A 3D image segmentation for lung cancer using V.Net architecture based deep convolutional networks

Hybrid CNN-transformer network for interactive learning of challenging musculoskeletal images

To facilitate the management of detonators, an automatic spotting system is proposed for detonator coded characters based on convolutional neural networks. The system contains a multi-scale detection network, a multi-label recognition network and a post-processing layer. An improved fully convolution network (FCN) is designed as the multi-scale detection network to obtain the accurate response map of the detonator image. Two subnetworks are parallel integrated into the FCN to perform a coarse-to-fine detection. An improved Jaccard loss function with a regularization term is defined to train the FCN. The region of interest (ROI) of the detonator image is achieved when the response map is post-processed by the post-processing layer. Finally, a modified multi-label network is used to recognize the detonator coded characters in the ROI. The experimental results indicate that the proposed system achieves a better spotting performance for detonator coded characters than the state-of-the-art text spotting methods in terms of accuracy and efficiency.

This paper introduces a deep architecture for segmenting 3D objects into their labeled semantic parts. Our architecture combines image-based Fully Convolutional Networks (FCNs) and surface-based Conditional Random Fields (CRFs) to yield coherent segmentations of 3D shapes. The image-based FCNs are used for efficient view-based reasoning about 3D object parts. Through a special projection layer, FCN outputs are effectively aggregated across multiple views and scales, then are projected onto the 3D object surfaces. Finally, a surface-based CRF combines the projected outputs with geometric consistency cues to yield coherent segmentations. The whole architecture (multi-view FCNs and CRF) is trained end-to-end. Our approach significantly outperforms the existing state-of-the-art methods in the currently largest segmentation benchmark (ShapeNet). Finally, we demonstrate promising segmentation results on noisy 3D shapes acquired from consumer-grade depth cameras.

Segmentation of tumor regions in H &E-stained slides is an important task for a pathologist while diagnosing different types of cancer, including oral squamous cell carcinoma (OSCC). Histological image segmentation is often constrained by the availability of labeled training data since labeling histological images is a highly skilled, complex, and time-consuming task. Thus, data augmentation strategies become essential to train convolutional neural networks models to overcome the overfitting problem when only a few training samples are available. This paper proposes a new data augmentation strategy, named Random Composition Augmentation (RCAug), to train fully convolutional networks (FCN) to segment OSCC tumor regions in H &E-stained histological images. Given the input image and their corresponding label, a pipeline with a random composition of geometric, distortion, color transfer, and generative image transformations is executed on the fly. Experimental evaluations were performed using an FCN-based method to segment OSCC regions through a set of different data augmentation transformations. By using RCAug, we improved the FCN-based segmentation method from 0.51 to 0.81 of intersection-over-union (IOU) in a whole slide image dataset and from 0.65 to 0.69 of IOU in a tissue microarray images dataset.

Morphological characterization of median nerve and transverse carpal ligament from ultrasound images using convolutional neural networks.

Optical pressure sensors based plantar image segmenting using an improved fully convolutional network

Staging third molar development is commonly used for age assessment in sub-adults. Current staging techniques are, at most, semi-automated and rely on manual interactions prone to operator variability. The aim of this study was to fully automate the staging process by employing the full potential of deep learning, using convolutional neural networks (CNNs) in every step of the procedure. The dataset used to train the CNNs consisted of 400 panoramic radiographs (OPGs), with 20 OPGs per developmental stage per sex, staged in consensus between three observers. The concepts of transfer learning, using pre-trained CNNs, and data augmentation were used to mitigate the issues when dealing with a limited dataset. In this work, a three-step procedure was proposed and the results were validated using fivefold cross-validation. First, a CNN localized the geometrical center of the lower left third molar, around which a square region of interest (ROI) was extracted. Second, another CNN segmented the third molar within the ROI. Third, a final CNN used both the ROI and the segmentation to classify the third molar into its developmental stage. The geometrical center of the third molar was found with an average Euclidean distance of 63 pixels. Third molars were segmented with an average Dice score of 93%. Finally, the developmental stages were classified with an accuracy of 54%, a mean absolute error of 0.69 stages, and a linear weighted Cohen's kappa coefficient of 0.79. The entire automated workflow on average took 2.72 s to compute, which is substantially faster than manual staging starting from the OPG. Taking into account the limited dataset size, this pilot study shows that the proposed fully automated approach shows promising results compared with manual staging.

Multi-grade brain tumor classification using deep CNN with extensive data augmentation

Early detection and treatment are crucial for recovery from cancer. Due to rapid advancement in medical imaging techniques, today doctors can scan various body parts from different perspectives to diagnose cancer or see the progress during a course of treatment. Such techniques are less painful and require less preparation and recovery. The recent evolution of AI, particularly deep learning algorithms have shown potential in computer-aided diagnosis of cancer. These include analysis of cancer images for detection of tumor region, prognosis, skin tissue inspection, etc. Convolutional Neural Network (CNN) based image processing techniques are showing promising results in the diagnosis of breast cancer, skin cancer, prostate cancer, lung cancer, etc. Literature shows many other CNN-based models such as feed-forward neural network, Deep CNN, Multi-Crop CNN, fully convolutional networks (FCNs), Deep Fully Convolutional Network (DFCNet), Recurrent neural networks, etc. The CNN focus solely on the image-specific features and hence require a lesser number of input parameters. A CNN model reduces the size of the input image vector without losing the features critical for making an accurate prediction. This makes it easier to process and reduces computational complexity. CNNs are also not sensitive to the object positioning in an image since the approximate position of image motifs relative to others is known. CNN deals with the variations in images through augmentation and other pre-processing techniques. This makes them robust to various straining conditions in images. This chapter presents an overview of a generic CNN architecture followed by a discussion on major advances in CNN models and their applications for cancer image analysis.

Accurate segmentation and delineation of the sub-tumor regions are very challenging tasks due to the nature of the tumor. Traditionally, convolutional neural networks (CNNs) have succeeded in achieving most promising performance for the segmentation of brain tumor; however, handcrafted features remain very important in identification of tumor's boundary regions accurately. The present work proposes a robust deep learning-based model with three different CNN architectures along with pre-defined handcrafted features for brain tumor segmentation, mainly to find out more prominent boundaries of the core and enhanced tumor regions. Generally, automatic CNN architecture does not use the pre-defined handcrafted features because it extracts the features automatically. In this present work, several pre-defined handcrafted features are computed from four MRI modalities (T2, FLAIR, T1c, and T1) with the help of additional handcrafted masks according to user interest and fed to the convolutional features (automatic features) to improve the overall performance of the proposed CNN model for tumor segmentation. Multi-pathway CNN is explored in this present work along with single-pathway CNN, which extracts simultaneously both local and global features to identify the accurate sub-regions of the tumor with the help of handcrafted features. The present work uses a cascaded CNN architecture, where the outcome of a CNN is considered as an additional input information to next subsequent CNNs. To extract the handcrafted features, convolutional operation was applied on the four MRI modalities with the help of several pre-defined masks to produce a predefined set of handcrafted features. The present work also investigates the usefulness of intensity normalization and data augmentation in pre-processing stage in order to handle the difficulties related to the imbalance of tumor labels. The proposed method is experimented on the BraST 2018 datasets and achieved promising results than the existing (currently published) methods with respect to different metrics such as specificity, sensitivity, and dice similarity coefficient (DSC) for complete, core, and enhanced tumor regions. Quantitatively, a notable gain is achieved around the boundaries of the sub-tumor regions using the proposed two-pathway CNN along with the handcrafted features. Graphical Abstract This data is mandatory. Please provide.

One of the methods for stratifying different molecular classes of breast cancer is the Nottingham prognostic index plus, which uses breast cancer relevant biomarkers to stain tumor tissues prepared on tissue microarray (TMA). To determine the molecular class of the tumor, pathologists will have to manually mark the nuclei activity biomarkers through a microscope and use a semi-quantitative assessment method to assign a histochemical score (H-Score) to each TMA core. Manually marking positively stained nuclei is a time-consuming, imprecise, and subjective process, which will lead to inter-observer and intra-observer discrepancies. In this paper, we present an end-to-end deep learning system, which directly predicts the H-Score automatically. Our system imitates the pathologists' decision process and uses one fully convolutional network (FCN) to extract all nuclei region (tumor and non-tumor), a second FCN to extract tumor nuclei region, and a multi-column convolutional neural network, which takes the outputs of the first two FCNs and the stain intensity description image as an input and acts as the high-level decision making mechanism to directly output the H-Score of the input TMA image. To the best of our knowledge, this is the first end-to-end system that takes a TMA image as the input and directly outputs a clinical score. We will present experimental results, which demonstrate that the H-Scores predicted by our model have very high and statistically significant correlation with experienced pathologists' scores and that the H-Score discrepancy between our algorithm and the pathologists is on par with the inter-subject discrepancy between the pathologists.

Objective: Accurate and fast automatic segmentation of organs is a key step for efficient planning for radiation therapy. In this paper, we propose the Multi-mode CNNs, which is for accurate and fast automatic segmentation of mandible, parotid glands, brainstem, optic nerves, cerebellum, eyes, lens, pituitary, thyroid, temporal lobes, brain and head respectively in 3D CT image of head and neck.Methods: The proposed Multi-mode CNNs consist of three convolutional neural networks. The first CNN is a simple classification network to distinguish slices of head and neck. It accelerates the next step by reducing the search space. The second network is a 3DCNN for locating the region of interest (ROI) of organs. It can enhance the robustness of the algorithm to CT images from different hospitals. The third network is a full convolution network (FCN) based on U-Net. This is a pixel-wise detailed segmented network to classify voxels in a region of interest and generate segmentation results. We used public and clinical datasets to evaluate our algorithm. The public datasets are from the MICCAI 2015 Head and Neck Auto Segmentation Grand Challenge. For the private datasets, we collected 3D CT images of 88 patients from A and B Hospital.Results: For the public datasets, our segmentation results of the nine organs in the challenge surpassed the first rank. For the private datasets, clinical trials have proved that it is effective for real image data in different hospitals. The average total segmentation time for one patient with above whole organs is less than one minute, which indicates proposed method having clinical value.Conclusion: The proposed Multi-mode CNNs can be used to accurate and fast automatic segmentation of organs in radiation therapy. It can assist doctors in outlining the organs during the planning of radiation therapy in the clinic.

Lung cancer is a dangerous disease that taking human life rapidly worldwide. The death of the people is increasing exponentially because of lung cancer. In order to reduce the disease and save a human's life, the automated system is needed. The purpose of the lung cancer detection system is able to detect and provide reliable information to doctors and clinicians from the medical image. To minimize this problem, many systems have been proposed by using different image processing techniques, machine learning, and deep learning techniques. A computed tomography (CT) imaging modality is an efficient technique for medical screening used for lung cancer detection and diagnosis. Physician and radiologist use the CT scan images to analyze, interpret and diagnose the lung cancer from lung tissues. However, in most cases, obtaining an accurate diagnosis result without using the extra medical tool known as a computer- Aid detection and Diagnosis (CAD) system is tedious work for many physicians. To obtain an accurate result from computer-aided diagnosis system lung segmentation methods are basic once. So in this project, we have used different lung segmentation and nodules segmentation methods. Our work has consisted of preprocessing, and lung segmentation by using thresholding, and also used the U-net model for detection of the candidate nodules of the patient’s lung CT scan and classification methodology. We have used a convolutional neural network and designed a 3D CNN model that has a 0.77% accuracy performance.

Automatic fetal brain extraction from 2D in utero fetal MRI slices using deep neural network

In this paper, a new convolution neural network method is proposed for the inspection and classification of galvanized stamping parts. Firstly, all workpieces are divided into normal and defective by image processing, and then the defective workpieces extracted from the region of interest (ROI) area are input to the trained fully convolutional networks (FCN). The network utilizes an end-to-end and pixel-to-pixel training convolution network that is currently the most advanced technology in semantic segmentation, predicts result of each pixel. Secondly, we mark the different pixel values of the workpiece, defect and background for the training image, and use the pixel value and the number of pixels to realize the recognition of the defects of the output picture. Finally, the defect area's threshold depended on the needs of the project is set to achieve the specific classification of the workpiece. The experiment results show that the proposed method can successfully achieve defect detection and classification of galvanized stamping parts under ordinary camera and illumination conditions, and its accuracy can reach 99.6%. Moreover, it overcomes the problem of complex image preprocessing and difficult feature extraction and performs better adaptability.