Automatic detection of Opisthorchis viverrini egg in stool examination using convolutional-based neural networks
Background Human opisthorchiasis is a dangerous infectious chronic disease distributed in many Asian areas in the water-basins of large rivers, Siberia, and Europe. The gold standard for human opisthorchiasis laboratory diagnosis is the routine examination of Opisthorchis spp. eggs under a microscop...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2024-01-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/16773.pdf |
| _version_ | 1797335989687943168 |
|---|---|
| author | Tongjit Thanchomnang Natthanai Chaibutr Wanchai Maleewong Penchom Janwan |
| author_facet | Tongjit Thanchomnang Natthanai Chaibutr Wanchai Maleewong Penchom Janwan |
| author_sort | Tongjit Thanchomnang |
| collection | DOAJ |
| description | Background Human opisthorchiasis is a dangerous infectious chronic disease distributed in many Asian areas in the water-basins of large rivers, Siberia, and Europe. The gold standard for human opisthorchiasis laboratory diagnosis is the routine examination of Opisthorchis spp. eggs under a microscope. Manual detection is laborious, time-consuming, and dependent on the microscopist’s abilities and expertise. Automatic screening of Opisthorchis spp. eggs with deep learning techniques is a useful diagnostic aid. Methods Herein, we propose a convolutional neural network (CNN) for classifying and automatically detecting O. viverrini eggs from digitized images. The image data acquisition was acquired from infected human feces and was processed using the gold standard formalin ethyl acetate concentration technique, and then captured under the microscope digital camera at 400x. Microscopic images containing artifacts and O.viverrini egg were augmented using image rotation, filtering, noising, and sharpening techniques. This augmentation increased the image dataset from 1 time to 36 times in preparation for the training and validation step. Furthermore, the overall dataset was subdivided into a training-validation and test set at an 80:20 ratio, trained with a five-fold cross-validation to test model stability. For model training, we customized a CNN for image classification. An object detection method was proposed using a patch search algorithm to detect eggs and their locations. A performance matrix was used to evaluate model efficiency after training and IoU analysis for object detection. Results The proposed model, initially trained on non-augmented data of artifacts (class 0) and O. viverrini eggs (class 1), showed limited performance with 50.0% accuracy, 25.0% precision, 50.0% recall, and a 33.0% F1-score. After implementing data augmentation, the model significantly improved, reaching 100% accuracy, precision, recall, and F1-score. Stability assessments using 5-fold cross-validation indicated better stability with augmented data, evidenced by an ROC-AUC metric improvement from 0.5 to 1.00. Compared to other models such as ResNet50, InceptionV3, VGG16, DenseNet121, and Xception, the proposed model, with a smaller file size of 2.7 MB, showed comparable perfect performance. In object detection, the augmented data-trained model achieved an IoU score over 0.5 in 139 out of 148 images, with an average IoU of 0.6947. Conclusion This study demonstrated the successful application of CNN in classifying and automating the detection of O. viverrini eggs in human stool samples. Our CNN model’s performance metrics and true positive detection rates were outstanding. This innovative application of deep learning can automate and improve diagnostic precision, speed, and efficiency, particularly in regions where O. viverrini infections are prevalent, thereby possibly improving infection sustainable control and treatment program. |
| first_indexed | 2024-03-08T08:47:27Z |
| format | Article |
| id | doaj.art-a1116fa1d9f44670b0fffee89a6ced35 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-08T08:47:27Z |
| publishDate | 2024-01-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-a1116fa1d9f44670b0fffee89a6ced352024-02-01T15:05:13ZengPeerJ Inc.PeerJ2167-83592024-01-0112e1677310.7717/peerj.16773Automatic detection of Opisthorchis viverrini egg in stool examination using convolutional-based neural networksTongjit Thanchomnang0Natthanai Chaibutr1Wanchai Maleewong2Penchom Janwan3Faculty of Medicine, Mahasarakham University, Maha Sarakham, ThailandMedical Innovation and Technology Program, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, ThailandDepartment of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, ThailandMedical Innovation and Technology Program, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, ThailandBackground Human opisthorchiasis is a dangerous infectious chronic disease distributed in many Asian areas in the water-basins of large rivers, Siberia, and Europe. The gold standard for human opisthorchiasis laboratory diagnosis is the routine examination of Opisthorchis spp. eggs under a microscope. Manual detection is laborious, time-consuming, and dependent on the microscopist’s abilities and expertise. Automatic screening of Opisthorchis spp. eggs with deep learning techniques is a useful diagnostic aid. Methods Herein, we propose a convolutional neural network (CNN) for classifying and automatically detecting O. viverrini eggs from digitized images. The image data acquisition was acquired from infected human feces and was processed using the gold standard formalin ethyl acetate concentration technique, and then captured under the microscope digital camera at 400x. Microscopic images containing artifacts and O.viverrini egg were augmented using image rotation, filtering, noising, and sharpening techniques. This augmentation increased the image dataset from 1 time to 36 times in preparation for the training and validation step. Furthermore, the overall dataset was subdivided into a training-validation and test set at an 80:20 ratio, trained with a five-fold cross-validation to test model stability. For model training, we customized a CNN for image classification. An object detection method was proposed using a patch search algorithm to detect eggs and their locations. A performance matrix was used to evaluate model efficiency after training and IoU analysis for object detection. Results The proposed model, initially trained on non-augmented data of artifacts (class 0) and O. viverrini eggs (class 1), showed limited performance with 50.0% accuracy, 25.0% precision, 50.0% recall, and a 33.0% F1-score. After implementing data augmentation, the model significantly improved, reaching 100% accuracy, precision, recall, and F1-score. Stability assessments using 5-fold cross-validation indicated better stability with augmented data, evidenced by an ROC-AUC metric improvement from 0.5 to 1.00. Compared to other models such as ResNet50, InceptionV3, VGG16, DenseNet121, and Xception, the proposed model, with a smaller file size of 2.7 MB, showed comparable perfect performance. In object detection, the augmented data-trained model achieved an IoU score over 0.5 in 139 out of 148 images, with an average IoU of 0.6947. Conclusion This study demonstrated the successful application of CNN in classifying and automating the detection of O. viverrini eggs in human stool samples. Our CNN model’s performance metrics and true positive detection rates were outstanding. This innovative application of deep learning can automate and improve diagnostic precision, speed, and efficiency, particularly in regions where O. viverrini infections are prevalent, thereby possibly improving infection sustainable control and treatment program.https://peerj.com/articles/16773.pdfHuman opisthorchiasisMicroscopic detectionConvolutional neural networksDeep learning |
| spellingShingle | Tongjit Thanchomnang Natthanai Chaibutr Wanchai Maleewong Penchom Janwan Automatic detection of Opisthorchis viverrini egg in stool examination using convolutional-based neural networks PeerJ Human opisthorchiasis Microscopic detection Convolutional neural networks Deep learning |
| title | Automatic detection of Opisthorchis viverrini egg in stool examination using convolutional-based neural networks |
| title_full | Automatic detection of Opisthorchis viverrini egg in stool examination using convolutional-based neural networks |
| title_fullStr | Automatic detection of Opisthorchis viverrini egg in stool examination using convolutional-based neural networks |
| title_full_unstemmed | Automatic detection of Opisthorchis viverrini egg in stool examination using convolutional-based neural networks |
| title_short | Automatic detection of Opisthorchis viverrini egg in stool examination using convolutional-based neural networks |
| title_sort | automatic detection of opisthorchis viverrini egg in stool examination using convolutional based neural networks |
| topic | Human opisthorchiasis Microscopic detection Convolutional neural networks Deep learning |
| url | https://peerj.com/articles/16773.pdf |
| work_keys_str_mv | AT tongjitthanchomnang automaticdetectionofopisthorchisviverriniegginstoolexaminationusingconvolutionalbasedneuralnetworks AT natthanaichaibutr automaticdetectionofopisthorchisviverriniegginstoolexaminationusingconvolutionalbasedneuralnetworks AT wanchaimaleewong automaticdetectionofopisthorchisviverriniegginstoolexaminationusingconvolutionalbasedneuralnetworks AT penchomjanwan automaticdetectionofopisthorchisviverriniegginstoolexaminationusingconvolutionalbasedneuralnetworks |