification experiments, a regression line was plotted using the results from commercial flow cytometry equipment as the standard concentration. The results show a regression line slope of 1.0005, an intercept of -0.025, and a determination coefficient of 0.9997, indicating high consistency between the two results.ConclusionThe ddPCR detection technique using the Filter Faster R-CNN model provides a robust detection method for ddPCR under various environmental conditions.
| S-EPMC10954537 | biostudies-literature
Project description:In this paper, we report our improvement on the prediction accuracy of pre-impact fall detection by applying a learning-based method on the real-time data from an IMU (inertial measurement unit)-sensor mounted on the waist, making it possible to achieve a high accuracy on a wearable device with the extracted features. Using the fixed threshold method is difficult for achieving satisfactory detection accuracy, due to various characteristics and behaviors in the movement of different individuals. In contrast, one could realize high-accuracy detection with machine learning-based methods, but it is difficult to apply them in the wearable devices due to the high hardware requirement. Our method merges the two methods above. We build a convolutional neural network (CNN) with a class activation mapping (CAM) method, which could highlight the class-specific region in the data and obtain a hot map of the fall data. After training on the MobiAct dataset, the model could achieve high-accuracy detection (95.55%) and obtain the region with high contributions to the classification. Then, we manually extract effective features and characteristics of this region and form our special threshold method, achieving pre-impact fall detection in real-world data. Consequently, our method achieves accuracy of 95.33% and a detection time of within 400 ms.
| S-EPMC7506847 | biostudies-literature
Project description:False information detection can detect false information in social media and reduce its negative impact on society. With the development of multimedia, the multimodal content contained in false information is increasing, so it is important to use multimodal features to detect false information. This paper mainly uses information from two modalities, text and image. The features extracted by the backbone network are not further processed in the previous work, and the problems of noise and information loss in the process of fusing multimodal features are ignored. This paper proposes a false information detection method based on Text-CNN and SE modules. We use Text-CNN to process the text and image features extracted by BERT and Swin-transformer to enhance the quality of the features. In addition, we use the modified SE module to fuse text and image features and reduce the noise in the fusion process. Meanwhile, we draw on the idea of residual networks to reduce information loss in the fusion process by concatenating the original features with the fused features. Our model improves accuracy by 6.5% and 2.0% on the Weibo dataset and Twitter dataset compared to the attention based multimodal factorized bilinear pooling. The comparative experimental results show that the proposed model can improve the accuracy of false information detection. The results of ablation experiments further demonstrate the effectiveness of each module in our model.
| S-EPMC9683577 | biostudies-literature
Project description:To evaluate changes in reproductive fitness of bacteria, e.g., after acquisition of antimicrobial resistance, a low-cost high-throughput method to analyze bacterial growth on agar is desirable for broad usability. In our bacterial quantitative fitness analysis (BaQFA), arrayed cultures are spotted on agar and photographed sequentially while growing. These time-lapse images are analyzed using a purpose-built open-source software to derive normalized image intensity (NI) values for each culture spot. Subsequently, a Gompertz growth model is fitted to NI values, and fitness is calculated from model parameters. To represent a range of clinically important pathogenic bacteria, we used different strains of Enterococcus faecium, Escherichia coli, and Staphylococcus aureus, with and without antimicrobial resistance. Relative competitive fitness (RCF) was defined as the mean fitness ratio of two strains growing competitively on one plate.BaQFA permitted the accurate construction of growth curves from bacteria grown on semisolid agar plates and fitting of Gompertz models. Normalized image intensity values showed a strong association with the total CFU/ml count per spotted culture (P < 0.001) for all strains of the three species. BaQFA showed relevant reproductive fitness differences between individual strains, suggesting substantially higher fitness of methicillin-resistant S. aureus JE2 than Cowan (RCF, 1.58; P < 0.001). Similarly, the vancomycin-resistant E. faecium ST172b showed higher competitive fitness than susceptible E. faecium ST172 (RCF, 1.59; P < 0.001). Our BaQFA method allows detection of fitness differences between bacterial strains and may help to estimate epidemiological antimicrobial persistence or contribute to the prediction of clinical outcomes in severe infections.IMPORTANCE Reproductive fitness of bacteria is a major factor in the evolution and persistence of antimicrobial resistance and may play an important role in severe infections. With a computational approach to quantify fitness in bacteria growing competitively on agar plates, our high-throughput method has been designed to obtain additional phenotypic data for antimicrobial resistance analysis at a low cost. Furthermore, our bacterial quantitative fitness analysis (BaQFA) enables the investigation of a link between bacterial fitness and clinical outcomes in severe invasive bacterial infections. This may allow future use of our method for patient management and risk stratification of clinical outcomes. Our proposed method uses open-source software and a hardware setup that can utilize consumer electronics. This will enable a wider community of researchers, including those from low-resource countries, where the burden of antimicrobial resistance is highest, to obtain valuable information about emerging bacterial strains.
| S-EPMC7857537 | biostudies-literature
Project description:Life-history traits are used as proxies of fitness in insects including Drosophila. Egg size is an adaptive and ecologically important trait potentially with genetic variation across different populations. However, the low throughput of manual measurement of egg size has hampered the widespread use of this trait in evolutionary biology and population genetics. We established a method for accurate and high throughput measurement of Drosophila egg size using large particle flow cytometry (LPFC). The size estimates using LPFC are accurate and highly correlated with the manual measurements. The measurement of egg size is high throughput (average of 214 eggs measured per minute) and viable eggs of a specific size can be sorted rapidly (average of 70 eggs per minute). Sorting by LPFC does not reduce the survival of eggs making it a suitable approach for sorting eggs for downstream analyses. This protocol can be applied to any organism within the detectable size range (10-1500 µm) of the large particle flow cytometers. We discuss the potential applications of this method and provide recommendations for optimizing the protocol for other organisms.
| S-EPMC9992389 | biostudies-literature
Project description:Object tracking based on the event-based camera or dynamic vision sensor (DVS) remains a challenging task due to the noise events, rapid change of event-stream shape, chaos of complex background textures, and occlusion. To address the challenges, this paper presents a robust event-stream object tracking method based on correlation filter mechanism and convolutional neural network (CNN) representation. In the proposed method, rate coding is used to encode the event-stream object. Feature representations from hierarchical convolutional layers of a pre-trained CNN are used to represent the appearance of the rate encoded event-stream object. Results prove that the proposed method not only achieves good tracking performance in many complicated scenes with noise events, complex background textures, occlusion, and intersected trajectories, but also is robust to variable scale, variable pose, and non-rigid deformations. In addition, the correlation filter-based method has the advantage of high speed. The proposed approach will promote the potential applications of these event-based vision sensors in autonomous driving, robots and many other high-speed scenes.
| S-EPMC6795673 | biostudies-literature
Project description:In object detection systems for autonomous driving, LIDAR sensors provide very useful information. However, problems occur because the object representation is greatly distorted by changes in distance. To solve this problem, we propose a LIDAR shape set that reconstructs the shape surrounding the object more clearly by using the LIDAR point information projected on the object. The LIDAR shape set restores object shape edges from a bird's eye view by filtering LIDAR points projected on a 2D pixel-based front view. In this study, we use this shape set for two purposes. The first is to supplement the shape set with a LIDAR Feature map, and the second is to divide the entire shape set according to the gradient of the depth and density to create a 2D and 3D bounding box proposal for each object. We present a multimodal fusion framework that classifies objects and restores the 3D pose of each object using enhanced feature maps and shape-based proposals. The network structure consists of a VGG -based object classifier that receives multiple inputs and a LIDAR-based Region Proposal Networks (RPN) that identifies object poses. It works in a very intuitive and efficient manner and can be extended to other classes other than vehicles. Our research has outperformed object classification accuracy (Average Precision, AP) and 3D pose restoration accuracy (3D bounding box recall rate) based on the latest studies conducted with KITTI data sets.
| S-EPMC5876686 | biostudies-literature
Project description:BackgroundA key objective in glaucoma is to identify those at risk of rapid progression and blindness. Recently, a novel first-in-man method for visualising apoptotic retinal cells called DARC (Detection-of-Apoptosing-Retinal-Cells) was reported. The aim was to develop an automatic CNN-aided method of DARC spot detection to enable prediction of glaucoma progression.MethodsAnonymised DARC images were acquired from healthy control (n=40) and glaucoma (n=20) Phase 2 clinical trial subjects (ISRCTN10751859) from which 5 observers manually counted spots. The CNN-aided algorithm was trained and validated using manual counts from control subjects, and then tested on glaucoma eyes.ResultsThe algorithm had 97.0% accuracy, 91.1% sensitivity and 97.1% specificity to spot detection when compared to manual grading of 50% controls. It was next tested on glaucoma patient eyes defined as progressing or stable based on a significant (p<0.05) rate of progression using OCT-retinal nerve fibre layer measurements at 18 months. It demonstrated 85.7% sensitivity, 91.7% specificity with AUC of 0.89, and a significantly (p=0.0044) greater DARC count in those patients who later progressed.ConclusionThis CNN-enabled algorithm provides an automated and objective measure of DARC, promoting its use as an AI-aided biomarker for predicting glaucoma progression and testing new drugs.
| S-EPMC7115906 | biostudies-literature
Project description:Faster Region-based Convolutional Network (Faster R-CNN) is a state-of-the-art object detection method. However, the object detection effect of Faster R-CNN is not good based on the Region Proposal Network (RPN). Inspired by RPN of Faster R-CNN, we propose a novel proposal generation method called Enhanced Region Proposal Network (ERPN). Four improvements are presented in ERPN. Firstly, our proposed deconvolutional feature pyramid network (DFPN) is introduced to improve the quality of region proposals. Secondly, novel anchor boxes are designed with interspersed scales and adaptive aspect ratios. Thereafter, the capability of object localization is increased. Thirdly, a particle swarm optimization (PSO) based support vector machine (SVM), termed PSO-SVM, is developed to distinguish the positive and negative anchor boxes. Fourthly, the classification part of multi-task loss function in RPN is improved. Consequently, the effect of classification loss is strengthened. In this study, our proposed ERPN is compared with five object detection methods on both PASCAL VOC and COCO data sets. For the VGG-16 model, our ERPN obtains 78.6% mAP on VOC 2007 data set, 74.4% mAP on VOC 2012 data set and 31.7% on COCO data set. The performance of ERPN is the best among the comparison object detection methods. Furthermore, the detection speed of ERPN is 5.8 fps. Additionally, ERPN obtains good effect on small object detection.
| S-EPMC6147513 | biostudies-literature