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:Ultra-high-speed imaging serves as a foundation for modern science. While in biomedicine, optical-fiber-based endoscopy is often required for in vivo applications, the combination of high speed with the fiber endoscopy, which is vital for exploring transient biomedical phenomena, still confronts some challenges. We propose all-fiber imaging at high speeds, which is achieved based on the transformation of two-dimensional spatial information into one-dimensional temporal pulsed streams by leveraging high intermodal dispersion in a multimode fiber. Neural networks are trained to reconstruct images from the temporal waveforms. It can not only detect content-aware images with high quality, but also detect images of different kinds from the training images with slightly reduced quality. The fiber probe can detect micron-scale objects with a high frame rate (15.4 Mfps) and large frame depth (10,000). This scheme combines high speeds with high mechanical flexibility and integration and may stimulate future research exploring various phenomena in vivo.
| S-EPMC8930987 | biostudies-literature
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:Smart, responsive materials are required in various advanced applications ranging from anti-counterfeiting to autonomous sensing. Colloidal crystals are a versatile material class for optically based sensing applications owing to their photonic stopband. A careful combination of materials synthesis and colloidal mesostructure rendered such systems helpful in responding to stimuli such as gases, humidity, or temperature. Here, an approach is demonstrated to simultaneously and independently measure the time and temperature solely based on the inherent material properties of complex colloidal crystal mixtures. An array of colloidal crystals, each featuring unique film formation kinetics, is fabricated. Combined with machine learning-enabled image analysis, the colloidal crystal arrays can autonomously record isothermal heating events - readout proceeds by acquiring photographs of the applied sensor using a standard smartphone camera. The concept shows how the progressing use of machine learning in materials science has the potential to allow non-classical forms of data acquisition and evaluation. This can provide novel insights into multiparameter systems and simplify applications of novel materials.
| S-EPMC10015860 | biostudies-literature
Project description:Novel functional materials enable fundamental breakthroughs across technological applications from clean energy to information processing1-11. From microchips to batteries and photovoltaics, discovery of inorganic crystals has been bottlenecked by expensive trial-and-error approaches. Concurrently, deep-learning models for language, vision and biology have showcased emergent predictive capabilities with increasing data and computation12-14. Here we show that graph networks trained at scale can reach unprecedented levels of generalization, improving the efficiency of materials discovery by an order of magnitude. Building on 48,000 stable crystals identified in continuing studies15-17, improved efficiency enables the discovery of 2.2 million structures below the current convex hull, many of which escaped previous human chemical intuition. Our work represents an order-of-magnitude expansion in stable materials known to humanity. Stable discoveries that are on the final convex hull will be made available to screen for technological applications, as we demonstrate for layered materials and solid-electrolyte candidates. Of the stable structures, 736 have already been independently experimentally realized. The scale and diversity of hundreds of millions of first-principles calculations also unlock modelling capabilities for downstream applications, leading in particular to highly accurate and robust learned interatomic potentials that can be used in condensed-phase molecular-dynamics simulations and high-fidelity zero-shot prediction of ionic conductivity.
| S-EPMC10700131 | biostudies-literature
Project description: Not available
| EMPIAR-10592 | biostudies-other
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: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:MotivationDeep learning attained excellent results in digital pathology recently. A challenge with its use is that high quality, representative training datasets are required to build robust models. Data annotation in the domain is labor intensive and demands substantial time commitment from expert pathologists. Active learning (AL) is a strategy to minimize annotation. The goal is to select samples from the pool of unlabeled data for annotation that improves model accuracy. However, AL is a very compute demanding approach. The benefits for model learning may vary according to the strategy used, and it may be hard for a domain specialist to fine tune the solution without an integrated interface.ResultsWe developed a framework that includes a friendly user interface along with run-time optimizations to reduce annotation and execution time in AL in digital pathology. Our solution implements several AL strategies along with our diversity-aware data acquisition (DADA) acquisition function, which enforces data diversity to improve the prediction performance of a model. In this work, we employed a model simplification strategy [Network Auto-Reduction (NAR)] that significantly improves AL execution time when coupled with DADA. NAR produces less compute demanding models, which replace the target models during the AL process to reduce processing demands. An evaluation with a tumor-infiltrating lymphocytes classification application shows that: (i) DADA attains superior performance compared to state-of-the-art AL strategies for different convolutional neural networks (CNNs), (ii) NAR improves the AL execution time by up to 4.3×, and (iii) target models trained with patches/data selected by the NAR reduced versions achieve similar or superior classification quality to using target CNNs for data selection.Availability and implementationSource code: https://github.com/alsmeirelles/DADA.
| S-EPMC10079352 | biostudies-literature
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