Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userCPNet: Cycle Prototype Network for Weakly-supervised 3D Renal Compartments Segmentation on CT Images
60
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Renal compartment segmentation on CT images targets on extracting the 3D structure of renal compartments from abdominal CTA images and is of great significance to the diagnosis and treatment for kidney diseases. However, due to the unclear compartment boundary, thin compartment structure and large anatomy variation of 3D kidney CT images, deep-learning based renal compartment segmentation is a challenging task. We propose a novel weakly supervised learning framework, Cycle Prototype Network, for 3D renal compartment segmentation. It has three innovations: 1) A Cycle Prototype Learning (CPL) is proposed to learn consistency for generalization. It learns from pseudo labels through the forward process and learns consistency regularization through the reverse process. The two processes make the model robust to noise and label-efficient. 2) We propose a Bayes Weakly Supervised Module (BWSM) based on cross-period prior knowledge. It learns prior knowledge from cross-period unlabeled data and perform error correction automatically, thus generates accurate pseudo labels. 3) We present a Fine Decoding Feature Extractor (FDFE) for fine-grained feature extraction. It combines global morphology information and local detail information to obtain feature maps with sharp detail, so the model will achieve fine segmentation on thin structures. Our model achieves Dice of 79.1% and 78.7% with only four labeled images, achieving a significant improvement by about 20% than typical prototype model PANet.
rate research
Read More
Coronavirus Disease 2019 (COVID-19) has spread aggressively across the world causing an existential health crisis. Thus, having a system that automatically detects COVID-19 in tomography (CT) images can assist in quantifying the severity of the illness. Unfortunately, labelling chest CT scans requires significant domain expertise, time, and effort. We address these labelling challenges by only requiring point annotations, a single pixel for each infected region on a CT image. This labeling scheme allows annotators to label a pixel in a likely infected region, only taking 1-3 seconds, as opposed to 10-15 seconds to segment a region. Conventionally, segmentation models train on point-level annotations using the cross-entropy loss function on these labels. However, these models often suffer from low precision. Thus, we propose a consistency-based (CB) loss function that encourages the output predictions to be consistent with spatial transformations of the input images. The experiments on 3 open-source COVID-19 datasets show that this loss function yields significant improvement over conventional point-level loss functions and almost matches the performance of models trained with full supervision with much less human effort. Code is available at: url{https://github.com/IssamLaradji/covid19_weak_supervision}.
One of the key challenges in the battle against the Coronavirus (COVID-19) pandemic is to detect and quantify the severity of the disease in a timely manner. Computed tomographies (CT) of the lungs are effective for assessing the state of the infection. Unfortunately, labeling CT scans can take a lot of time and effort, with up to 150 minutes per scan. We address this challenge introducing a scalable, fast, and accurate active learning system that accelerates the labeling of CT scan images. Conventionally, active learning methods require the labelers to annotate whole images with full supervision, but that can lead to wasted efforts as many of the annotations could be redundant. Thus, our system presents the annotator with unlabeled regions that promise high information content and low annotation cost. Further, the system allows annotators to label regions using point-level supervision, which is much cheaper to acquire than per-pixel annotations. Our experiments on open-source COVID-19 datasets show that using an entropy-based method to rank unlabeled regions yields to significantly better results than random labeling of these regions. Also, we show that labeling small regions of images is more efficient than labeling whole images. Finally, we show that with only 7% of the labeling effort required to label the whole training set gives us around 90% of the performance obtained by training the model on the fully annotated training set. Code is available at: url{https://github.com/IssamLaradji/covid19_active_learning}.
An outbreak of a novel coronavirus disease (i.e., COVID-19) has been recorded in Wuhan, China since late December 2019, which subsequently became pandemic around the world. Although COVID-19 is an acutely treated disease, it can also be fatal with a risk of fatality of 4.03% in China and the highest of 13.04% in Algeria and 12.67% Italy (as of 8th April 2020). The onset of serious illness may result in death as a consequence of substantial alveolar damage and progressive respiratory failure. Although laboratory testing, e.g., using reverse transcription polymerase chain reaction (RT-PCR), is the golden standard for clinical diagnosis, the tests may produce false negatives. Moreover, under the pandemic situation, shortage of RT-PCR testing resources may also delay the following clinical decision and treatment. Under such circumstances, chest CT imaging has become a valuable tool for both diagnosis and prognosis of COVID-19 patients. In this study, we propose a weakly supervised deep learning strategy for detecting and classifying COVID-19 infection from CT images. The proposed method can minimise the requirements of manual labelling of CT images but still be able to obtain accurate infection detection and distinguish COVID-19 from non-COVID-19 cases. Based on the promising results obtained qualitatively and quantitatively, we can envisage a wide deployment of our developed technique in large-scale clinical studies.
3D complete renal structures(CRS) segmentation targets on segmenting the kidneys, tumors, renal arteries and veins in one inference. Once successful, it will provide preoperative plans and intraoperative guidance for laparoscopic partial nephrectomy(LPN), playing a key role in the renal cancer treatment. However, no success has been reported in 3D CRS segmentation due to the complex shapes of renal structures, low contrast and large anatomical variation. In this study, we utilize the adversarial ensemble learning and propose Ensemble Multi-condition GAN(EnMcGAN) for 3D CRS segmentation for the first time. Its contribution is three-fold. 1)Inspired by windowing, we propose the multi-windowing committee which divides CTA image into multiple narrow windows with different window centers and widths enhancing the contrast for salient boundaries and soft tissues. And then, it builds an ensemble segmentation model on these narrow windows to fuse the segmentation superiorities and improve whole segmentation quality. 2)We propose the multi-condition GAN which equips the segmentation model with multiple discriminators to encourage the segmented structures meeting their real shape conditions, thus improving the shape feature extraction ability. 3)We propose the adversarial weighted ensemble module which uses the trained discriminators to evaluate the quality of segmented structures, and normalizes these evaluation scores for the ensemble weights directed at the input image, thus enhancing the ensemble results. 122 patients are enrolled in this study and the mean Dice coefficient of the renal structures achieves 84.6%. Extensive experiments with promising results on renal structures reveal powerful segmentation accuracy and great clinical significance in renal cancer treatment.
The reconstruction of three-dimensional models of coronary arteries is of great significance for the localization, evaluation and diagnosis of stenosis and plaque in the arteries, as well as for the assisted navigation of interventional surgery. In the clinical practice, physicians use a few angles of coronary angiography to capture arterial images, so it is of great practical value to perform 3D reconstruction directly from coronary angiography images. However, this is a very difficult computer vision task due to the complex shape of coronary blood vessels, as well as the lack of data set and key point labeling. With the rise of deep learning, more and more work is being done to reconstruct 3D models of human organs from medical images using deep neural networks. We propose an adversarial and generative way to reconstruct three dimensional coronary artery models, from two different views of angiographic images of coronary arteries. With 3D fully supervised learning and 2D weakly supervised learning schemes, we obtained reconstruction accuracies that outperform state-of-art techniques.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
