Deep learning approach to describe and classify fungi microscopic images.
Ontology highlight
ABSTRACT:
SUBMITTER: Zielinski B
PROVIDER: S-EPMC7326179 | biostudies-literature | 2020
REPOSITORIES: biostudies-literature
Publications
Deep learning approach to describe and classify fungi microscopic images.
Zieliński Bartosz B Sroka-Oleksiak Agnieszka A Rymarczyk Dawid D Piekarczyk Adam A Brzychczy-Włoch Monika M
PloS one 20200630 6
Preliminary diagnosis of fungal infections can rely on microscopic examination. However, in many cases, it does not allow unambiguous identification of the species due to their visual similarity. Therefore, it is usually necessary to use additional biochemical tests. That involves additional costs and extends the identification process up to 10 days. Such a delay in the implementation of targeted therapy may be grave in consequence as the mortality rate for immunosuppressed patients is high. In ...[more]
Similar Datasets
Project description:BACKGROUND:Melanoma results in the vast majority of skin cancer deaths during the last decades, even though this disease accounts for only one percent of all skin cancers' instances. The survival rates of melanoma from early to terminal stages is more than fifty percent. Therefore, having the right information at the right time by early detection with monitoring skin lesions to find potential problems is essential to surviving this type of cancer. RESULTS:An approach to classify skin lesions using deep learning for early detection of melanoma in a case-based reasoning (CBR) system is proposed. This approach has been employed for retrieving new input images from the case base of the proposed system DePicT Melanoma Deep-CLASS to support users with more accurate recommendations relevant to their requested problem (e.g., image of affected area). The efficiency of our system has been verified by utilizing the ISIC Archive dataset in analysis of skin lesion classification as a benign and malignant melanoma. The kernel of DePicT Melanoma Deep-CLASS is built upon a convolutional neural network (CNN) composed of sixteen layers (excluding input and ouput layers), which can be recursively trained and learned. Our approach depicts an improved performance and accuracy in testing on the ISIC Archive dataset. CONCLUSIONS:Our methodology derived from a deep CNN, generates case representations for our case base to use in the retrieval process. Integration of this approach to DePicT Melanoma CLASS, significantly improving the efficiency of its image classification and the quality of the recommendation part of the system. The proposed method has been tested and validated on 1796 dermoscopy images. Analyzed results indicate that it is efficient on malignancy detection.
| S-EPMC7068864 | biostudies-literature
Project description:Efficient and accurate methods of analysis are needed for the huge amount of biological data that have accumulated in various research fields, including genomics, phenomics, and genetics. Artificial intelligence (AI)-based analysis is one promising method to manipulate biological data. To this end, various algorithms have been developed and applied in fields such as disease diagnosis, species classification, and object prediction. In the field of phenomics, classification of accessions and variants is important for basic science and industrial applications. To construct AI-based classification models, three types of phenotypic image data were generated from 156 Brassica rapa core collections, and classification analyses were carried out using four different convolutional neural network architectures. The results of lateral view data showed higher accuracy compared with top view data. Furthermore, the relatively low accuracy of ResNet50 architecture suggested that definition and estimation of similarity index of phenotypic data were required before the selection of deep learning architectures.
| S-EPMC8511822 | biostudies-literature
Project description:Stitched fluorescence microscope images inevitably exist in various types of stripes or artifacts caused by uncertain factors such as optical devices or specimens, which severely affects the image quality and downstream quantitative analysis. Here, we present a deep learning-based Stripe Self-Correction method, so-called SSCOR. Specifically, we propose a proximity sampling scheme and adversarial reciprocal self-training paradigm that enable SSCOR to utilize stripe-free patches sampled from the stitched microscope image itself to correct their adjacent stripe patches. Comparing to off-the-shelf approaches, SSCOR can not only adaptively correct non-uniform, oblique, and grid stripes, but also remove scanning, bubble, and out-of-focus artifacts, achieving the state-of-the-art performance across different imaging conditions and modalities. Moreover, SSCOR does not require any physical parameter estimation, patch-wise manual annotation, or raw stitched information in the correction process. This provides an intelligent prior-free image restoration solution for microscopists or even microscope companies, thus ensuring more precise biomedical applications for researchers.
| S-EPMC10480181 | biostudies-literature
Project description:Deep learning emerges as a powerful tool for analyzing medical images. Retinal disease detection by using computer-aided diagnosis from fundus image has emerged as a new method. We applied deep learning convolutional neural network by using MatConvNet for an automated detection of multiple retinal diseases with fundus photographs involved in STructured Analysis of the REtina (STARE) database. Dataset was built by expanding data on 10 categories, including normal retina and nine retinal diseases. The optimal outcomes were acquired by using a random forest transfer learning based on VGG-19 architecture. The classification results depended greatly on the number of categories. As the number of categories increased, the performance of deep learning models was diminished. When all 10 categories were included, we obtained results with an accuracy of 30.5%, relative classifier information (RCI) of 0.052, and Cohen's kappa of 0.224. Considering three integrated normal, background diabetic retinopathy, and dry age-related macular degeneration, the multi-categorical classifier showed accuracy of 72.8%, 0.283 RCI, and 0.577 kappa. In addition, several ensemble classifiers enhanced the multi-categorical classification performance. The transfer learning incorporated with ensemble classifier of clustering and voting approach presented the best performance with accuracy of 36.7%, 0.053 RCI, and 0.225 kappa in the 10 retinal diseases classification problem. First, due to the small size of datasets, the deep learning techniques in this study were ineffective to be applied in clinics where numerous patients suffering from various types of retinal disorders visit for diagnosis and treatment. Second, we found that the transfer learning incorporated with ensemble classifiers can improve the classification performance in order to detect multi-categorical retinal diseases. Further studies should confirm the effectiveness of algorithms with large datasets obtained from hospitals.
| S-EPMC5667846 | biostudies-literature
Project description:Intravascular ultrasound (IVUS) imaging is widely used for diagnostic imaging in interventional cardiology. The detection and quantification of atherosclerosis from acquired images is typically performed manually by medical experts or by virtual histology IVUS (VH-IVUS) software. VH-IVUS analyzes backscattered radio frequency (RF) signals to provide a color-coded tissue map, and is the method of choice for assessing atherosclerotic plaque in situ. However, a significant amount of tissue cannot be analyzed in reasonable time because the method can be applied just once per cardiac cycle. Furthermore, only hardware and software compatible with RF signal acquisition and processing may be used. We present an image-based tissue characterization method that can be applied to entire acquisition sequences post hoc for the assessment of diseased vessels. The pixel-based method utilizes domain knowledge of arterial pathology and physiology, and leverages technological advances of convolutional neural networks to segment diseased vessel walls into the same tissue classes as virtual histology using only grayscale IVUS images. The method was trained and tested on patches extracted from VH-IVUS images acquired from several patients, and achieved overall accuracy of 93.5% for all segmented tissue. Imposing physically-relevant spatial constraints driven by domain knowledge was key to achieving such strong performance. This enriched approach offers capabilities akin to VH-IVUS without the constraints of RF signals or limited once-per-cycle analysis, offering superior potential information acquisition speed, reduced hardware and software requirements, and more widespread applicability. Such an approach may well yield promise for future clinical and research applications.
| S-EPMC7845913 | biostudies-literature
Project description:PurposeHistological analysis of artery tissue samples is a widely used method for diagnosis and quantification of cardiovascular diseases. However, the variable and labor-intensive tissue staining procedures hinder efficient and informative histological image analysis.ProceduresIn this study, we developed a deep learning-based method to transfer bright-field microscopic images of unlabeled tissue sections into equivalent bright-field images of histologically stained versions of the same samples. We trained a convolutional neural network to build maps between the unstained images and histologically stained images using a conditional generative adversarial network model.ResultsThe results of a blind evaluation by board-certified pathologists illustrate that the virtual staining and standard histological staining images of rat carotid artery tissue sections and those involving different types of stains showed no major differences. Quantification of virtual and histological H&E staining in carotid artery tissue sections showed that the relative errors of intima thickness, intima area, and media area were lower than 1.6 %, 5.6 %, and 12.7 %, respectively. The training time of deep learning network was 12.857 h with 1800 training patches and 200 epoches.ConclusionsThis virtual staining method significantly mitigates the typically laborious and time-consuming histological staining procedures and could be augmented with other label-free microscopic imaging modalities.
| S-EPMC7497459 | biostudies-literature
Project description:Topological features such as persistence diagrams and their functional approximations like persistence images (PIs) have been showing substantial promise for machine learning and computer vision applications. This is greatly attributed to the robustness topological representations provide against different types of physical nuisance variables seen in real-world data, such as view-point, illumination, and more. However, key bottlenecks to their large scale adoption are computational expenditure and difficulty incorporating them in a differentiable architecture. We take an important step in this paper to mitigate these bottlenecks by proposing a novel one-step approach to generate PIs directly from the input data. We design two separate convolutional neural network architectures, one designed to take in multi-variate time series signals as input and another that accepts multi-channel images as input. We call these networks Signal PI-Net and Image PI-Net respectively. To the best of our knowledge, we are the first to propose the use of deep learning for computing topological features directly from data. We explore the use of the proposed PI-Net architectures on two applications: human activity recognition using tri-axial accelerometer sensor data and image classification. We demonstrate the ease of fusion of PIs in supervised deep learning architectures and speed up of several orders of magnitude for extracting PIs from data. Our code is available at https://github.com/anirudhsom/PI-Net.
| S-EPMC7521829 | biostudies-literature
Project description:Pulmonary fissure detection in computed tomography (CT) is a critical component for automatic lobar segmentation. The majority of fissure detection methods use feature descriptors that are hand-crafted, low-level, and have local spatial extent. The design of such feature detectors is typically targeted toward normal fissure anatomy, yielding low sensitivity to weak, and abnormal fissures that are common in clinical data sets. Furthermore, local features commonly suffer from low specificity, as the complex textures in the lung can be indistinguishable from the fissure when the global context is not considered. We propose a supervised discriminative learning framework for simultaneous feature extraction and classification. The proposed framework, called FissureNet, is a coarse-to-fine cascade of two convolutional neural networks. The coarse-to-fine strategy alleviates the challenges associated with training a network to segment a thin structure that represents a small fraction of the image voxels. FissureNet was evaluated on a cohort of 3706 subjects with inspiration and expiration 3DCT scans from the COPDGene clinical trial and a cohort of 20 subjects with 4DCT scans from a lung cancer clinical trial. On both data sets, FissureNet showed superior performance compared with a deep learning approach using the U-Net architecture and a Hessian-based fissure detection method in terms of area under the precision-recall curve (PR-AUC). The overall PR-AUC for FissureNet, U-Net, and Hessian on the COPDGene (lung cancer) data set was 0.980 (0.966), 0.963 (0.937), and 0.158 (0.182), respectively. On a subset of 30 COPDGene scans, FissureNet was compared with a recently proposed advanced fissure detection method called derivative of sticks (DoS) and showed superior performance with a PR-AUC of 0.991 compared with 0.668 for DoS.
| S-EPMC6318012 | biostudies-literature
Project description:While outdoor advertisements are common features within towns and cities, they may reinforce social inequalities in health. Vulnerable populations in deprived areas may have greater exposure to fast food, gambling and alcohol advertisements, which may encourage their consumption. Understanding who is exposed and evaluating potential policy restrictions requires a substantial manual data collection effort. To address this problem we develop a deep learning workflow to automatically extract and classify unhealthy advertisements from street-level images. We introduce the Liverpool [Formula: see text] Street View (LIV360SV) dataset for evaluating our workflow. The dataset contains 25,349, 360 degree, street-level images collected via cycling with a GoPro Fusion camera, recorded Jan 14th-18th 2020. 10,106 advertisements were identified and classified as food (1335), alcohol (217), gambling (149) and other (8405). We find evidence of social inequalities with a larger proportion of food advertisements located within deprived areas and those frequented by students. Our project presents a novel implementation for the incidental classification of street view images for identifying unhealthy advertisements, providing a means through which to identify areas that can benefit from tougher advertisement restriction policies for tackling social inequalities.
| S-EPMC7921635 | biostudies-literature
Project description:Provocative heart disease is related to ventricular arrhythmias (VA). Ventricular tachyarrhythmia is an irregular and fast heart rhythm that emerges from inappropriate electrical impulses in the ventricles of the heart. Different types of arrhythmias are associated with different patterns, which can be identified. An electrocardiogram (ECG) is the major analytical tool used to interpret and record ECG signals. ECG signals are nonlinear and difficult to interpret and analyze. We propose a new deep learning approach for the detection of VA. Initially, the ECG signals are transformed into images that have not been done before. Later, these images are normalized and utilized to train the AlexNet, VGG-16 and Inception-v3 deep learning models. Transfer learning is performed to train a model and extract the deep features from different output layers. After that, the features are fused by a concatenation approach, and the best features are selected using a heuristic entropy calculation approach. Finally, supervised learning classifiers are utilized for final feature classification. The results are evaluated on the MIT-BIH dataset and achieved an accuracy of 97.6% (using Cubic Support Vector Machine as a final stage classifier).
| S-EPMC7959637 | biostudies-literature