superior-auto-identification-trypanosome-parasites-using-hybrid-deep

Superior Auto-Identification of Trypanosome Parasites by Using a Hybrid Deep-Learning Model

Trypanosomiasis is a significant public health problem in several regions across the world, including South Asia and Southeast Asia. The identification of ...

King Mongkut’s Institute of Technology Ladkrabang

Microscopic observation of mosquito species, which is the basis of morphological identification, is a time-consuming and challenging process, particularly owing to the different skills and experience of public health personnel. We present deep learning models based on the well-known you-only-look-once (YOLO) algorithm. This model can be used to simultaneously classify and localize the images to identify the species of the gender of field-caught mosquitoes. The results indicated that the concatenated two YOLO v3 model exhibited the optimal performance in identifying the mosquitoes, as the mosquitoes were relatively small objects compared with the large proportional environment image. The robustness testing of the proposed model yielded a mean average precision and sensitivity of 99% and 92.4%, respectively. The model exhibited high performance in terms of the specificity and accuracy, with an extremely low rate of misclassification. The area under the receiver operating characteristic curve (AUC) was 0.958 ± 0.011, which further demonstrated the model accuracy. Thirteen classes were detected with an accuracy of 100% based on a confusion matrix. Nevertheless, the relatively low detection rates for the two species were likely a result of the limited number of wild-caught biological samples available. The proposed model can help establish the population densities of mosquito vectors in remote areas to predict disease outbreaks in advance.

Deep learning approaches for challenging species and gender identification of mosquito vectors.

The infection of an avian malaria parasite (Plasmodium gallinaceum) in domestic chickens presents a major threat to the poultry industry because it causes economic loss in both the quality and quantity of meat and egg production. Computer-aided diagnosis has been developed to automatically identify avian malaria infections and classify the blood infection stage development. In this study, four types of deep convolutional neural networks, namely Darknet, Darknet19, Darknet19-448 and Densenet201 are used to classify P. gallinaceum blood stages. We randomly collected a dataset of 12,761 single-cell images consisting of three parasite stages from ten-infected blood films stained by Giemsa. All images were confirmed by three well-trained examiners. The study mainly compared several image classification models and used both qualitative and quantitative data for the evaluation of the proposed models. In the model-wise comparison, the four neural network models gave us high values with a mean average accuracy of at least 97%. The Darknet can reproduce a superior performance in the classification of the P. gallinaceum development stages across any other model architectures. Furthermore, the Darknet has the best performance in multiple class-wise classification, with average values of greater than 99% in accuracy, specificity, and sensitivity. It also has a low misclassification rate (< 1%) than the other three models. Therefore, the model is more suitable in the classification of P. gallinaceum blood stages. The findings could help us create a fast-screening method to help non-experts in field studies where there is a lack of specialized instruments for avian malaria diagnostics.

Classification for avian malaria parasite Plasmodium gallinaceum blood stages by using deep convolutional neural networks.

This paper outlines a system for detecting printing errors and misidentifications on hard disk drive sliders, which may contribute to shipping tracking problems and incorrect product delivery to end users. A deep-learning-based technique is proposed for determining the printed identity of a slider serial number from images captured by a digital camera. Our approach starts with image preprocessing methods that deal with differences in lighting and printing positions and then progresses to deep learning character detection based on the You-Only-Look-Once (YOLO) v4 algorithm and finally character classification. For character classification, four convolutional neural networks (CNN) were compared for accuracy and effectiveness: DarkNet-19, EfficientNet-B0, ResNet-50, and DenseNet-201. Experimenting on almost 15,000 photographs yielded accuracy greater than 99% on four CNN networks, proving the feasibility of the proposed technique. The EfficientNet-B0 network outperformed highly qualified human readers with the best recovery rate (98.4%) and fastest inference time (256.91 ms).

A Deep Learning System for Recognizing and Recovering Contaminated Slider Serial Numbers in Hard Disk Manufacturing Processes.

DNA double-strand breaks (DSBs) are the most lethal form of damage to cells from irradiation. γ-H2AX (phosphorylated form of H2AX histone variant) has become one of the most reliable and sensitive biomarkers of DNA DSBs. However, the γ-H2AX foci assay still has limitations in the time consumed for manual scoring and possible variability between scorers. This study proposed a novel automated foci scoring method using a deep convolutional neural network based on a You-Only-Look-Once (YOLO) algorithm to quantify γ-H2AX foci in peripheral blood samples. FociRad, a two-stage deep learning approach, consisted of mononuclear cell (MNC) and γ-H2AX foci detections. Whole blood samples were irradiated with X-rays from a 6 MV linear accelerator at 1, 2, 4 or 6 Gy. Images were captured using confocal microscopy. Then, dose-response calibration curves were established and implemented with unseen dataset. The results of the FociRad model were comparable with manual scoring. MNC detection yielded 96.6% accuracy, 96.7% sensitivity and 96.5% specificity. γ-H2AX foci detection showed very good F1 scores (> 0.9). Implementation of calibration curve in the range of 0-4 Gy gave mean absolute difference of estimated doses less than 1 Gy compared to actual doses. In addition, the evaluation times of FociRad were very short (< 0.5 min per 100 images), while the time for manual scoring increased with the number of foci. In conclusion, FociRad was the first automated foci scoring method to use a YOLO algorithm with high detection performance and fast evaluation time, which opens the door for large-scale applications in radiation triage.

A deep learning model (FociRad) for automated detection of γ-H2AX foci and radiation dose estimation.

Both the ABO and Rhesus (Rh) blood groups play crucial roles in blood transfusion medicine. Herein, we report a simple and low-cost paper-based analytical device (PAD) for phenotyping red blood cell (RBC) antigens. Using this Rh typing format, 5 Rh antigens on RBCs can be simultaneously detected and macroscopically visualized within 12 min. The proposed Rh phenotyping relies on the presence or absence of hemagglutination in the sample zones after immobilizing the antibodies targeting each Rh antigen. The PAD was optimized in terms of filter paper type, antibodies, and distance of the visualization zone. In this study, the optimal conditions were Whatman filter paper Grade 4; anti-D, -C, -E, -c, and -e antibodies; RBC suspension of 30%; and a visualization zone of 1 cm above the sample zone. The accuracy of simultaneously phenotyping the five Rh RBC antigens in the blood samples (n = 4692) was 99.19%, comparable with the accuracy of the gold-standard tube method used by blood bank laboratories in several regions of Thailand. Furthermore, decision making based on this method can be assisted by deep learning. After implementing a two-stage objective detection algorithm (YOLO v4-tiny) and classification model (DenseNet-201), the ambiguous images (n = 48) were interpreted with 100% accuracy. The PAD integrated with customized-region convolutional neural networks can reduce the interpretation discrepancies in RBC antigen phenotyping in any laboratory.

Simultaneous phenotyping of five Rh red blood cell antigens on a paper-based analytical device combined with deep learning for rapid and accurate interpretation.

Thin films of silk fibroin were prepared by solvent evaporation from calcium chloride/ethanol aqueous solution. The influence of alcohol treatments on thermal, mechanical and optical properties of silk-fibroin-based film is presented. To understand the conformal structure of the alcohol-treated silk fibroin film, the IR spectral decomposition method is employed. The optical properties especially the optical transparency, haze and fluorescence emission of alcohol-treated silk fibroin film is systematically investigated together with the conformal structure to understand the effect of the fibril such as the beta-sheet influencing the optical properties. Monohydric alcohol treatment increased beta-turn content in the regenerated silk fibroin structure. These affected the amount of light diffusion and scattering within silk-fibroin films. With alcohol-treatment, all the silk-fibroin films exhibit exceptional optical transparency (>90%) with different levels of optical haze (2.56-14.17%). In particular, ethanol-treated silk-fibroin films contain the highest content of beta-turns (22.8%). The ethanol-treated silk-fibroin films displayed a distinct interference of oscillating crests and troughs in the UV-Vis transmittance spectra, thereby showing the lowest optical haze of 2.56%. In contrast, the silk-fibroin films treated with methanol and propanol exhibit the highest (14.17%) and second-highest (10.29%) optical transmittance haze, respectively. The beta-turn content of the silk-fibroin films treated with methanol is the lowest (20.5%). These results show the relationship between the beta-turn content and optical haze properties. The results manifestly provide a method to manufacture exceptional optically transparent silk-fibroin films with adjustable light diffusion and scattering which can be designed to meet specific applications with the potential to provide UV-shielding protection  monohydric alcohol treatment.

Influence of alcohol treatments on properties of silk-fibroin-based films for highly optically transparent coating applications.

This research focuses on the development of environmentally friendly textile-based shielding composites, from micro-sized and nanosized BiO particles, against ionizing radiation. Polyester fabric dyne-coated with either micro- or nano-BiO particles shields some X-rays but the effectiveness is poor. With only ∼58% uptake of micro-sized BiO particles dyeing on polyester fabric, the insufficient amount of BiO leaded to the low density of particles, resulting in only 30% of X-ray shielding at 80 kVp. Cotton fabric coated with either micro- or nano-BiO/poly(vinyl alcohol) (PVA) composites, on the other hand, demonstrated the capacity to attenuate X-ray generated by high diagnostic X-ray tube voltages of 70-100 kVp, in compliance with medical protection requirements. The X-ray attenuation performance of cotton fabric coated with either micro-BiO/PVA or nano-BiO/PVA nanocomposite decreased progressively with increasing tube acceleration voltages, however their ionizing radiation-shielding performance enhanced with the number of fabric layers. Interestingly, for all X-ray tube voltages evaluated, the micro-BiO/PVA composite outperformed the nano- BiO/PVA composite in terms of X-ray shielding. At a weight ratio of 66.7% BiO, 10 layers of cotton fabric coated with micro- BiO/PVA composite can attenuate 90, 85, and 80% of X-ray photons at 70, 80, and 100 kVp, respectively. As a result, these less harmful X-ray shielding materials have the potential to replace lead-based composites, which are highly toxic to human health and have negative environmental consequences.

Evaluation of Micro- and Nano-Bismuth(III) Oxide Coated Fabric for Environmentally Friendly X-Ray Shielding Materials.

Object detection is a new artificial intelligence approach to morphological recognition and labeling parasitic pathogens. Due to the lack of equipment and trained personnel, artificial intelligence innovation for searching various parasitic products in stool examination will enable patients in remote areas of undeveloped countries to access diagnostic services. Because object detection is a developing approach that has been tested for its effectiveness in detecting intestinal parasitic objects such as protozoan cysts and helminthic eggs, it is suitable for use in rural areas where many factors supporting laboratory testing are still lacking. Based on the literatures, the YOLOv4-Tiny produces faster results and uses less memory with the support of low-end GPU devices. In comparison to the YOLOv3 and YOLOv3-Tiny models, this study aimed to propose an automated object detection approach, specifically the YOLOv4-Tiny model, for automatic recognition of intestinal parasitic products in stools.

Automatic recognition of parasitic products in stool examination using object detection approach.

Mosquito-borne diseases such as dengue fever and malaria are the top 10 leading causes of death in low-income countries. Control measure for the mosquito population plays an essential role in the fight against the disease. Currently, several intervention strategies; chemical-, biological-, mechanical- and environmental methods remain under development and need further improvement in their effectiveness. Although, a conventional entomological surveillance, required a microscope and taxonomic key for identification by professionals, is a key strategy to evaluate the population growth of these mosquitoes, these techniques are tedious, time-consuming, labor-intensive, and reliant on skillful and well-trained personnel. Here, we proposed an automatic screening, namely the deep metric learning approach and its inference under the image-retrieval process with Euclidean distance-based similarity. We aimed to develop the optimized model to find suitable miners and suggested the robustness of the proposed model by evaluating it with unseen data under a 20-returned image system. During the model development, well-trained ResNet34 are outstanding and no performance difference when comparing five data miners that showed up to 98% in its precision even after testing the model with both image sources: stereomicroscope and mobile phone cameras. The robustness of the proposed-trained model was tested with secondary unseen data which showed different environmental factors such as lighting, image scales, background colors and zoom levels. Nevertheless, our proposed neural network still has great performance with greater than 95% for sensitivity and precision, respectively. Also, the area under the ROC curve given the learning system seems to be practical and empirical with its value greater than 0.960. The results of the study may be used by public health authorities to locate mosquito vectors nearby. If used in the field, our research tool in particular is believed to accurately represent a real-world scenario.

Article	Year
Deep learning approaches for challenging species and gender identification of mosquito vectors. Scientific reports\| PubMed ID: 33649429	2021
Classification for avian malaria parasite Plasmodium gallinaceum blood stages by using deep convolutional neural networks. Scientific reports\| PubMed ID: 34413434	2021
A Deep Learning System for Recognizing and Recovering Contaminated Slider Serial Numbers in Hard Disk Manufacturing Processes. Sensors (Basel, Switzerland)\| PubMed ID: 34577468	2021
A deep learning model (FociRad) for automated detection of γ-H2AX foci and radiation dose estimation. Scientific reports\| PubMed ID: 35365702	2022
Simultaneous phenotyping of five Rh red blood cell antigens on a paper-based analytical device combined with deep learning for rapid and accurate interpretation. Analytica chimica acta\| PubMed ID: 35491041	2022
Influence of alcohol treatments on properties of silk-fibroin-based films for highly optically transparent coating applications. RSC advances\| PubMed ID: 35493649	2020
Evaluation of Micro- and Nano-Bismuth(III) Oxide Coated Fabric for Environmentally Friendly X-Ray Shielding Materials. ACS omega\| PubMed ID: 35990472	2022
Automatic recognition of parasitic products in stool examination using object detection approach. PeerJ. Computer science\| PubMed ID: 36092001	2022
Automatic identification of medically important mosquitoes using embedded learning approach-based image-retrieval system. Scientific reports\| PubMed ID: 37391476	2023

Siridech Boonsang

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