ASLseg: Adapting SAM in the Loop for Semi-supervised Liver Tumor Segmentation

Liver tumor segmentation is essential for computer-aided diagnosis, surgical planning, and prognosis evaluation. However, obtaining and maintaining a large-scale dataset with dense annotations is challenging. Semi-Supervised Learning (SSL) is a common technique to address these challenges. Recently, Segment Anything Model (SAM) has shown promising performance in some medical image segmentation tasks, but it performs poorly for liver tumor segmentation. In this paper, we propose a novel semi-supervised framework, named ASLseg, which can effectively adapt the SAM to the SSL setting and combine both domain-specific and general knowledge of liver tumors. Specifically, the segmentation model trained with a specific SSL paradigm provides the generated pseudo-labels as prompts to the fine-tuned SAM. An adaptation network is then used to refine the SAM-predictions and generate higher-quality pseudo-labels. Finally, the reliable pseudo-labels are selected to expand the labeled set for iterative training. Extensive experiments on the LiTS dataset demonstrate overwhelming performance of our ASLseg.

Super-Resolution on Rotationally Scanned Photoacoustic Microscopy Images Incorporating Scanning Prior

Photoacoustic Microscopy (PAM) images integrating the advantages of optical contrast and acoustic resolution have been widely used in brain studies. However, there exists a trade-off between scanning speed and image resolution. Compared with traditional raster scanning, rotational scanning provides good opportunities for fast PAM imaging by optimizing the scanning mechanism. Recently, there is a trend to incorporate deep learning into the scanning process to further increase the scanning speed.Yet, most such attempts are performed for raster scanning while those for rotational scanning are relatively rare. In this study, we propose a novel and well-performing super-resolution framework for rotational scanning-based PAM imaging. To eliminate adjacent rows' displacements due to subject motion or high-frequency scanning distortion,we introduce a registration module across odd and even rows in the preprocessing and incorporate displacement degradation in the training. Besides, gradient-based patch selection is proposed to increase the probability of blood vessel patches being selected for training. A Transformer-based network with a global receptive field is applied for better performance. Experimental results on both synthetic and real datasets demonstrate the effectiveness and generalizability of our proposed framework for rotationally scanned PAM images'super-resolution, both quantitatively and qualitatively. Code is available at https://github.com/11710615/PAMSR.git.

Unlock the Power: Competitive Distillation for Multi-Modal Large Language Models

Recently, multi-modal content generation has attracted lots of attention from researchers by investigating the utilization of visual instruction tuning based on large language models (LLMs). To enhance the performance and generalization ability of such LLMs, the practice of distilling knowledge from pretrained multi-modal models (a.k.a. teachers) to more compact multi-modal LLMs (students) has gained considerable interest. However, the prevailing paradigm of instructiontuning in multi-modal LLMs knowledge distillation is resource-intensive and unidirectional, neglecting the potential for mutual feedback between the student and teacher models. Thus, we propose an innovative Competitive Multi-modal Distillation framework (CoMD), which captures bidirectional feedback between teacher and student models and continually updates the multi-modal capabilities that the student model has learned. It comprises two stages: multi-modal pre-training and multi-modal competitive distillation. The first stage pre-trains the student model on a large number of filtered multi-modal datasets. The second stage facilitates a bidirectional knowledge transfer between the student and teacher models. Our experimental analysis of diverse datasets shows that our knowledge transfer method consistently improves the capabilities of the student model. Finally, the 7B-sized student model after four distillations surpassed the current state-of-the-art model LLaVA-13B on the ScienceQA and LLaVA Test dataset, also outperforms other strong baselines in the zero-shot setting.

PRIOR: Prototype Representation Joint Learning from Medical Images and Reports

Contrastive learning based vision-language joint pre-training has emerged as a successful representation learning strategy. In this paper, we present a prototype representation learning framework incorporating both global and local alignment between medical images and reports. In contrast to standard global multi-modality alignment methods, we employ a local alignment module for fine-grained representation. Furthermore, a cross-modality conditional reconstruction module is designed to interchange information across modalities in the training phase by reconstructing masked images and reports. For reconstructing long reports, a sentence-wise prototype memory bank is constructed, enabling the network to focus on low-level localized visual and high-level clinical linguistic features. Additionally, a non-auto-regressive generation paradigm is proposed for reconstructing non-sequential reports. Experimental results on five downstream tasks, including supervised classification, zero-shot classification, image-to-text retrieval, semantic segmentation, and object detection, show the proposed method outperforms other state-of-the-art methods across multiple datasets and under different dataset size settings. The code is available at https://github.com/QtacierP/PRIOR.

Single-shot 3D photoacoustic computed tomography with a densely packed array for transcranial functional imaging

Photoacoustic computed tomography (PACT) is emerging as a new technique for functional brain imaging, primarily due to its capabilities in label-free hemodynamic imaging. Despite its potential, the transcranial application of PACT has encountered hurdles, such as acoustic attenuations and distortions by the skull and limited light penetration through the skull. To overcome these challenges, we have engineered a PACT system that features a densely packed hemispherical ultrasonic transducer array with 3072 channels, operating at a central frequency of 1 MHz. This system allows for single-shot 3D imaging at a rate equal to the laser repetition rate, such as 20 Hz. We have achieved a single-shot light penetration depth of approximately 9 cm in chicken breast tissue utilizing a 750 nm laser (withstanding 3295-fold light attenuation and still retaining an SNR of 74) and successfully performed transcranial imaging through an ex vivo human skull using a 1064 nm laser. Moreover, we have proven the capacity of our system to perform single-shot 3D PACT imaging in both tissue phantoms and human subjects. These results suggest that our PACT system is poised to unlock potential for real-time, in vivo transcranial functional imaging in humans.

JOINEDTrans: Prior Guided Multi-task Transformer for Joint Optic Disc/Cup Segmentation and Fovea Detection

Deep learning-based image segmentation and detection models have largely improved the efficiency of analyzing retinal landmarks such as optic disc (OD), optic cup (OC), and fovea. However, factors including ophthalmic disease-related lesions and low image quality issues may severely complicate automatic OD/OC segmentation and fovea detection. Most existing works treat the identification of each landmark as a single task, and take into account no prior information. To address these issues, we propose a prior guided multi-task transformer framework for joint OD/OC segmentation and fovea detection, named JOINEDTrans. JOINEDTrans effectively combines various spatial features of the fundus images, relieving the structural distortions induced by lesions and other imaging issues. It contains a segmentation branch and a detection branch. To be noted, we employ an encoder pretrained in a vessel segmentation task to effectively exploit the positional relationship among vessel, OD/OC, and fovea, successfully incorporating spatial prior into the proposed JOINEDTrans framework. There are a coarse stage and a fine stage in JOINEDTrans. In the coarse stage, OD/OC coarse segmentation and fovea heatmap localization are obtained through a joint segmentation and detection module. In the fine stage, we crop regions of interest for subsequent refinement and use predictions obtained in the coarse stage to provide additional information for better performance and faster convergence. Experimental results demonstrate that JOINEDTrans outperforms existing state-of-the-art methods on the publicly available GAMMA, REFUGE, and PALM fundus image datasets. We make our code available at https://github.com/HuaqingHe/JOINEDTrans

Unifying and Personalizing Weakly-supervised Federated Medical Image Segmentation via Adaptive Representation and Aggregation

Federated learning (FL) enables multiple sites to collaboratively train powerful deep models without compromising data privacy and security. The statistical heterogeneity (e.g., non-IID data and domain shifts) is a primary obstacle in FL, impairing the generalization performance of the global model. Weakly supervised segmentation, which uses sparsely-grained (i.e., point-, bounding box-, scribble-, block-wise) supervision, is increasingly being paid attention to due to its great potential of reducing annotation costs. However, there may exist label heterogeneity, i.e., different annotation forms across sites. In this paper, we propose a novel personalized FL framework for medical image segmentation, named FedICRA, which uniformly leverages heterogeneous weak supervision via adaptIve Contrastive Representation and Aggregation. Concretely, to facilitate personalized modeling and to avoid confusion, a channel selection based site contrastive representation module is employed to adaptively cluster intra-site embeddings and separate inter-site ones. To effectively integrate the common knowledge from the global model with the unique knowledge from each local model, an adaptive aggregation module is applied for updating and initializing local models at the element level. Additionally, a weakly supervised objective function that leverages a multiscale tree energy loss and a gated CRF loss is employed to generate more precise pseudo-labels and further boost the segmentation performance. Through extensive experiments on two distinct medical image segmentation tasks of different modalities, the proposed FedICRA demonstrates overwhelming performance over other state-of-the-art personalized FL methods. Its performance even approaches that of fully supervised training on centralized data. Our code and data are available at https://github.com/llmir/FedICRA.

Learning Enhancement From Degradation: A Diffusion Model For Fundus Image Enhancement

The quality of a fundus image can be compromised by numerous factors, many of which are challenging to be appropriately and mathematically modeled. In this paper, we introduce a novel diffusion model based framework, named Learning Enhancement from Degradation (LED), for enhancing fundus images. Specifically, we first adopt a data-driven degradation framework to learn degradation mappings from unpaired high-quality to low-quality images. We then apply a conditional diffusion model to learn the inverse enhancement process in a paired manner. The proposed LED is able to output enhancement results that maintain clinically important features with better clarity. Moreover, in the inference phase, LED can be easily and effectively integrated with any existing fundus image enhancement framework. We evaluate the proposed LED on several downstream tasks with respect to various clinically-relevant metrics, successfully demonstrating its superiority over existing state-of-the-art methods both quantitatively and qualitatively. The source code is available at https://github.com/QtacierP/LED.

UNO-QA: An Unsupervised Anomaly-Aware Framework with Test-Time Clustering for OCTA Image Quality Assessment

Medical image quality assessment (MIQA) is a vital prerequisite in various medical image analysis applications. Most existing MIQA algorithms are fully supervised that request a large amount of annotated data. However, annotating medical images is time-consuming and labor-intensive. In this paper, we propose an unsupervised anomaly-aware framework with test-time clustering for optical coherence tomography angiography (OCTA) image quality assessment in a setting wherein only a set of high-quality samples are accessible in the training phase. Specifically, a feature-embedding-based low-quality representation module is proposed to quantify the quality of OCTA images and then to discriminate between outstanding quality and non-outstanding quality. Within the non-outstanding quality class, to further distinguish gradable images from ungradable ones, we perform dimension reduction and clustering of multi-scale image features extracted by the trained OCTA quality representation network. Extensive experiments are conducted on one publicly accessible dataset sOCTA-3*3-10k, with superiority of our proposed framework being successfully established.

YoloCurvSeg: You Only Label One Noisy Skeleton for Vessel-style Curvilinear Structure Segmentation

Weakly-supervised learning (WSL) has been proposed to alleviate the conflict between data annotation cost and model performance through employing sparsely-grained (i.e., point-, box-, scribble-wise) supervision and has shown promising performance, particularly in the image segmentation field. However, it is still a very challenging problem due to the limited supervision, especially when only a small number of labeled samples are available. Additionally, almost all existing WSL segmentation methods are designed for star-convex structures which are very different from curvilinear structures such as vessels and nerves. In this paper, we propose a novel sparsely annotated segmentation framework for curvilinear structures, named YoloCurvSeg, based on image synthesis. A background generator delivers image backgrounds that closely match real distributions through inpainting dilated skeletons. The extracted backgrounds are then combined with randomly emulated curves generated by a Space Colonization Algorithm-based foreground generator and through a multilayer patch-wise contrastive learning synthesizer. In this way, a synthetic dataset with both images and curve segmentation labels is obtained, at the cost of only one or a few noisy skeleton annotations. Finally, a segmenter is trained with the generated dataset and possibly an unlabeled dataset. The proposed YoloCurvSeg is evaluated on four publicly available datasets (OCTA500, CORN, DRIVE and CHASEDB1) and the results show that YoloCurvSeg outperforms state-of-the-art WSL segmentation methods by large margins. With only one noisy skeleton annotation (respectively 0.14%, 0.02%, 1.4%, and 0.65% of the full annotation), YoloCurvSeg achieves more than 97% of the fully-supervised performance on each dataset. Code and datasets will be released at https://github.com/llmir/YoloCurvSeg.