Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userCross-Modality Multi-Atlas Segmentation Using Deep Neural Networks
134
0
0.0
(
0
)
Added by
Wangbin Ding
Publication date
2020
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
Both image registration and label fusion in the multi-atlas segmentation (MAS) rely on the intensity similarity between target and atlas images. However, such similarity can be problematic when target and atlas images are acquired using different imaging protocols. High-level structure information can provide reliable similarity measurement for cross-modality images when cooperating with deep neural networks (DNNs). This work presents a new MAS framework for cross-modality images, where both image registration and label fusion are achieved by DNNs. For image registration, we propose a consistent registration network, which can jointly estimate forward and backward dense displacement fields (DDFs). Additionally, an invertible constraint is employed in the network to reduce the correspondence ambiguity of the estimated DDFs. For label fusion, we adapt a few-shot learning network to measure the similarity of atlas and target patches. Moreover, the network can be seamlessly integrated into the patch-based label fusion. The proposed framework is evaluated on the MM-WHS dataset of MICCAI 2017. Results show that the framework is effective in both cross-modality registration and segmentation.
rate research
Read More
Objective: A new image instance segmentation method is proposed to segment individual glands (instances) in colon histology images. This process is challenging since the glands not only need to be segmented from a complex background, they must also be individually identified. Methods: We leverage the idea of image-to-image prediction in recent deep learning by designing an algorithm that automatically exploits and fuses complex multichannel information - regional, location, and boundary cues - in gland histology images. Our proposed algorithm, a deep multichannel framework, alleviates heavy feature design due to the use of convolutional neural networks and is able to meet multifarious requirements by altering channels. Results: Compared with methods reported in the 2015 MICCAI Gland Segmentation Challenge and other currently prevalent instance segmentation methods, we observe state-of-the-art results based on the evaluation metrics. Conclusion: The proposed deep multichannel algorithm is an effective method for gland instance segmentation. Significance: The generalization ability of our model not only enable the algorithm to solve gland instance segmentation problems, but the channel is also alternative that can be replaced for a specific task.
The findings of splenomegaly, abnormal enlargement of the spleen, is a non-invasive clinical biomarker for liver and spleen disease. Automated segmentation methods are essential to efficiently quantify splenomegaly from clinically acquired abdominal magnetic resonance imaging (MRI) scans. However, the task is challenging due to (1) large anatomical and spatial variations of splenomegaly, (2) large inter- and intra-scan intensity variations on multi-modal MRI, and (3) limited numbers of labeled splenomegaly scans. In this paper, we propose the Splenomegaly Segmentation Network (SS-Net) to introduce the deep convolutional neural network (DCNN) approaches in multi-modal MRI splenomegaly segmentation. Large convolutional kernel layers were used to address the spatial and anatomical variations, while the conditional generative adversarial networks (GAN) were employed to leverage the segmentation performance of SS-Net in an end-to-end manner. A clinically acquired cohort containing both T1-weighted (T1w) and T2-weighted (T2w) MRI splenomegaly scans was used to train and evaluate the performance of multi-atlas segmentation (MAS), 2D DCNN networks, and a 3D DCNN network. From the experimental results, the DCNN methods achieved superior performance to the state-of-the-art MAS method. The proposed SS-Net method achieved the highest median and mean Dice scores among investigated baseline DCNN methods.
Weakly supervised learning has emerged as an appealing alternative to alleviate the need for large labeled datasets in semantic segmentation. Most current approaches exploit class activation maps (CAMs), which can be generated from image-level annotations. Nevertheless, resulting maps have been demonstrated to be highly discriminant, failing to serve as optimal proxy pixel-level labels. We present a novel learning strategy that leverages self-supervision in a multi-modal image scenario to significantly enhance original CAMs. In particular, the proposed method is based on two observations. First, the learning of fully-supervised segmentation networks implicitly imposes equivariance by means of data augmentation, whereas this implicit constraint disappears on CAMs generated with image tags. And second, the commonalities between image modalities can be employed as an efficient self-supervisory signal, correcting the inconsistency shown by CAMs obtained across multiple modalities. To effectively train our model, we integrate a novel loss function that includes a within-modality and a cross-modality equivariant term to explicitly impose these constraints during training. In addition, we add a KL-divergence on the class prediction distributions to facilitate the information exchange between modalities, which, combined with the equivariant regularizers further improves the performance of our model. Exhaustive experiments on the popular multi-modal BRATS dataset demonstrate that our approach outperforms relevant recent literature under the same learning conditions.
We use a well-known deep neural network framework, called Mask R-CNN, for identification of solar filaments in full-disk H-alpha images from Big Bear Solar Observatory (BBSO). The image data, collected from BBSOs archive, are integrated with the spatiotemporal metadata of filaments retrieved from the Heliophysics Events Knowledgebase (HEK) system. This integrated data is then treated as the ground-truth in the training process of the model. The available spatial metadata are the output of a currently running filament-detection module developed and maintained by the Feature Finding Team; an international consortium selected by NASA. Despite the known challenges in the identification and characterization of filaments by the existing module, which in turn are inherited into any other module that intends to learn from such outputs, Mask R-CNN shows promising results. Trained and validated on two years worth of BBSO data, this model is then tested on the three following years. Our case-by-case and overall analyses show that Mask R-CNN can clearly compete with the existing module and in some cases even perform better. Several cases of false positives and false negatives, that are correctly segmented by this model are also shown. The overall advantages of using the proposed model are two-fold: First, deep neural networks performance generally improves as more annotated data, or better annotations are provided. Second, such a model can be scaled up to detect other solar events, as well as a single multi-purpose module. The results presented in this study introduce a proof of concept in benefits of employing deep neural networks for detection of solar events, and in particular, filaments.
Segmentation of white matter lesions and deep grey matter structures is an important task in the quantification of magnetic resonance imaging in multiple sclerosis. In this paper we explore segmentation solutions based on convolutional neural networks (CNNs) for providing fast, reliable segmentations of lesions and grey-matter structures in multi-modal MR imaging, and the performance of these methods when applied to out-of-centre data. We trained two state-of-the-art fully convolutional CNN architectures on the 2016 MSSEG training dataset, which was annotated by seven independent human raters: a reference implementation of a 3D Unet, and a more recently proposed 3D-to-2D architecture (DeepSCAN). We then retrained those methods on a larger dataset from a single centre, with and without labels for other brain structures. We quantified changes in performance owing to dataset shift, and changes in performance by adding the additional brain-structure labels. We also compared performance with freely available reference methods. Both fully-convolutional CNN methods substantially outperform other approaches in the literature when trained and evaluated in cross-validation on the MSSEG dataset, showing agreement with human raters in the range of human inter-rater variability. Both architectures showed drops in performance when trained on single-centre data and tested on the MSSEG dataset. When trained with the addition of weak anatomical labels derived from Freesurfer, the performance of the 3D Unet degraded, while the performance of the DeepSCAN net improved. Overall, the DeepSCAN network predicting both lesion and anatomical labels was the best-performing network examined.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
