Semantic segmentation of microscopic neuroanatomical data by combining topological priors with encoder-decoder deep networks.
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ABSTRACT:
SUBMITTER: Banerjee S
PROVIDER: S-EPMC8486300 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Motivation3D neuron segmentation is a key step for the neuron digital reconstruction, which is essential for exploring brain circuits and understanding brain functions. However, the fine line-shaped nerve fibers of neuron could spread in a large region, which brings great computational cost to the neuron segmentation. Meanwhile, the strong noises and disconnected nerve fibers bring great challenges to the task.ResultsIn this paper, we propose a 3D wavelet and deep learning based 3D neuron segmentation method. The neuronal image is first partitioned into neuronal cubes to simplify the segmentation task. Then, we design 3D WaveUNet, the first 3D wavelet integrated encoder-decoder network, to segment the nerve fibers in the cubes; the wavelets could assist the deep networks in suppressing data noises and connecting the broken fibers. We also produce a Neuronal Cube Dataset (NeuCuDa) using the biggest available annotated neuronal image dataset, BigNeuron, to train 3D WaveUNet. Finally, the nerve fibers segmented in cubes are assembled to generate the complete neuron, which is digitally reconstructed using an available automatic tracing algorithm. The experimental results show that our neuron segmentation method could completely extract the target neuron in noisy neuronal images. The integrated 3D wavelets can efficiently improve the performance of 3D neuron segmentation and reconstruction.AvailabilityThe data and codes for this work are available at https://github.com/LiQiufu/3D-WaveUNet.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC8756182 | biostudies-literature
Project description:Weeds in agricultural farms are aggressive growers which compete for nutrition and other resources with the crop and reduce production. The increasing use of chemicals to control them has inadvertent consequences to the human health and the environment. In this work, a novel neural network training method combining semantic graphics for data annotation and an advanced encoder-decoder network for (a) automatic crop line detection and (b) weed (wild millet) detection in paddy fields is proposed. The detected crop lines act as a guiding line for an autonomous weeding robot for inter-row weeding, whereas the detection of weeds enables autonomous intra-row weeding. The proposed data annotation method, semantic graphics, is intuitive, and the desired targets can be annotated easily with minimal labor. Also, the proposed "extended skip network" is an improved deep convolutional encoder-decoder neural network for efficient learning of semantic graphics. Quantitative evaluations of the proposed method demonstrated an increment of 6.29% and 6.14% in mean intersection over union (mIoU), over the baseline network on the task of paddy line detection and wild millet detection, respectively. The proposed method also leads to a 3.56% increment in mIoU and a significantly higher recall compared to a popular bounding box-based object detection approach on the task of wild-millet detection.
| S-EPMC6837080 | biostudies-literature
Project description:IntroductionMultiple positron emission tomography (PET) tracers are available for amyloid imaging, posing a significant challenge to consensus interpretation and quantitative analysis. We accordingly developed and validated a deep learning model as a harmonization strategy.MethodA Residual Inception Encoder-Decoder Neural Network was developed to harmonize images between amyloid PET image pairs made with Pittsburgh Compound-B and florbetapir tracers. The model was trained using a dataset with 92 subjects with 10-fold cross validation and its generalizability was further examined using an independent external dataset of 46 subjects.ResultsSignificantly stronger between-tracer correlations (P < .001) were observed after harmonization for both global amyloid burden indices and voxel-wise measurements in the training cohort and the external testing cohort.DiscussionWe proposed and validated a novel encoder-decoder based deep model to harmonize amyloid PET imaging data from different tracers. Further investigation is ongoing to improve the model and apply to additional tracers.
| S-EPMC9360199 | biostudies-literature
Project description:Autonomous harvesters can be used for the timely cultivation of high-value crops such as strawberries, where the robots have the capability to identify ripe and unripe crops. However, the real-time segmentation of strawberries in an unbridled farming environment is a challenging task due to fruit occlusion by multiple trusses, stems, and leaves. In this work, we propose a possible solution by constructing a dynamic feature selection mechanism for convolutional neural networks (CNN). The proposed building block namely a dense attention module (DAM) controls the flow of information between the convolutional encoder and decoder. DAM enables hierarchical adaptive feature fusion by exploiting both inter-channel and intra-channel relationships and can be easily integrated into any existing CNN to obtain category-specific feature maps. We validate our attention module through extensive ablation experiments. In addition, a dataset is collected from different strawberry farms and divided into four classes corresponding to different maturity levels of fruits and one is devoted to background. Quantitative analysis of the proposed method showed a 4.1% and 2.32% increase in mean intersection over union, over existing state-of-the-art semantic segmentation models and other attention modules respectively, while simultaneously retaining a processing speed of 53 frames per second.
| S-EPMC7937933 | biostudies-literature
Project description:This work presents the application of an Encoder-Decoder convolutional neural network (ED-CNN) model to automatically segment COVID-19 computerised tomography (CT) data. By doing so we are producing an alternative model to current literature, which is easy to follow and reproduce, making it more accessible for real-world applications as little training would be required to use this. Our simple approach achieves results comparable to those of previously published studies, which use more complex deep-learning networks. We demonstrate a high-quality automated segmentation prediction of thoracic CT scans that correctly delineates the infected regions of the lungs. This segmentation automation can be used as a tool to speed up the contouring process, either to check manual contouring in place of a peer checking, when not possible or to give a rapid indication of infection to be referred for further treatment, thus saving time and resources. In contrast, manual contouring is a time-consuming process in which a professional would contour each patient one by one to be later checked by another professional. The proposed model uses approximately 49 k parameters while others average over 1,000 times more parameters. As our approach relies on a very compact model, shorter training times are observed, which make it possible to easily retrain the model using other data and potentially afford "personalised medicine" workflows. The model achieves similarity scores of Specificity (Sp) = 0.996 ± 0.001, Accuracy (Acc) = 0.994 ± 0.002 and Mean absolute error (MAE) = 0.0075 ± 0.0005.
| S-EPMC11323195 | biostudies-literature
Project description:BackgroundNuclear segmentation is an important step for profiling aberrant regions of histology sections. If nuclear segmentation can be resolved, then new biomarkers of nuclear phenotypes and their organization can be predicted for the application of precision medicine. However, segmentation is a complex problem as a result of variations in nuclear geometry (e.g., size, shape), nuclear type (e.g., epithelial, fibroblast), nuclear phenotypes (e.g., vesicular, aneuploidy), and overlapping nuclei. The problem is further complicated as a result of variations in sample preparation (e.g., fixation, staining). Our hypothesis is that (i) deep learning techniques can learn complex phenotypic signatures that rise in tumor sections, and (ii) fusion of different representations (e.g., regions, boundaries) contributes to improved nuclear segmentation.ResultsWe have demonstrated that training of deep encoder-decoder convolutional networks overcomes complexities associated with multiple nuclear phenotypes, where we evaluate alternative architecture of deep learning for an improved performance against the simplicity of the design. In addition, improved nuclear segmentation is achieved by color decomposition and combining region- and boundary-based features through a fusion network. The trained models have been evaluated against approximately 19,000 manually annotated nuclei, and object-level Precision, Recall, F1-score and Standard Error are reported with the best F1-score being 0.91. Raw training images, annotated images, processed images, and source codes are released as a part of the Additional file 1.ConclusionsThere are two intrinsic barriers in nuclear segmentation to H&E stained images, which correspond to the diversity of nuclear phenotypes and perceptual boundaries between adjacent cells. We demonstrate that (i) the encoder-decoder architecture can learn complex phenotypes that include the vesicular type; (ii) delineation of overlapping nuclei is enhanced by fusion of region- and edge-based networks; (iii) fusion of ENets produces an improved result over the fusion of UNets; and (iv) fusion of networks is better than multitask learning. We suggest that our protocol enables processing a large cohort of whole slide images for applications in precision medicine.
| S-EPMC6081825 | biostudies-literature
Project description:Although increasing hidden layers can improve the ability of a neural network in modeling complex nonlinear relationships, deep layers may result in degradation of accuracy due to the problem of vanishing gradient. Accuracy degradation limits the applications of deep neural networks to predict continuous variables with a small sample size and/or weak or little invariance to translations. Inspired by residual convolutional neural network in computer vision, we developed an encoder-decoder full residual deep network to robustly regress and predict complex spatiotemporal variables. We embedded full shortcuts from each encoding layer to its corresponding decoding layer in a systematic encoder-decoder architecture for efficient residual mapping and error signal propagation. We demonstrated, theoretically and experimentally, that the proposed network structure with full residual connections can successfully boost the backpropagation of signals and improve learning outcomes. This novel method has been extensively evaluated and compared with four commonly used methods (i.e., plain neural network, cascaded residual autoencoder, generalized additive model, and XGBoost) across different testing cases for continuous variable predictions. For model evaluation, we focused on spatiotemporal imputation of satellite aerosol optical depth with massive nonrandomness missingness and spatiotemporal estimation of atmospheric fine particulate matter [Formula: see text] (PM2.5). Compared with the other approaches, our method achieved the state-of-the-art accuracy, had less bias in predicting extreme values, and generated more realistic spatial surfaces. This encoder-decoder full residual deep network can be an efficient and powerful tool in a variety of applications that involve complex nonlinear relationships of continuous variables, varying sample sizes, and spatiotemporal data with weak or little invariance to translation.
| S-EPMC8665903 | biostudies-literature
Project description:BackgroundHigh throughput non-destructive phenotyping is emerging as a significant approach for phenotyping germplasm and breeding populations for the identification of superior donors, elite lines, and QTLs. Detection and counting of spikes, the grain bearing organs of wheat, is critical for phenomics of a large set of germplasm and breeding lines in controlled and field conditions. It is also required for precision agriculture where the application of nitrogen, water, and other inputs at this critical stage is necessary. Further, counting of spikes is an important measure to determine yield. Digital image analysis and machine learning techniques play an essential role in non-destructive plant phenotyping analysis.ResultsIn this study, an approach based on computer vision, particularly object detection, to recognize and count the number of spikes of the wheat plant from the digital images is proposed. For spike identification, a novel deep-learning network, SpikeSegNet, has been developed by combining two proposed feature networks: Local Patch extraction Network (LPNet) and Global Mask refinement Network (GMRNet). In LPNet, the contextual and spatial features are learned at the local patch level. The output of LPNet is a segmented mask image, which is further refined at the global level using GMRNet. Visual (RGB) images of 200 wheat plants were captured using LemnaTec imaging system installed at Nanaji Deshmukh Plant Phenomics Centre, ICAR-IARI, New Delhi. The precision, accuracy, and robustness (F1 score) of the proposed approach for spike segmentation are found to be 99.93%, 99.91%, and 99.91%, respectively. For counting the number of spikes, "analyse particles"-function of imageJ was applied on the output image of the proposed SpikeSegNet model. For spike counting, the average precision, accuracy, and robustness are 99%, 95%, and 97%, respectively. SpikeSegNet approach is tested for robustness with illuminated image dataset, and no significant difference is observed in the segmentation performance.ConclusionIn this study, a new approach called as SpikeSegNet has been proposed based on combined digital image analysis and deep learning techniques. A dedicated deep learning approach has been developed to identify and count spikes in the wheat plants. The performance of the approach demonstrates that SpikeSegNet is an effective and robust approach for spike detection and counting. As detection and counting of wheat spikes are closely related to the crop yield, and the proposed approach is also non-destructive, it is a significant step forward in the area of non-destructive and high-throughput phenotyping of wheat.
| S-EPMC7079463 | biostudies-literature
Project description:Automatic lung lesion segmentation of chest computer tomography (CT) scans is considered a pivotal stage toward accurate diagnosis and severity measurement of COVID-19. Traditional U-shaped encoder-decoder architecture and its variants suffer from diminutions of contextual information in pooling/upsampling operations with increased semantic gaps among encoded and decoded feature maps as well as instigate vanishing gradient problems for its sequential gradient propagation that result in suboptimal performance. Moreover, operating with 3-D CT volume poses further limitations due to the exponential increase of computational complexity making the optimization difficult. In this article, an automated COVID-19 lesion segmentation scheme is proposed utilizing a highly efficient neural network architecture, namely CovSegNet, to overcome these limitations. Additionally, a two-phase training scheme is introduced where a deeper 2-D network is employed for generating region-of-interest (ROI)-enhanced CT volume followed by a shallower 3-D network for further enhancement with more contextual information without increasing computational burden. Along with the traditional vertical expansion of Unet, we have introduced horizontal expansion with multistage encoder-decoder modules for achieving optimum performance. Additionally, multiscale feature maps are integrated into the scale transition process to overcome the loss of contextual information. Moreover, a multiscale fusion module is introduced with a pyramid fusion scheme to reduce the semantic gaps between subsequent encoder/decoder modules while facilitating the parallel optimization for efficient gradient propagation. Outstanding performances have been achieved in three publicly available datasets that largely outperform other state-of-the-art approaches. The proposed scheme can be easily extended for achieving optimum segmentation performances in a wide variety of applications. Impact Statement-With lower sensitivity (60-70%), elongated testing time, and a dire shortage of testing kits, traditional RTPCR based COVID-19 diagnostic scheme heavily relies on postCT based manual inspection for further investigation. Hence, automating the process of infected lesions extraction from chestCT volumes will be major progress for faster accurate diagnosis of COVID-19. However, in challenging conditions with diffused, blurred, and varying shaped edges of COVID-19 lesions, conventional approaches fail to provide precise segmentation of lesions that can be deleterious for false estimation and loss of information. The proposed scheme incorporating an efficient neural network architecture (CovSegNet) overcomes the limitations of traditional approaches that provide significant improvement of performance (8.4% in averaged dice measurement scale) over two datasets. Therefore, this scheme can be an effective, economical tool for the physicians for faster infection analysis to greatly reduce the spread and massive death toll of this deadly virus through mass-screening.
| S-EPMC8545036 | biostudies-literature
Project description:Neuroprosthetic brain-computer interfaces are systems that decode neural activity into useful control signals for effectors, such as a cursor on a computer screen. It has long been recognized that both the user and decoding system can adapt to increase the accuracy of the end effector. Co-adaptation is the process whereby a user learns to control the system in conjunction with the decoder adapting to learn the user's neural patterns. We provide a mathematical framework for co-adaptation and relate co-adaptation to the joint optimization of the user's control scheme ("encoding model") and the decoding algorithm's parameters. When the assumptions of that framework are respected, co-adaptation cannot yield better performance than that obtainable by an optimal initial choice of fixed decoder, coupled with optimal user learning. For a specific case, we provide numerical methods to obtain such an optimized decoder. We demonstrate our approach in a model brain-computer interface system using an online prosthesis simulator, a simple human-in-the-loop pyschophysics setup which provides a non-invasive simulation of the BCI setting. These experiments support two claims: that users can learn encoders matched to fixed, optimal decoders and that, once learned, our approach yields expected performance advantages.
| S-EPMC4451011 | biostudies-literature