Graph Flow: Cross-layer Graph Flow Distillation for Dual Efficient Medical Image Segmentation

With the development of deep convolutional neural networks, medical image segmentation has achieved a series of breakthroughs in recent years. However, the higher-performance convolutional neural networks always mean numerous parameters and high computation costs, which will hinder the applications in clinical scenarios. Meanwhile, the scarceness of large-scale annotated medical image datasets further impedes the application of high-performance networks. To tackle these problems, we propose Graph Flow, a comprehensive knowledge distillation framework, for both network-efficiency and annotation-efficiency medical image segmentation. Specifically, our core Graph Flow Distillation transfer the essence of cross-layer variations from a well-trained cumbersome teacher network to a non-trained compact student network. In addition, an unsupervised Paraphraser Module is designed to purify the knowledge of the teacher network, which is also beneficial for the stabilization of training procedure. Furthermore, we build a unified distillation framework by integrating the adversarial distillation and the vanilla logits distillation, which can further refine the final predictions of the compact network. Extensive experiments conducted on Gastric Cancer Segmentation Dataset and Synapse Multi-organ Segmentation Dataset demonstrate the prominent ability of our method which achieves state-of-the-art performance on these different-modality and multi-category medical image datasets. Moreover, we demonstrate the effectiveness of our Graph Flow through a new semi-supervised paradigm for dual efficient medical image segmentation. Our code will be available at Graph Flow

CiT-Net: Convolutional Neural Networks Hand in Hand with Vision Transformers for Medical Image Segmentation

The hybrid architecture of convolutional neural networks (CNNs) and Transformer are very popular for medical image segmentation. However, it suffers from two challenges. First, although a CNNs branch can capture the local image features using vanilla convolution, it cannot achieve adaptive feature learning. Second, although a Transformer branch can capture the global features, it ignores the channel and cross-dimensional self-attention, resulting in a low segmentation accuracy on complex-content images. To address these challenges, we propose a novel hybrid architecture of convolutional neural networks hand in hand with vision Transformers (CiT-Net) for medical image segmentation. Our network has two advantages. First, we design a dynamic deformable convolution and apply it to the CNNs branch, which overcomes the weak feature extraction ability due to fixed-size convolution kernels and the stiff design of sharing kernel parameters among different inputs. Second, we design a shifted-window adaptive complementary attention module and a compact convolutional projection. We apply them to the Transformer branch to learn the cross-dimensional long-term dependency for medical images. Experimental results show that our CiT-Net provides better medical image segmentation results than popular SOTA methods. Besides, our CiT-Net requires lower parameters and less computational costs and does not rely on pre-training. The code is publicly available at https://github.com/SR0920/CiT-Net

Catheter segmentation in X-ray fluoroscopy using synthetic data and transfer learning with light U-nets

Background and objectivesAutomated segmentation and tracking of surgical instruments and catheters under X-ray fluoroscopy hold the potential for enhanced image guidance in catheter-based endovascular procedures. This article presents a novel method for real-time segmentation of catheters and guidewires in 2d X-ray images. We employ Convolutional Neural Networks (CNNs) and propose a transfer learning approach, using synthetic fluoroscopic images, to develop a lightweight version of the U-Net architecture. Our strategy, requiring a small amount of manually annotated data, streamlines the training process and results in a U-Net model, which achieves comparable performance to the state-of-the-art segmentation, with a decreased number of trainable parameters. MethodsThe proposed transfer learning approach exploits high-fidelity synthetic images generated from real fluroscopic backgrounds. We implement a two-stage process, initial end-to-end training and fine-tuning, to develop two versions of our model, using synthetic and phantom fluoroscopic images independently. A small number of manually annotated in-vivo images is employed to fine-tune the deepest 7 layers of the U-Net architecture, producing a network specialized for pixel-wise catheter/guidewire segmentation. The network takes as input a single grayscale image and outputs the segmentation result as a binary mask against the background. ResultsEvaluation is carried out with images from in-vivo fluoroscopic video sequences from six endovascular procedures, with different surgical setups. We validate the effectiveness of developing the U-Net models using synthetic data, in tests where fine-tuning and testing in-vivo takes place both by dividing data from all procedures into independent fine-tuning/testing subsets as well as by using different in-vivo sequences. Accurate catheter/guidewire segmentation (average Dice coefficient of ~ 0.55, ~ 0.26 and ~ 0.17) is obtained with both U-Net models. Compared to the state-of-the-art CNN models, the proposed U-Net achieves comparable performance ( ± 5% average Dice coefficients) in terms of segmentation accuracy, while yielding a 84% reduction of the testing time. This adds flexibility for real-time operation and makes our network adaptable to increased input resolution. ConclusionsThis work presents a new approach in the development of CNN models for pixel-wise segmentation of surgical catheters in X-ray fluoroscopy, exploiting synthetic images and transfer learning. Our methodology reduces the need for manually annotating large volumes of data for training. This represents an important advantage, given that manual pixel-wise annotations is a key bottleneck in developing CNN segmentation models. Combined with a simplified U-Net model, our work yields significant advantages compared to current state-of-the-art solutions

Mobile-PolypNet: Lightweight Colon Polyp Segmentation Network for Low-Resource Settings

Colon polyps, small clump of cells on the lining of the colon, can lead to colorectal cancer (CRC), one of the leading types of cancer globally. Hence, early detection of these polyps automatically is crucial in the prevention of CRC. The deep learning models proposed for the detection and segmentation of colorectal polyps are resource-consuming. This paper proposes a lightweight deep learning model for colorectal polyp segmentation that achieved state-of-the-art accuracy while significantly reducing the model size and complexity. The proposed deep learning autoencoder model employs a set of state-of-the-art architectural blocks and optimization objective functions to achieve the desired efficiency. The model is trained and tested on five publicly available colorectal polyp segmentation datasets (CVC-ClinicDB, CVC-ColonDB, EndoScene, Kvasir, and ETIS). We also performed ablation testing on the model to test various aspects of the autoencoder architecture. We performed the model evaluation by using most of the common image-segmentation metrics. The backbone model achieved a DICE score of 0.935 on the Kvasir dataset and 0.945 on the CVC-ClinicDB dataset, improving the accuracy by 4.12% and 5.12%, respectively, over the current state-of-the-art network, while using 88 times fewer parameters, 40 times less storage space, and being computationally 17 times more efficient. Our ablation study showed that the addition of ConvSkip in the autoencoder slightly improves the model\u27s performance but it was not significant (-value = 0.815)

MA-SAM: Modality-agnostic SAM Adaptation for 3D Medical Image Segmentation

The Segment Anything Model (SAM), a foundation model for general image segmentation, has demonstrated impressive zero-shot performance across numerous natural image segmentation tasks. However, SAM's performance significantly declines when applied to medical images, primarily due to the substantial disparity between natural and medical image domains. To effectively adapt SAM to medical images, it is important to incorporate critical third-dimensional information, i.e., volumetric or temporal knowledge, during fine-tuning. Simultaneously, we aim to harness SAM's pre-trained weights within its original 2D backbone to the fullest extent. In this paper, we introduce a modality-agnostic SAM adaptation framework, named as MA-SAM, that is applicable to various volumetric and video medical data. Our method roots in the parameter-efficient fine-tuning strategy to update only a small portion of weight increments while preserving the majority of SAM's pre-trained weights. By injecting a series of 3D adapters into the transformer blocks of the image encoder, our method enables the pre-trained 2D backbone to extract third-dimensional information from input data. The effectiveness of our method has been comprehensively evaluated on four medical image segmentation tasks, by using 10 public datasets across CT, MRI, and surgical video data. Remarkably, without using any prompt, our method consistently outperforms various state-of-the-art 3D approaches, surpassing nnU-Net by 0.9%, 2.6%, and 9.9% in Dice for CT multi-organ segmentation, MRI prostate segmentation, and surgical scene segmentation respectively. Our model also demonstrates strong generalization, and excels in challenging tumor segmentation when prompts are used. Our code is available at: https://github.com/cchen-cc/MA-SAM