Deep learning-based automated and universal bubble detection and mask extraction in complex two-phase flows

AbstractWhile investigating multiphase flows experimentally, the spatiotemporal variation in the interfacial shape between different phases must be measured to analyze the transport phenomena. For this, numerous image processing techniques have been proposed, showing good performance. However, they require trial-and-error optimization of thresholding parameters, which are not universal for all experimental conditions; thus, their accuracy is highly dependent on human experience, and the overall processing cost is high. Motivated by the remarkable improvements in deep learning-based image processing, we trained the Mask R-CNN to develop an automated bubble detection and mask extraction tool that works universally in gas–liquid two-phase flows. The training dataset was rigorously optimized to improve the model performance and delay overfitting with a finite amount of data. The range of detectable bubble size (particularly smaller bubbles) could be extended using a customized weighted loss function. Validation with different bubbly flows yields promising results, with AP50reaching 98%. Even while testing with bubble-swarm flows not included in the training set, the model detects more than 95% of the bubbles, which is equivalent or superior to conventional image processing methods. The pure processing speed for mask extraction is more than twice as fast as conventional approaches, even without counting the time required for tedious threshold parameter tuning. The present bubble detection and mask extraction tool is available online (https://github.com/ywflow/BubMask).

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Effectiveness of transfer learning for enhancing tumor classification with a convolutional neural network on frozen sections

Scientific Reports ◽

10.1038/s41598-020-78129-0 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Young-Gon Kim ◽

Sungchul Kim ◽

Cristina Eunbee Cho ◽

In Hye Song ◽

Hee Jin Lee ◽

...

Keyword(s):

Neural Network ◽

Deep Learning ◽

Convolutional Neural Network ◽

Transfer Learning ◽

Frozen Section ◽

Medical Center ◽

External Validation ◽

Model Performance ◽

Classification Model ◽

Training Dataset

AbstractFast and accurate confirmation of metastasis on the frozen tissue section of intraoperative sentinel lymph node biopsy is an essential tool for critical surgical decisions. However, accurate diagnosis by pathologists is difficult within the time limitations. Training a robust and accurate deep learning model is also difficult owing to the limited number of frozen datasets with high quality labels. To overcome these issues, we validated the effectiveness of transfer learning from CAMELYON16 to improve performance of the convolutional neural network (CNN)-based classification model on our frozen dataset (N = 297) from Asan Medical Center (AMC). Among the 297 whole slide images (WSIs), 157 and 40 WSIs were used to train deep learning models with different dataset ratios at 2, 4, 8, 20, 40, and 100%. The remaining, i.e., 100 WSIs, were used to validate model performance in terms of patch- and slide-level classification. An additional 228 WSIs from Seoul National University Bundang Hospital (SNUBH) were used as an external validation. Three initial weights, i.e., scratch-based (random initialization), ImageNet-based, and CAMELYON16-based models were used to validate their effectiveness in external validation. In the patch-level classification results on the AMC dataset, CAMELYON16-based models trained with a small dataset (up to 40%, i.e., 62 WSIs) showed a significantly higher area under the curve (AUC) of 0.929 than those of the scratch- and ImageNet-based models at 0.897 and 0.919, respectively, while CAMELYON16-based and ImageNet-based models trained with 100% of the training dataset showed comparable AUCs at 0.944 and 0.943, respectively. For the external validation, CAMELYON16-based models showed higher AUCs than those of the scratch- and ImageNet-based models. Model performance for slide feasibility of the transfer learning to enhance model performance was validated in the case of frozen section datasets with limited numbers.

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InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification

BMC Bioinformatics ◽

10.1186/s12859-021-04037-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Dominik Jens Elias Waibel ◽

Sayedali Shetab Boushehri ◽

Carsten Marr

Keyword(s):

Image Processing ◽

Deep Learning ◽

Specific Problem ◽

State Of The Art ◽

Image Data ◽

Semantic Segmentation ◽

Parameter Tuning ◽

Cellular Processes ◽

Minimal Effort ◽

Instance Segmentation

Abstract Background Deep learning contributes to uncovering molecular and cellular processes with highly performant algorithms. Convolutional neural networks have become the state-of-the-art tool to provide accurate and fast image data processing. However, published algorithms mostly solve only one specific problem and they typically require a considerable coding effort and machine learning background for their application. Results We have thus developed InstantDL, a deep learning pipeline for four common image processing tasks: semantic segmentation, instance segmentation, pixel-wise regression and classification. InstantDL enables researchers with a basic computational background to apply debugged and benchmarked state-of-the-art deep learning algorithms to their own data with minimal effort. To make the pipeline robust, we have automated and standardized workflows and extensively tested it in different scenarios. Moreover, it allows assessing the uncertainty of predictions. We have benchmarked InstantDL on seven publicly available datasets achieving competitive performance without any parameter tuning. For customization of the pipeline to specific tasks, all code is easily accessible and well documented. Conclusions With InstantDL, we hope to empower biomedical researchers to conduct reproducible image processing with a convenient and easy-to-use pipeline.

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A Deep Learning-Based Fragment Detection Approach for the Arena Fragmentation Test

Applied Sciences ◽

10.3390/app10144744 ◽

2020 ◽

Vol 10 (14) ◽

pp. 4744

Author(s):

Hyukzae Lee ◽

Jonghee Kim ◽

Chanho Jung ◽

Yongchan Park ◽

Woong Park ◽

...

Keyword(s):

Image Processing ◽

Deep Learning ◽

Object Detection ◽

High Speed ◽

Detection Algorithm ◽

Learning Technologies ◽

Experimental Conditions ◽

Fragmentation Test ◽

Detection Approach ◽

Previous Image

The arena fragmentation test (AFT) is one of the tests used to design an effective warhead. Conventionally, complex and expensive measuring equipment is used for testing a warhead and measuring important factors such as the size, velocity, and the spatial distribution of fragments where the fragments penetrate steel target plates. In this paper, instead of using specific sensors and equipment, we proposed the use of a deep learning-based object detection algorithm to detect fragments in the AFT. To this end, we acquired many high-speed videos and built an AFT image dataset with bounding boxes of warhead fragments. Our method fine-tuned an existing object detection network named the Faster R-convolutional neural network (CNN) on this dataset with modification of the network’s anchor boxes. We also employed a novel temporal filtering method, which was demonstrated as an effective non-fragment filtering scheme in our recent previous image processing-based fragment detection approach, to capture only the first penetrating fragments from all detected fragments. We showed that the performance of the proposed method was comparable to that of a sensor-based system under the same experimental conditions. We also demonstrated that the use of deep learning technologies in the task of AFT significantly enhanced the performance via a quantitative comparison between our proposed method and our recent previous image processing-based method. In other words, our proposed method outperformed the previous image processing-based method. The proposed method produced outstanding results in terms of finding the exact fragment positions.

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Improving generalization of deep learning models for diagnostic pathology by increasing variability in training data: experiments on osteosarcoma subtypes

10.1101/2020.09.10.20192294 ◽

2020 ◽

Author(s):

Haiming Tang ◽

Nanfei Sun ◽

Steven Shen

Keyword(s):

Deep Learning ◽

Model Performance ◽

High Variability ◽

Training Data ◽

Classification Model ◽

Training Dataset ◽

Learning Models ◽

Diagnostic Pathology ◽

Model Generalization ◽

Histopathological Images

Artificial intelligence (AI) has an emerging progress in diagnostic pathology. A large number of studies of applying deep learning models to histopathological images have been published in recent years. While many studies claim high accuracies, they may fall into the pitfalls of overfitting and lack of generalization due to the high variability of the histopathological images. We use the example of Osteosarcoma to illustrate the pitfalls and how the addition of model input variability can help improve model performance. We use the publicly available osteosarcoma dataset to retrain a previously published classification model for osteosarcoma. We partition the same set of images into the training and testing datasets differently than the original study: the test dataset consists of images from one patient while the training dataset consists images of all other patients. The performance of the model on the test set using the new partition schema declines dramatically, indicating a lack of model generalization and overfitting.We also show the influence of training data variability on model performance by collecting a minimal dataset of 10 osteosarcoma subtypes as well as benign tissues and benign bone tumors of differentiation. We show the additions of more and more subtypes into the training data step by step under the same model schema yield a series of coherent models with increasing performances. In conclusion, we bring forward data preprocessing and collection tactics for histopathological images of high variability to avoid the pitfalls of overfitting and build deep learning models of higher generalization abilities.

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Three-Dimensional Reconstruction of Bubble Distribution in Two-Phase Flows With Metaball Technique

Volume 1: Fora, Parts A, B, C, and D ◽

10.1115/fedsm2003-45218 ◽

2003 ◽

Author(s):

Toru Furukawa ◽

Yassin A. Hassan ◽

Javier Ortiz-Villafuerte

Keyword(s):

Image Processing ◽

Three Dimensional ◽

Bubbly Flows ◽

Reconstruction Method ◽

Three Dimensional Reconstruction ◽

Two Phase Flows ◽

Two Phase ◽

Real Experiment ◽

Bubble Distribution ◽

Dimensional Reconstruction

A three-dimensional reconstruction method using shadowgraphy for complex shaped bubbly flows is proposed. Bubble distribution is represented by a metaball object. Metaballs have the capability of representing smooth but complex surfaces. The fundamental strategy is searching the optimal metaball object equivalent to the original bubble distribution. The method does not assume that every bubble has a certain size or shape, therefore, intensive image processing on shadow images is not required. This method has applied to both synthetic bubble shadow images and those obtained from a real experiment, and the results indicate the potential ability of bubble reconstruction.

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