Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userVerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images
117
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms towards labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the the results of this evaluation and further investigate the performance-variation at vertebra-level, scan-level, and at different fields-of-view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The content and code concerning VerSe can be accessed at: https://github.com/anjany/verse.
rate research
Read More
Purpose: To use and test a labelling algorithm that operates on two-dimensional (2D) reformations, rather than three-dimensional (3D) data to locate and identify vertebrae. Methods: We improved the Btrfly Net (described by Sekuboyina et al) that works on sagittal and coronal maximum intensity projections (MIP) and augmented it with two additional components: spine-localization and adversarial a priori-learning. Furthermore, we explored two variants of adversarial training schemes that incorporated the anatomical a priori knowledge into the Btrfly Net. We investigated the superiority of the proposed approach for labelling vertebrae on three datasets: a public benchmarking dataset of 302 CT scans and two in-house datasets with a total of 238 CT scans. We employed Wilcoxon signed-rank test to compute the statistical significance of the improvement in performance observed due to various architectural components in our approach. Results: On the public dataset, our approach using the described Btrfly(pe-eb) network performed on par with current state-of-the-art methods achieving a statistically significant (p < .001) vertebrae identification rate of 88.5+/-0.2 % and localization distances of less than 7-mm. On the in-house datasets that had a higher inter-scan data variability, we obtained an identification rate of 85.1+/-1.2%. Conclusion: An identification performance comparable to existing 3D approaches was achieved when labelling vertebrae on 2D MIPs. The performance was further improved using the proposed adversarial training regime that effectively enforced local spine a priori knowledge during training. Lastly, spine-localization increased the generalizability of our approach by homogenizing the content in the MIPs.
Automatic segmentation of organs-at-risk (OAR) in computed tomography (CT) is an essential part of planning effective treatment strategies to combat lung and esophageal cancer. Accurate segmentation of organs surrounding tumours helps account for the variation in position and morphology inherent across patients, thereby facilitating adaptive and computer-assisted radiotherapy. Although manual delineation of OARs is still highly prevalent, it is prone to errors due to complex variations in the shape and position of organs across patients, and low soft tissue contrast between neighbouring organs in CT images. Recently, deep convolutional neural networks (CNNs) have gained tremendous traction and achieved state-of-the-art results in medical image segmentation. In this paper, we propose a deep learning framework to segment OARs in thoracic CT images, specifically for the: heart, esophagus, trachea and aorta. Our approach employs dilated convolutions and aggregated residual connections in the bottleneck of a U-Net styled network, which incorporates global context and dense information. Our method achieved an overall Dice score of 91.57% on 20 unseen test samples from the ISBI 2019 SegTHOR challenge.
Assigning geospatial objects with specific categories at the pixel level is a fundamental task in remote sensing image analysis. Along with rapid development in sensor technologies, remotely sensed images can be captured at multiple spatial resolutions (MSR) with information content manifested at different scales. Extracting information from these MSR images represents huge opportunities for enhanced feature representation and characterisation. However, MSR images suffer from two critical issues: 1) increased scale variation of geo-objects and 2) loss of detailed information at coarse spatial resolutions. To bridge these gaps, in this paper, we propose a novel scale-aware neural network (SaNet) for semantic segmentation of MSR remotely sensed imagery. SaNet deploys a densely connected feature network (DCFPN) module to capture high-quality multi-scale context, such that the scale variation is handled properly and the quality of segmentation is increased for both large and small objects. A spatial feature recalibration (SFR) module is further incorporated into the network to learn intact semantic content with enhanced spatial relationships, where the negative effects of information loss are removed. The combination of DCFPN and SFR allows SaNet to learn scale-aware feature representation, which outperforms the existing multi-scale feature representation. Extensive experiments on three semantic segmentation datasets demonstrated the effectiveness of the proposed SaNet in cross-resolution segmentation.
This paper presents a method for automatic segmentation, localization, and identification of vertebrae in arbitrary 3D CT images. Many previous works do not perform the three tasks simultaneously even though requiring a priori knowledge of which part of the anatomy is visible in the 3D CT images. Our method tackles all these tasks in a single multi-stage framework without any assumptions. In the first stage, we train a 3D Fully Convolutional Networks to find the bounding boxes of the cervical, thoracic, and lumbar vertebrae. In the second stage, we train an iterative 3D Fully Convolutional Networks to segment individual vertebrae in the bounding box. The input to the second networks have an auxiliary channel in addition to the 3D CT images. Given the segmented vertebra regions in the auxiliary channel, the networks output the next vertebra. The proposed method is evaluated in terms of segmentation, localization, and identification accuracy with two public datasets of 15 3D CT images from the MICCAI CSI 2014 workshop challenge and 302 3D CT images with various pathologies introduced in [1]. Our method achieved a mean Dice score of 96%, a mean localization error of 8.3 mm, and a mean identification rate of 84%. In summary, our method achieved better performance than all existing works in all the three metrics.
Multi-focus image fusion (MFIF) has attracted considerable interests due to its numerous applications. While much progress has been made in recent years with efforts on developing various MFIF algorithms, some issues significantly hinder the fair and comprehensive performance comparison of MFIF methods, such as the lack of large-scale test set and the random choices of objective evaluation metrics in the literature. To solve these issues, this paper presents a multi-focus image fusion benchmark (MFIFB) which consists a test set of 105 image pairs, a code library of 30 MFIF algorithms, and 20 evaluation metrics. MFIFB is the first benchmark in the field of MFIF and provides the community a platform to compare MFIF algorithms fairly and comprehensively. Extensive experiments have been conducted using the proposed MFIFB to understand the performance of these algorithms. By analyzing the experimental results, effective MFIF algorithms are identified. More importantly, some observations on the status of the MFIF field are given, which can help to understand this field better.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
