CellSeg1: Robust Cell Segmentation with One Training Image

Recent trends in cell segmentation have shifted towards universal models to handle diverse cell morphologies and imaging modalities. However, for continuously emerging cell types and imaging techniques, these models still require hundreds or thousands of annotated cells for fine-tuning. We introduce CellSeg1, a practical solution for segmenting cells of arbitrary morphology and modality with a few dozen cell annotations in 1 image. By adopting Low-Rank Adaptation of the Segment Anything Model (SAM), we achieve robust cell segmentation. Tested on 19 diverse cell datasets, CellSeg1 trained on 1 image achieved 0.81 average mAP at 0.5 IoU, performing comparably to existing models trained on over 500 images. It also demonstrated superior generalization in cross-dataset tests on TissueNet. We found that high-quality annotation of a few dozen densely packed cells of varied sizes is key to effective segmentation. CellSeg1 provides an efficient solution for cell segmentation with minimal annotation effort.

Shape Transformation Driven by Active Contour for Class-Imbalanced Semi-Supervised Medical Image Segmentation

Annotating 3D medical images demands expert knowledge and is time-consuming. As a result, semi-supervised learning (SSL) approaches have gained significant interest in 3D medical image segmentation. The significant size differences among various organs in the human body lead to imbalanced class distribution, which is a major challenge in the real-world application of these SSL approaches. To address this issue, we develop a novel Shape Transformation driven by Active Contour (STAC), that enlarges smaller organs to alleviate imbalanced class distribution across different organs. Inspired by curve evolution theory in active contour methods, STAC employs a signed distance function (SDF) as the level set function, to implicitly represent the shape of organs, and deforms voxels in the direction of the steepest descent of SDF (i.e., the normal vector). To ensure that the voxels far from expansion organs remain unchanged, we design an SDF-based weight function to control the degree of deformation for each voxel. We then use STAC as a data-augmentation process during the training stage. Experimental results on two benchmark datasets demonstrate that the proposed method significantly outperforms some state-of-the-art methods. Source code is publicly available at https://github.com/GuGuLL123/STAC.

Shape-intensity knowledge distillation for robust medical image segmentation

Many medical image segmentation methods have achieved impressive results. Yet, most existing methods do not take into account the shape-intensity prior information. This may lead to implausible segmentation results, in particular for images of unseen datasets. In this paper, we propose a novel approach to incorporate joint shape-intensity prior information into the segmentation network. Specifically, we first train a segmentation network (regarded as the teacher network) on class-wise averaged training images to extract valuable shape-intensity information, which is then transferred to a student segmentation network with the same network architecture as the teacher via knowledge distillation. In this way, the student network regarded as the final segmentation model can effectively integrate the shape-intensity prior information, yielding more accurate segmentation results. Despite its simplicity, experiments on five medical image segmentation tasks of different modalities demonstrate that the proposed Shape-Intensity Knowledge Distillation (SIKD) consistently improves several baseline models (including recent MaxStyle and SAMed) under intra-dataset evaluation, and significantly improves the cross-dataset generalization ability. The code is available at https://github.com/whdong-whu/SIKD.

Progressive Retinal Image Registration via Global and Local Deformable Transformations

Retinal image registration plays an important role in the ophthalmological diagnosis process. Since there exist variances in viewing angles and anatomical structures across different retinal images, keypoint-based approaches become the mainstream methods for retinal image registration thanks to their robustness and low latency. These methods typically assume the retinal surfaces are planar, and adopt feature matching to obtain the homography matrix that represents the global transformation between images. Yet, such a planar hypothesis inevitably introduces registration errors since retinal surface is approximately curved. This limitation is more prominent when registering image pairs with significant differences in viewing angles. To address this problem, we propose a hybrid registration framework called HybridRetina, which progressively registers retinal images with global and local deformable transformations. For that, we use a keypoint detector and a deformation network called GAMorph to estimate the global transformation and local deformable transformation, respectively. Specifically, we integrate multi-level pixel relation knowledge to guide the training of GAMorph. Additionally, we utilize an edge attention module that includes the geometric priors of the images, ensuring the deformation field focuses more on the vascular regions of clinical interest. Experiments on two widely-used datasets, FIRE and FLoRI21, show that our proposed HybridRetina significantly outperforms some state-of-the-art methods. The code is available at https://github.com/lyp-deeplearning/awesome-retinal-registration.

HFGS: 4D Gaussian Splatting with Emphasis on Spatial and Temporal High-Frequency Components for Endoscopic Scene Reconstruction

Robot-assisted minimally invasive surgery benefits from enhancing dynamic scene reconstruction, as it improves surgical outcomes. While Neural Radiance Fields (NeRF) have been effective in scene reconstruction, their slow inference speeds and lengthy training durations limit their applicability. To overcome these limitations, 3D Gaussian Splatting (3D-GS) based methods have emerged as a recent trend, offering rapid inference capabilities and superior 3D quality. However, these methods still struggle with under-reconstruction in both static and dynamic scenes. In this paper, we propose HFGS, a novel approach for deformable endoscopic reconstruction that addresses these challenges from spatial and temporal frequency perspectives. Our approach incorporates deformation fields to better handle dynamic scenes and introduces Spatial High-Frequency Emphasis Reconstruction (SHF) to minimize discrepancies in spatial frequency spectra between the rendered image and its ground truth. Additionally, we introduce Temporal High-Frequency Emphasis Reconstruction (THF) to enhance dynamic awareness in neural rendering by leveraging flow priors, focusing optimization on motion-intensive parts. Extensive experiments on two widely used benchmarks demonstrate that HFGS achieves superior rendering quality. Our code will be available.

Spatial-aware Attention Generative Adversarial Network for Semi-supervised Anomaly Detection in Medical Image

Medical anomaly detection is a critical research area aimed at recognizing abnormal images to aid in diagnosis.Most existing methods adopt synthetic anomalies and image restoration on normal samples to detect anomaly. The unlabeled data consisting of both normal and abnormal data is not well explored. We introduce a novel Spatial-aware Attention Generative Adversarial Network (SAGAN) for one-class semi-supervised generation of health images.Our core insight is the utilization of position encoding and attention to accurately focus on restoring abnormal regions and preserving normal regions. To fully utilize the unlabelled data, SAGAN relaxes the cyclic consistency requirement of the existing unpaired image-to-image conversion methods, and generates high-quality health images corresponding to unlabeled data, guided by the reconstruction of normal images and restoration of pseudo-anomaly images.Subsequently, the discrepancy between the generated healthy image and the original image is utilized as an anomaly score.Extensive experiments on three medical datasets demonstrate that the proposed SAGAN outperforms the state-of-the-art methods.

Position-Guided Prompt Learning for Anomaly Detection in Chest X-Rays

Anomaly detection in chest X-rays is a critical task. Most methods mainly model the distribution of normal images, and then regard significant deviation from normal distribution as anomaly. Recently, CLIP-based methods, pre-trained on a large number of medical images, have shown impressive performance on zero/few-shot downstream tasks. In this paper, we aim to explore the potential of CLIP-based methods for anomaly detection in chest X-rays. Considering the discrepancy between the CLIP pre-training data and the task-specific data, we propose a position-guided prompt learning method. Specifically, inspired by the fact that experts diagnose chest X-rays by carefully examining distinct lung regions, we propose learnable position-guided text and image prompts to adapt the task data to the frozen pre-trained CLIP-based model. To enhance the model's discriminative capability, we propose a novel structure-preserving anomaly synthesis method within chest x-rays during the training process. Extensive experiments on three datasets demonstrate that our proposed method outperforms some state-of-the-art methods. The code of our implementation is available at https://github.com/sunzc-sunny/PPAD.

Development of Skip Connection in Deep Neural Networks for Computer Vision and Medical Image Analysis: A Survey

Deep learning has made significant progress in computer vision, specifically in image classification, object detection, and semantic segmentation. The skip connection has played an essential role in the architecture of deep neural networks,enabling easier optimization through residual learning during the training stage and improving accuracy during testing. Many neural networks have inherited the idea of residual learning with skip connections for various tasks, and it has been the standard choice for designing neural networks. This survey provides a comprehensive summary and outlook on the development of skip connections in deep neural networks. The short history of skip connections is outlined, and the development of residual learning in deep neural networks is surveyed. The effectiveness of skip connections in the training and testing stages is summarized, and future directions for using skip connections in residual learning are discussed. Finally, we summarize seminal papers, source code, models, and datasets that utilize skip connections in computer vision, including image classification, object detection, semantic segmentation, and image reconstruction. We hope this survey could inspire peer researchers in the community to develop further skip connections in various forms and tasks and the theory of residual learning in deep neural networks. The project page can be found at https://github.com/apple1986/Residual_Learning_For_Images

MoreStyle: Relax Low-frequency Constraint of Fourier-based Image Reconstruction in Generalizable Medical Image Segmentation

The task of single-source domain generalization (SDG) in medical image segmentation is crucial due to frequent domain shifts in clinical image datasets. To address the challenge of poor generalization across different domains, we introduce a Plug-and-Play module for data augmentation called MoreStyle. MoreStyle diversifies image styles by relaxing low-frequency constraints in Fourier space, guiding the image reconstruction network. With the help of adversarial learning, MoreStyle further expands the style range and pinpoints the most intricate style combinations within latent features. To handle significant style variations, we introduce an uncertainty-weighted loss. This loss emphasizes hard-to-classify pixels resulting only from style shifts while mitigating true hard-to-classify pixels in both MoreStyle-generated and original images. Extensive experiments on two widely used benchmarks demonstrate that the proposed MoreStyle effectively helps to achieve good domain generalization ability, and has the potential to further boost the performance of some state-of-the-art SDG methods.

WIA-LD2ND: Wavelet-based Image Alignment for Self-supervised Low-Dose CT Denoising

In clinical examinations and diagnoses, low-dose computed tomography (LDCT) is crucial for minimizing health risks compared with normal-dose computed tomography (NDCT). However, reducing the radiation dose compromises the signal-to-noise ratio, leading to degraded quality of CT images. To address this, we analyze LDCT denoising task based on experimental results from the frequency perspective, and then introduce a novel self-supervised CT image denoising method called WIA-LD2ND, only using NDCT data. The proposed WIA-LD2ND comprises two modules: Wavelet-based Image Alignment (WIA) and Frequency-Aware Multi-scale Loss (FAM). First, WIA is introduced to align NDCT with LDCT by mainly adding noise to the high-frequency components, which is the main difference between LDCT and NDCT. Second, to better capture high-frequency components and detailed information, Frequency-Aware Multi-scale Loss (FAM) is proposed by effectively utilizing multi-scale feature space. Extensive experiments on two public LDCT denoising datasets demonstrate that our WIA-LD2ND, only uses NDCT, outperforms existing several state-of-the-art weakly-supervised and self-supervised methods.