Automatic Brain Tumor Segmentation using Cascaded Anisotropic Convolutional Neural Networks

A cascade of fully convolutional neural networks is proposed to segment multi-modal Magnetic Resonance (MR) images with brain tumor into background and three hierarchical regions: whole tumor, tumor core and enhancing tumor core. The cascade is designed to decompose the multi-class segmentation problem into a sequence of three binary segmentation problems according to the subregion hierarchy. The whole tumor is segmented in the first step and the bounding box of the result is used for the tumor core segmentation in the second step. The enhancing tumor core is then segmented based on the bounding box of the tumor core segmentation result. Our networks consist of multiple layers of anisotropic and dilated convolution filters, and they are combined with multi-view fusion to reduce false positives. Residual connections and multi-scale predictions are employed in these networks to boost the segmentation performance. Experiments with BraTS 2017 validation set show that the proposed method achieved average Dice scores of 0.7859, 0.9050, 0.8378 for enhancing tumor core, whole tumor and tumor core, respectively. The corresponding values for BraTS 2017 testing set were 0.7831, 0.8739, and 0.7748, respectively.Comment: 12 pages, 5 figures. MICCAI Brats Challenge 201

Semi-supervised Pathological Image Segmentation via Cross Distillation of Multiple Attentions

Segmentation of pathological images is a crucial step for accurate cancer diagnosis. However, acquiring dense annotations of such images for training is labor-intensive and time-consuming. To address this issue, Semi-Supervised Learning (SSL) has the potential for reducing the annotation cost, but it is challenged by a large number of unlabeled training images. In this paper, we propose a novel SSL method based on Cross Distillation of Multiple Attentions (CDMA) to effectively leverage unlabeled images. Firstly, we propose a Multi-attention Tri-branch Network (MTNet) that consists of an encoder and a three-branch decoder, with each branch using a different attention mechanism that calibrates features in different aspects to generate diverse outputs. Secondly, we introduce Cross Decoder Knowledge Distillation (CDKD) between the three decoder branches, allowing them to learn from each other's soft labels to mitigate the negative impact of incorrect pseudo labels in training. Additionally, uncertainty minimization is applied to the average prediction of the three branches, which further regularizes predictions on unlabeled images and encourages inter-branch consistency. Our proposed CDMA was compared with eight state-of-the-art SSL methods on the public DigestPath dataset, and the experimental results showed that our method outperforms the other approaches under different annotation ratios. The code is available at \href{https://github.com/HiLab-git/CDMA}{https://github.com/HiLab-git/CDMA.}Comment: Provisional Accepted by MICCAI 202

Conjugate Calculation of Gas Turbine Vanes Cooled with Leading Edge Films

AbstractConjugate calculation methodology is used to simulate the C3X gas turbine vanes cooled with leading edge films of “shower-head” type. By comparing calculated results of different turbulence models with the measured data, it is clear that calculation with the transition model can better simulate the flow and heat transfer in the boundary layers with leading edge film cooling. In the laminar boundary layers, on the upstream suction side, the film cooling flow presents 3D turbulent characteristics before transition, which quickly disappear on the downstream suction side owing to its intensified mixing with hot gas boundary layer after transition. On the pressure side, the film cooling flow retains the 3D turbulent characteristics all the time because the local boundary layers' consistent laminar flow retains a smooth mixing of the cooling flow and the hot gas. The temperature gradients formed between the cooled metallic vane and the hot gas can improve the stability of the boundary layer flow because the gradients possess a self stable convective structure

Magnetic anisotropy in hole-doped superconducting Ba 0.67K 0.33Fe 2As2 probed by polarized inelastic neutron scattering

We use polarized inelastic neutron scattering (INS) to study spin excitations of optimally hole-doped superconductor Ba$_{0.67}$K$_{0.33}$Fe$_2$As$_{2}$ ($T_c=38$ K). In the normal state, the imaginary part of the dynamic susceptibility, $\chi^{\prime\prime}(Q,\omega)$, shows magnetic anisotropy for energies below $\sim$7 meV with c-axis polarized spin excitations larger than that of the in-plane component. Upon entering into the superconducting state, previous unpolarized INS experiments have shown that spin gaps at $\sim$5 and 0.75 meV open at wave vectors $Q=(0.5,0.5,0)$ and $(0.5,0.5,1)$, respectively, with a broad neutron spin resonance at $E_r=15$ meV. Our neutron polarization analysis reveals that the large difference in spin gaps is purely due to different spin gaps in the c-axis and in-plane polarized spin excitations, resulting resonance with different energy widths for the c-axis and in-plane spin excitations. The observation of spin anisotropy in both opitmally electron and hole-doped BaFe$_2$As$_2$ is due to their proximity to the AF ordered BaFe$_2$As$_2$ where spin anisotropy exists below $T_N$.Comment: 5 pages, 4 figure

Semi-supervised Medical Image Segmentation through Dual-task Consistency

Deep learning-based semi-supervised learning (SSL) algorithms have led to promising results in medical images segmentation and can alleviate doctors' expensive annotations by leveraging unlabeled data. However, most of the existing SSL algorithms in literature tend to regularize the model training by perturbing networks and/or data. Observing that multi/dual-task learning attends to various levels of information which have inherent prediction perturbation, we ask the question in this work: can we explicitly build task-level regularization rather than implicitly constructing networks- and/or data-level perturbation-and-transformation for SSL? To answer this question, we propose a novel dual-task-consistency semi-supervised framework for the first time. Concretely, we use a dual-task deep network that jointly predicts a pixel-wise segmentation map and a geometry-aware level set representation of the target. The level set representation is converted to an approximated segmentation map through a differentiable task transform layer. Simultaneously, we introduce a dual-task consistency regularization between the level set-derived segmentation maps and directly predicted segmentation maps for both labeled and unlabeled data. Extensive experiments on two public datasets show that our method can largely improve the performance by incorporating the unlabeled data. Meanwhile, our framework outperforms the state-of-the-art semi-supervised medical image segmentation methods. Code is available at: https://github.com/Luoxd1996/DTCComment: 9 pages, 4 figure

Aleatoric uncertainty estimation with test-time augmentation for medical image segmentation with convolutional neural networks

Despite the state-of-the-art performance for medical image segmentation, deep convolutional neural networks (CNNs) have rarely provided uncertainty estimations regarding their segmentation outputs, e.g., model (epistemic) and image-based (aleatoric) uncertainties. In this work, we analyze these different types of uncertainties for CNN-based 2D and 3D medical image segmentation tasks. We additionally propose a test-time augmentation-based aleatoric uncertainty to analyze the effect of different transformations of the input image on the segmentation output. Test-time augmentation has been previously used to improve segmentation accuracy, yet not been formulated in a consistent mathematical framework. Hence, we also propose a theoretical formulation of test-time augmentation, where a distribution of the prediction is estimated by Monte Carlo simulation with prior distributions of parameters in an image acquisition model that involves image transformations and noise. We compare and combine our proposed aleatoric uncertainty with model uncertainty. Experiments with segmentation of fetal brains and brain tumors from 2D and 3D Magnetic Resonance Images (MRI) showed that 1) the test-time augmentation-based aleatoric uncertainty provides a better uncertainty estimation than calculating the test-time dropout-based model uncertainty alone and helps to reduce overconfident incorrect predictions, and 2) our test-time augmentation outperforms a single-prediction baseline and dropout-based multiple predictions.Comment: 13 pages, 8 figures, accepted by NeuroComputin

MIS-FM: 3D Medical Image Segmentation using Foundation Models Pretrained on a Large-Scale Unannotated Dataset

Pretraining with large-scale 3D volumes has a potential for improving the segmentation performance on a target medical image dataset where the training images and annotations are limited. Due to the high cost of acquiring pixel-level segmentation annotations on the large-scale pretraining dataset, pretraining with unannotated images is highly desirable. In this work, we propose a novel self-supervised learning strategy named Volume Fusion (VF) for pretraining 3D segmentation models. It fuses several random patches from a foreground sub-volume to a background sub-volume based on a predefined set of discrete fusion coefficients, and forces the model to predict the fusion coefficient of each voxel, which is formulated as a self-supervised segmentation task without manual annotations. Additionally, we propose a novel network architecture based on parallel convolution and transformer blocks that is suitable to be transferred to different downstream segmentation tasks with various scales of organs and lesions. The proposed model was pretrained with 110k unannotated 3D CT volumes, and experiments with different downstream segmentation targets including head and neck organs, thoracic/abdominal organs showed that our pretrained model largely outperformed training from scratch and several state-of-the-art self-supervised training methods and segmentation models. The code and pretrained model are available at https://github.com/openmedlab/MIS-FM.Comment: 13 pages, 8 figure