3D AGSE-VNet: an automatic brain tumor MRI data segmentation framework

Background Glioma is the most common brain malignant tumor, with a high morbidity rate and a mortality rate of more than three percent, which seriously endangers human health. The main method of acquiring brain tumors in the clinic is MRI. Segmentation of brain tumor regions from multi-modal MRI scan images is helpful for treatment inspection, post-diagnosis monitoring, and effect evaluation of patients. However, the common operation in clinical brain tumor segmentation is still manual segmentation, lead to its time-consuming and large performance difference between different operators, a consistent and accurate automatic segmentation method is urgently needed. With the continuous development of deep learning, researchers have designed many automatic segmentation algorithms; however, there are still some problems: (1) The research of segmentation algorithm mostly stays on the 2D plane, this will reduce the accuracy of 3D image feature extraction to a certain extent. (2) MRI images have gray-scale offset fields that make it difficult to divide the contours accurately. Methods To meet the above challenges, we propose an automatic brain tumor MRI data segmentation framework which is called AGSE-VNet. In our study, the Squeeze and Excite (SE) module is added to each encoder, the Attention Guide Filter (AG) module is added to each decoder, using the channel relationship to automatically enhance the useful information in the channel to suppress the useless information, and use the attention mechanism to guide the edge information and remove the influence of irrelevant information such as noise. Results We used the BraTS2020 challenge online verification tool to evaluate our approach. The focus of verification is that the Dice scores of the whole tumor, tumor core and enhanced tumor are 0.68, 0.85 and 0.70, respectively. Conclusion Although MRI images have different intensities, AGSE-VNet is not affected by the size of the tumor, and can more accurately extract the features of the three regions, it has achieved impressive results and made outstanding contributions to the clinical diagnosis and treatment of brain tumor patients.

Two-Stage Segmentation Framework Based on Distance Transformation

With the rise of deep learning, using deep learning to segment lesions and assist in diagnosis has become an effective means to promote clinical medical analysis. However, the partial volume effect of organ tissues leads to unclear and blurred edges of ROI in medical images, making it challenging to achieve high-accuracy segmentation of lesions or organs. In this paper, we assume that the distance map obtained by performing distance transformation on the ROI edge can be used as a weight map to make the network pay more attention to the learning of the ROI edge region. To this end, we design a novel framework to flexibly embed the distance map into the two-stage network to improve left atrium MRI segmentation performance. Furthermore, a series of distance map generation methods are proposed and studied to reasonably explore how to express the weight of assisting network learning. We conduct thorough experiments to verify the effectiveness of the proposed segmentation framework, and experimental results demonstrate that our hypothesis is feasible.

Lesion Segmentation Framework Based on Convolutional Neural Networks with Dual Attention Mechanism

Computational intelligence has been widely used in medical information processing. The deep learning methods, especially, have many successful applications in medical image analysis. In this paper, we proposed an end-to-end medical lesion segmentation framework based on convolutional neural networks with a dual attention mechanism, which integrates both fully and weakly supervised segmentation. The weakly supervised segmentation module achieves accurate lesion segmentation by using bounding-box labels of lesion areas, which solves the problem of the high cost of pixel-level labels with lesions in the medical images. In addition, a dual attention mechanism is introduced to enhance the network’s ability for visual feature learning. The dual attention mechanism (channel and spatial attention) can help the network pay attention to feature extraction from important regions. Compared with the current mainstream method of weakly supervised segmentation using pseudo labels, it can greatly reduce the gaps between ground-truth labels and pseudo labels. The final experimental results show that our proposed framework achieved more competitive performances on oral lesion dataset, and our framework further extended to dermatological lesion segmentation.

SDFCNv2: An Improved FCN Framework for Remote Sensing Images Semantic Segmentation

Semantic segmentation is a fundamental task in remote sensing image analysis (RSIA). Fully convolutional networks (FCNs) have achieved state-of-the-art performance in the task of semantic segmentation of natural scene images. However, due to distinctive differences between natural scene images and remotely-sensed (RS) images, FCN-based semantic segmentation methods from the field of computer vision cannot achieve promising performances on RS images without modifications. In previous work, we proposed an RS image semantic segmentation framework SDFCNv1, combined with a majority voting postprocessing method. Nevertheless, it still has some drawbacks, such as small receptive field and large number of parameters. In this paper, we propose an improved semantic segmentation framework SDFCNv2 based on SDFCNv1, to conduct optimal semantic segmentation on RS images. We first construct a novel FCN model with hybrid basic convolutional (HBC) blocks and spatial-channel-fusion squeeze-and-excitation (SCFSE) modules, which occupies a larger receptive field and fewer network model parameters. We also put forward a data augmentation method based on spectral-specific stochastic-gamma-transform-based (SSSGT-based) during the model training process to improve generalizability of our model. Besides, we design a mask-weighted voting decision fusion postprocessing algorithm for image segmentation on overlarge RS images. We conducted several comparative experiments on two public datasets and a real surveying and mapping dataset. Extensive experimental results demonstrate that compared with the SDFCNv1 framework, our SDFCNv2 framework can increase the mIoU metric by up to 5.22% while only using about half of parameters.