Accurate 3D Cell Segmentation using Deep Feature and CRF Refinement

We consider the problem of accurately identifying cell boundaries and labeling individual cells in confocal microscopy images, specifically, 3D image stacks of cells with tagged cell membranes. Precise identification of cell boundaries, their shapes, and quantifying inter-cellular space leads to a better understanding of cell morphogenesis. Towards this, we outline a cell segmentation method that uses a deep neural network architecture to extract a confidence map of cell boundaries, followed by a 3D watershed algorithm and a final refinement using a conditional random field. In addition to improving the accuracy of segmentation compared to other state-of-the-art methods, the proposed approach also generalizes well to different datasets without the need to retrain the network for each dataset. Detailed experimental results are provided, and the source code is available on GitHub.Comment: 5 pages, 5 figures, 3 table

Improving 3D U-Net for Brain Tumor Segmentation by Utilizing Lesion Prior

We propose a novel, simple and effective method to integrate lesion prior and a 3D U-Net for improving brain tumor segmentation. First, we utilize the ground-truth brain tumor lesions from a group of patients to generate the heatmaps of different types of lesions. These heatmaps are used to create the volume-of-interest (VOI) map which contains prior information about brain tumor lesions. The VOI map is then integrated with the multimodal MR images and input to a 3D U-Net for segmentation. The proposed method is evaluated on a public benchmark dataset, and the experimental results show that the proposed feature fusion method achieves an improvement over the baseline methods. In addition, our proposed method also achieves a competitive performance compared to state-of-the-art methods.Comment: 5 pages, 4 figures, 1 table, LNCS forma

Improving Patch-Based Convolutional Neural Networks for MRI Brain Tumor Segmentation by Leveraging Location Information.

The manual brain tumor annotation process is time consuming and resource consuming, therefore, an automated and accurate brain tumor segmentation tool is greatly in demand. In this paper, we introduce a novel method to integrate location information with the state-of-the-art patch-based neural networks for brain tumor segmentation. This is motivated by the observation that lesions are not uniformly distributed across different brain parcellation regions and that a locality-sensitive segmentation is likely to obtain better segmentation accuracy. Toward this, we use an existing brain parcellation atlas in the Montreal Neurological Institute (MNI) space and map this atlas to the individual subject data. This mapped atlas in the subject data space is integrated with structural Magnetic Resonance (MR) imaging data, and patch-based neural networks, including 3D U-Net and DeepMedic, are trained to classify the different brain lesions. Multiple state-of-the-art neural networks are trained and integrated with XGBoost fusion in the proposed two-level ensemble method. The first level reduces the uncertainty of the same type of models with different seed initializations, and the second level leverages the advantages of different types of neural network models. The proposed location information fusion method improves the segmentation performance of state-of-the-art networks including 3D U-Net and DeepMedic. Our proposed ensemble also achieves better segmentation performance compared to the state-of-the-art networks in BraTS 2017 and rivals state-of-the-art networks in BraTS 2018. Detailed results are provided on the public multimodal brain tumor segmentation (BraTS) benchmarks

Carbon monoxide may enhance bile secretion by increasing glutathione excretion and Mrp2 expression in rats

AbstractBackgroundNitric oxide (NO) donors have been reported to induce choleresis via an increased excretion of glutathione. The effects of another gas molecule, carbon monoxide (CO), on bile formation are, however, inconsistent among previous reports. We investigated the sequential changes of bile output and the biliary contents in rats with or without CO supplementation to elucidate the mechanism of CO on bile excretion.MethodsDichloromethane (DCM) was gastrically fed to male Sprague–Dawley rats to yield CO by liver biotransformation. The rats were divided into DCM-treated (n = 7), DCM plus L-NAME-treated (n = 6), and corn oil-treated-(n = 8) groups. Bile samples were collected hourly to examine the flow rate and bile content. Serum levels of nitrite and nitrate 4 hours after DCM supplementation with or without NO synthase (NOS) inhibition were measured by capillary electrophoresis. The expression of hepatic inducible NOS was evaluated by Western blotting 6 hours after DCM administration.ResultsLevels of carboxyhemoglobin rose to around 10% at 4 hours after DCM supplementation and were maintained until the end of the experiments. Bile flow increased after DCM supplementation and was associated with a concomitant increase of biliary glutathione and higher hepatic multidrug resistance-associated protein 2 (Mrp2) expression. Hepatic inducible NOS expression and serum nitrate/nitrite levels were also increased. Treatment with an NOS inhibitor (L-NAME) abolished the CO-induced glutathione excretion and choleresis, but not Mrp2 expression.ConclusionThe present study demonstrated that CO enhanced biliary output in conjunction with NO by increasing the biliary excretion of glutathione. The increment in biliary glutathione was associated with an increased expression of hepatic Mrp2

An All Deep System for Badminton Game Analysis

The CoachAI Badminton 2023 Track1 initiative aim to automatically detect events within badminton match videos. Detecting small objects, especially the shuttlecock, is of quite importance and demands high precision within the challenge. Such detection is crucial for tasks like hit count, hitting time, and hitting location. However, even after revising the well-regarded shuttlecock detecting model, TrackNet, our object detection models still fall short of the desired accuracy. To address this issue, we've implemented various deep learning methods to tackle the problems arising from noisy detectied data, leveraging diverse data types to improve precision. In this report, we detail the detection model modifications we've made and our approach to the 11 tasks. Notably, our system garnered a score of 0.78 out of 1.0 in the challenge.Comment: Golden Award for IJCAI CoachAI Challenge 2023: Team NTNUEE AIoTLa

α-Lactosylceramide Protects Against iNKT-Mediated Murine Airway Hyperreactivity and Liver Injury Through Competitive Inhibition of Cd1d Binding.

Invariant natural killer T (iNKT) cells, which are activated by T cell receptor (TCR)-dependent recognition of lipid-based antigens presented by the CD1d molecule, have been shown to participate in the pathogenesis of many diseases, including asthma and liver injury. Previous studies have shown the inhibition of iNKT cell activation using lipid antagonists can attenuate iNKT cell-induced disease pathogenesis. Hence, the development of iNKT cell-targeted glycolipids can facilitate the discovery of new therapeutics. In this study, we synthesized and evaluated α-lactosylceramide (α-LacCer), an α-galactosylceramide (α-GalCer) analog with lactose substitution for the galactose head and a shortened acyl chain in the ceramide tail, toward iNKT cell activation. We demonstrated that α-LacCer was a weak inducer for both mouse and human iNKT cell activation and cytokine production, and the iNKT induction by α-LacCer was CD1d-dependent. However, when co-administered with α-GalCer, α-LacCer inhibited α-GalCer-induced IL-4 and IFN-γ production from iNKT cells. Consequently, α-LacCer also ameliorated both α-GalCer and GSL-1-induced airway hyperreactivity and α-GalCer-induced neutrophilia when co-administered in vivo. Furthermore, we were able to inhibit the increases of ConA-induced AST, ALT and IFN-γ serum levels through α-LacCer pre-treatment, suggesting α-LacCer could protect against ConA-induced liver injury. Mechanistically, we discerned that α-LacCer suppressed α-GalCer-stimulated cytokine production through competing for CD1d binding. Since iNKT cells play a critical role in the development of AHR and liver injury, the inhibition of iNKT cell activation by α-LacCer present a possible new approach in treating iNKT cell-mediated diseases

Corrigendum: Improving Patch-Based Convolutional Neural Networks for MRI Brain Tumor Segmentation by Leveraging Location Information.

[This corrects the article DOI: 10.3389/fnins.2019.01449.]