Changchun Yang

Yidong Zhao, Changchun Yang, Artur Schweidtmann et al.

The self-configuring nnU-Net has achieved leading performance in a large range of medical image segmentation challenges. It is widely considered as the model of choice and a strong baseline for medical image segmentation. However, despite its extraordinary performance, nnU-Net does not supply a measure of uncertainty to indicate its possible failure. This can be problematic for large-scale image segmentation applications, where data are heterogeneous and nnU-Net may fail without notice. In this work, we introduce a novel method to estimate nnU-Net uncertainty for medical image segmentation. We propose a highly effective scheme for posterior sampling of weight space for Bayesian uncertainty estimation. Different from previous baseline methods such as Monte Carlo Dropout and mean-field Bayesian Neural Networks, our proposed method does not require a variational architecture and keeps the original nnU-Net architecture intact, thereby preserving its excellent performance and ease of use. Additionally, we boost the segmentation performance over the original nnU-Net via marginalizing multi-modal posterior models. We applied our method on the public ACDC and M&M datasets of cardiac MRI and demonstrated improved uncertainty estimation over a range of baseline methods. The proposed method further strengthens nnU-Net for medical image segmentation in terms of both segmentation accuracy and quality control.

Yuetan Chu, Yilan Zhang, Zhongyi Han et al.

Foundation models have recently attracted significant attention for their impressive generalizability across diverse downstream tasks. However, these models are demonstrated to exhibit great limitations in representing high-frequency components and fine-grained details. In many medical imaging tasks, the precise representation of such information is crucial due to the inherently intricate anatomical structures, sub-visual features, and complex boundaries involved. Consequently, the limited representation of prevalent foundation models can result in significant performance degradation or even failure in these tasks. To address these challenges, we propose a novel pretraining strategy, named Frequency-advanced Representation Autoencoder (Frepa). Through high-frequency masking and low-frequency perturbation combined with adversarial learning, Frepa encourages the encoder to effectively represent and preserve high-frequency components in the image embeddings. Additionally, we introduce an innovative histogram-equalized image masking strategy, extending the Masked Autoencoder approach beyond ViT to other architectures such as Swin Transformer and convolutional networks. We develop Frepa across nine medical modalities and validate it on 32 downstream tasks for both 2D images and 3D volume data. Without fine-tuning, Frepa can outperform other self-supervised pretraining methods and, in some cases, even surpasses task-specific trained models. This improvement is particularly significant for tasks involving fine-grained details, such as achieving up to a +15% increase in DSC for retina vessel segmentation and a +7% increase in IoU for lung nodule detection. Further experiments quantitatively reveal that Frepa enables superior high-frequency representations and preservation in the embeddings, underscoring its potential for developing more generalized and universal medical image foundation models.

Changchun Yang, Hengrong Lan, Fei Gao

If light passes through the body tissues, focusing only on areas where treatment needs, such as tumors, will revolutionize many biomedical imaging and therapy technologies. So how to focus light through deep inhomogeneous tissues overcoming scattering is Holy Grail in biomedical areas. In this paper, we use deep learning to learn and accelerate the process of phase pre-compensation using wavefront shaping. We present an approach (LoftGAN, light only focuses on treatment needs) for learning the relationship between phase domain X and speckle domain Y . Our goal is not just to learn an inverse mapping F:Y->X such that we can know the corresponding X needed for imaging Y like most work, but also to make focusing that is susceptible to disturbances more robust and precise by ensuring that the phase obtained can be forward mapped back to speckle. So we introduce different constraints to enforce F(Y)=X and H(F(Y))=Y with the transmission mapping H:X->Y. Both simulation and physical experiments are performed to investigate the effects of light focusing to demonstrate the effectiveness of our method and comparative experiments prove the crucial improvement of robustness and precision. Codes are available at https://github.com/ChangchunYang/LoftGAN.

Changchun Yang, Hengrong Lan, Feng Gao et al.

Machine learning has been developed dramatically and witnessed a lot of applications in various fields over the past few years. This boom originated in 2009, when a new model emerged, that is, the deep artificial neural network, which began to surpass other established mature models on some important benchmarks. Later, it was widely used in academia and industry. Ranging from image analysis to natural language processing, it fully exerted its magic and now become the state-of-the-art machine learning models. Deep neural networks have great potential in medical imaging technology, medical data analysis, medical diagnosis and other healthcare issues, and is promoted in both pre-clinical and even clinical stages. In this review, we performed an overview of some new developments and challenges in the application of machine learning to medical image analysis, with a special focus on deep learning in photoacoustic imaging. The aim of this review is threefold: (i) introducing deep learning with some important basics, (ii) reviewing recent works that apply deep learning in the entire ecological chain of photoacoustic imaging, from image reconstruction to disease diagnosis, (iii) providing some open source materials and other resources for researchers interested in applying deep learning to photoacoustic imaging.

Hengrong Lan, Juze Zhang, Changchun Yang et al.

Photoacoustic (PA) computed tomography (PACT) shows great potentials in various preclinical and clinical applications. A great number of measurements are the premise that obtains a high-quality image, which implies a low imaging rate or a high system cost. The artifacts or sidelobes could pollute the image if we decrease the number of measured channels or limit the detected view. In this paper, a novel compressed sensing method for PACT using an untrained neural network is proposed, which decreases half number of the measured channels and recoveries enough details. This method uses a neural network to reconstruct without the requirement for any additional learning based on the deep image prior. The model can reconstruct the image only using a few detections with gradient descent. Our method can cooperate with other existing regularization, and further improve the quality. In addition, we introduce a shape prior to easily converge the model to the image. We verify the feasibility of untrained network based compressed sensing in PA image reconstruction, and compare this method with a conventional method using total variation minimization. The experimental results show that our proposed method outperforms 32.72% (SSIM) with the traditional compressed sensing method in the same regularization. It could dramatically reduce the requirement for the number of transducers, by sparsely sampling the raw PA data, and improve the quality of PA image significantly.

Mengjie Guo, Hengrong Lan, Changchun Yang et al.

Photoacoustic (PA) imaging is a biomedical imaging modality capable of acquiring high-contrast images of optical absorption at depths much greater than traditional optical imaging techniques. However, practical instrumentation and geometry limit the number of available acoustic sensors surrounding the imaging target, which results in the sparsity of sensor data. Conventional PA image reconstruction methods give severe artifacts when they are applied directly to the sparse PA data. In this paper, we firstly propose to employ a novel signal processing method to make sparse PA raw data more suitable for the neural network, concurrently speeding up image reconstruction. Then we propose Attention Steered Network (AS-Net) for PA reconstruction with multi-feature fusion. AS-Net is validated on different datasets, including simulated photoacoustic data from fundus vasculature phantoms and experimental data from in vivo fish and mice. Notably, the method is also able to eliminate some artifacts present in the ground truth for in vivo data. Results demonstrated that our method provides superior reconstructions at a faster speed.

Hengrong Lan, Changchun Yang, Fei Gao

Photoacoustic (PA) computed tomography (PACT) reconstructs the initial pressure distribution from raw PA signals. The standard reconstruction of medical image could cause the artifacts due to interferences or ill-posed setup. Recently, deep learning has been used to reconstruct the PA image with ill-posed conditions. Most works remove the artifacts from image domain, and compensate the limited-view from dataset. In this paper, we propose a jointed feature fusion framework (JEFF-Net) based on deep learning to reconstruct the PA image using limited-view data. The cross-domain features from limited-view position-wise data and the reconstructed image are fused by a backtracked supervision. Specifically, our results could generate superior performance, whose artifacts are drastically reduced in the output compared to ground-truth (full-view reconstructed result). In this paper, a quarter position-wise data (32 channels) is fed into model, which outputs another 3-quarters-view data (96 channels). Moreover, two novel losses are designed to restrain the artifacts by sufficiently manipulating superposed data. The numerical and in-vivo results have demonstrated the superior performance of our method to reconstruct the full-view image without artifacts. Finally, quantitative evaluations show that our proposed method outperformed the ground-truth in some metrics.

Hengrong Lan, Daohuai Jiang, Changchun Yang et al.

Photoacoustic imaging (PAI) is an emerging non-invasive imaging modality combining the advantages of deep ultrasound penetration and high optical contrast. Image reconstruction is an essential topic in PAI, which is unfortunately an ill-posed problem due to the complex and unknown optical/acoustic parameters in tissue. Conventional algorithms used in PAI (e.g., delay-and-sum) provide a fast solution while many artifacts remain, especially for linear array probe with limited-view issue. Convolutional neural network (CNN) has shown state-of-the-art results in computer vision, and more and more work based on CNN has been studied in medical image processing recently. In this paper, we present a non-iterative scheme filling the gap between existing direct-processing and post-processing methods, and propose a new framework Y-Net: a CNN architecture to reconstruct the PA image by optimizing both raw data and beamformed images once. The network connected two encoders with one decoder path, which optimally utilizes more information from raw data and beamformed image. The results of the test set showed good performance compared with conventional reconstruction algorithms and other deep learning methods. Our method is also validated with experiments both in-vitro and in vivo, which still performs better than other existing methods. The proposed Y-Net architecture also has high potential in medical image reconstruction for other imaging modalities beyond PAI.