DeepCell Kiosk: scaling deep learning-enabled cellular image analysis with Kubernetes.
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ABSTRACT:
SUBMITTER: Bannon D
PROVIDER: S-EPMC8759612 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundDeep learning using convolutional neural networks (CNN) has achieved significant results in various fields that use images. Deep learning can automatically extract features from data, and CNN extracts image features by convolution processing. We assumed that increasing the image size using interpolation methods would result in an effective feature extraction. To investigate how interpolation methods change as the number of data increases, we examined and compared the effectiveness of data augmentation by inversion or rotation with image augmentation by interpolation when the image data for training were small. Further, we clarified whether image augmentation by interpolation was useful for CNN training. To examine the usefulness of interpolation methods in medical images, we used a Gender01 data set, which is a sex classification data set, on chest radiographs. For comparison of image enlargement using an interpolation method with data augmentation by inversion and rotation, we examined the results of two- and four-fold enlargement using a Bilinear method.ResultsThe average classification accuracy improved by expanding the image size using the interpolation method. The biggest improvement was noted when the number of training data was 100, and the average classification accuracy of the training model with the original data was 0.563. However, upon increasing the image size by four times using the interpolation method, the average classification accuracy significantly improved to 0.715. Compared with the data augmentation by inversion and rotation, the model trained using the Bilinear method showed an improvement in the average classification accuracy by 0.095 with 100 training data and 0.015 with 50,000 training data. Comparisons of the average classification accuracy of the chest X-ray images showed a stable and high-average classification accuracy using the interpolation method.ConclusionTraining the CNN by increasing the image size using the interpolation method is a useful method. In the future, we aim to conduct additional verifications using various medical images to further clarify the reason why image size is important.
| S-EPMC7924688 | biostudies-literature
Project description:The widespread adoption of whole slide imaging has increased the demand for effective and efficient gigapixel image analysis. Deep learning is at the forefront of computer vision, showcasing significant improvements over previous methodologies on visual understanding. However, whole slide images have billions of pixels and suffer from high morphological heterogeneity as well as from different types of artifacts. Collectively, these impede the conventional use of deep learning. For the clinical translation of deep learning solutions to become a reality, these challenges need to be addressed. In this paper, we review work on the interdisciplinary attempt of training deep neural networks using whole slide images, and highlight the different ideas underlying these methodologies.
| S-EPMC6882930 | biostudies-literature
Project description:Deep learning algorithms have become the first choice as an approach to medical image analysis, face recognition, and emotion recognition. In this survey, several deep-learning-based approaches applied to breast cancer, cervical cancer, brain tumor, colon and lung cancers are studied and reviewed. Deep learning has been applied in almost all of the imaging modalities used for cervical and breast cancers and MRIs for the brain tumor. The result of the review process indicated that deep learning methods have achieved state-of-the-art in tumor detection, segmentation, feature extraction and classification. As presented in this paper, the deep learning approaches were used in three different modes that include training from scratch, transfer learning through freezing some layers of the deep learning network and modifying the architecture to reduce the number of parameters existing in the network. Moreover, the application of deep learning to imaging devices for the detection of various cancer cases has been studied by researchers affiliated to academic and medical institutes in economically developed countries; while, the study has not had much attention in Africa despite the dramatic soar of cancer risks in the continent.
| S-EPMC8321208 | biostudies-literature
Project description:Quantitative analysis of dynamic processes in living cells using time-lapse microscopy requires not only accurate tracking of every particle in the images, but also reliable extraction of biologically relevant parameters from the resulting trajectories. Whereas many methods exist to perform the tracking task, there is still a lack of robust solutions for subsequent parameter extraction and analysis. Here a novel method is presented to address this need. It uses for the first time a deep learning approach to segment single particle trajectories into consistent tracklets (trajectory segments that exhibit one type of motion) and then performs moment scaling spectrum analysis of the tracklets to estimate the number of mobility classes and their associated parameters, providing rich fundamental knowledge about the behavior of the particles under study. Experiments on in-house datasets as well as publicly available particle tracking data for a wide range of proteins with different dynamic behavior demonstrate the broad applicability of the method.
| S-EPMC6868130 | biostudies-literature
Project description: Not available
| EMPIAR-10592 | biostudies-other
Project description:Automated segmentation of cellular electron microscopy (EM) datasets remains a challenge. Supervised deep learning (DL) methods that rely on region-of-interest (ROI) annotations yield models that fail to generalize to unrelated datasets. Newer unsupervised DL algorithms require relevant pre-training images, however, pre-training on currently available EM datasets is computationally expensive and shows little value for unseen biological contexts, as these datasets are large and homogeneous. To address this issue, we present CEM500K, a nimble 25 GB dataset of 0.5 × 106 unique 2D cellular EM images curated from nearly 600 three-dimensional (3D) and 10,000 two-dimensional (2D) images from >100 unrelated imaging projects. We show that models pre-trained on CEM500K learn features that are biologically relevant and resilient to meaningful image augmentations. Critically, we evaluate transfer learning from these pre-trained models on six publicly available and one newly derived benchmark segmentation task and report state-of-the-art results on each. We release the CEM500K dataset, pre-trained models and curation pipeline for model building and further expansion by the EM community. Data and code are available at https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10592/ and https://git.io/JLLTz.
| S-EPMC8032397 | biostudies-literature
Project description:Diabetes is a globally prevalent disease that can cause visible microvascular complications such as diabetic retinopathy and macular edema in the human eye retina, the images of which are today used for manual disease screening and diagnosis. This labor-intensive task could greatly benefit from automatic detection using deep learning technique. Here we present a deep learning system that identifies referable diabetic retinopathy comparably or better than presented in the previous studies, although we use only a small fraction of images (<1/4) in training but are aided with higher image resolutions. We also provide novel results for five different screening and clinical grading systems for diabetic retinopathy and macular edema classification, including state-of-the-art results for accurately classifying images according to clinical five-grade diabetic retinopathy and for the first time for the four-grade diabetic macular edema scales. These results suggest, that a deep learning system could increase the cost-effectiveness of screening and diagnosis, while attaining higher than recommended performance, and that the system could be applied in clinical examinations requiring finer grading.
| S-EPMC6656880 | biostudies-other
Project description:With the ever-increasing societal dependence on electricity, one of the critical tasks in power supply is maintaining the power line infrastructure. In the process of making informed, cost-effective, and timely decisions, maintenance engineers must rely on human-created, heterogeneous, structured, and also largely unstructured information. The maturing research on vision-based power line inspection driven by advancements in deep learning offers first possibilities to move towards more holistic, automated, and safe decision-making. However, (current) research focuses solely on the extraction of information rather than its implementation in decision-making processes. The paper addresses this shortcoming by designing, instantiating, and evaluating a holistic deep-learning-enabled image-based decision support system artifact for power line maintenance at a German distribution system operator in southern Germany. Following the design science research paradigm, two main components of the artifact are designed: A deep-learning-based model component responsible for automatic fault detection of power line parts as well as a user-oriented interface responsible for presenting the captured information in a way that enables more informed decisions. As a basis for both components, preliminary design requirements are derived from literature and the application field. Drawing on justificatory knowledge from deep learning as well as decision support systems, tentative design principles are derived. Based on these design principles, a prototype of the artifact is implemented that allows for rigorous evaluation of the design knowledge in multiple evaluation episodes, covering different angles. Through a technical experiment the technical novelty of the artifact’s capability to capture selected faults (regarding insulators and safety pins) in unmanned aerial vehicle (UAV)-captured image data (model component) is validated. Subsequent interviews, surveys, and workshops in a natural environment confirm the usefulness of the model as well as the user interface component. The evaluation provides evidence that (1) the image processing approach manages to address the gap of power line component inspection and (2) that the proposed holistic design knowledge for image-based decision support systems enables more informed decision-making. The paper therefore contributes to research and practice in three ways. First, the technical feasibility to detect certain maintenance-intensive parts of power lines with the help of unique UAV image data is shown. Second, the distribution system operators’ specific problem is solved by supporting decisions in maintenance with the proposed image-based decision support system. Third, precise design knowledge for image-based decision support systems is formulated that can inform future system designs of a similar nature. Supplementary Information The online version contains supplementary material available at 10.1007/s12599-022-00745-z.
| S-EPMC8973684 | biostudies-literature
Project description:Fast and selective isolation of single cells with unique spatial and morphological traits remains a technical challenge. We address this by establishing high speed image-enabled cell sorting (ICS), which records multicolor fluorescence images, and sorts cells based on measurements from image data at speeds up to 15,000 events per second. We combine ICS with CRISPR-pooled screens to identify novel regulators of the NF-κB pathway, enabling the completion of genome-wide image- based screens in around nine hours of run-time.
2022-01-20 | GSE167944 | GEO
Project description:Artificial intelligence, deep convolutional neural networks, and deep learning are all niche terms that are increasingly appearing in scientific presentations as well as in the general media. In this review, we focus on deep learning and how it is applied to microscopy image data of cells and tissue samples. Starting with an analogy to neuroscience, we aim to give the reader an overview of the key concepts of neural networks, and an understanding of how deep learning differs from more classical approaches for extracting information from image data. We aim to increase the understanding of these methods, while highlighting considerations regarding input data requirements, computational resources, challenges, and limitations. We do not provide a full manual for applying these methods to your own data, but rather review previously published articles on deep learning in image cytometry, and guide the readers toward further reading on specific networks and methods, including new methods not yet applied to cytometry data. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
| S-EPMC6590257 | biostudies-literature