Extracellular recordings are transient voltage fluctuations in the vicinity of neurons, serving as a fundamental modality in neuroscience for decoding brain activity at single-neuron resolution. Spike sorting, the process of attributing each detected spike to its corresponding neuron, is a pivotal step in brain sensing pipelines. However, it remains challenging under low signal-to-noise ratio (SNR), electrode drift, and cross-session variability. In this paper, we propose HuiduRep, a robust self-supervised representation learning framework that extracts discriminative and generalizable features from extracellular recordings. By integrating contrastive learning with a denoising autoencoder, HuiduRep learns latent representations robust to noise and drift. With HuiduRep, we develop a spike sorting pipeline that clusters spike representations without ground truth labels. Experiments on hybrid and real-world datasets demonstrate that HuiduRep achieves strong robustness. Furthermore, the pipeline significantly outperforms state-of-the-art tools such as KiloSort4 and MountainSort5 on accuracy and precision on diverse datasets. These findings demonstrate the potential of self-supervised spike representation learning as a foundational tool for robust and generalizable processing of extracellular recordings.

The intima-media thickness (IMT) of the carotid artery is commonly used for monitoring atherosclerosis. However, the intima-media complex (IMC) segmentation for the IMT calculation is a tedious task due to confused IMC boundaries and class-imbalance issues. In this paper, we propose an automatic method named CSM-Net for the joint segmentation of IMC on near and far walls, and Lumen in carotid ultrasound images. In the encoder-decoder CSM-Net, firstly, the cascaded dilated convolutions combined with the squeeze-excitation module are introduced for exploiting more contextual features on the last encoder layer. Secondly, a multi-scale triple spatial attention module is utilized for capturing serviceable features on each decoder layer. Lastly, a weighted hybrid loss function is employed to resolve the class-imbalance issue. Experiments are performed on a private dataset of 100 images from one center using the 10-fold cross-validation, the results of the proposed method on the IMC Dice, Lumen Dice, Precision, Recall, and F1 metrics are 0.814 ±0.061,0.941 ±0.024,0.911 ±0.044,0.916 ±0.039, and 0.913 ±0.027, respectively, which precede some cutting-edge methods. The proposed method may be useful for the IMC segmentation of carotid ultrasound images in the clinic.

The quality of a blastocyst directly determines the embryo's implantation potential, thus making it essential to objectively and accurately identify the blastocyst morphology. In this work, we propose an automatic framework named I2CNet to perform the blastocyst segmentation task in human embryo images. The I2CNet contains two components: IntrA-Class Context Module (IACCM) and InteR-Class Context Module (IRCCM). The IACCM aggregates the representations of specific areas sharing the same category for each pixel, where the categorized regions are learned under the supervision of the groundtruth. This aggregation decomposes a K-category recognition task into K recognition tasks of two labels while maintaining the ability of garnering intra-class features. In addition, the IRCCM is designed based on the blastocyst morphology to compensate for inter-class information which is gradually gathered from inside out. Meanwhile, a weighted mapping function is applied to facilitate edges of the inter classes and stimulate some hard samples. Eventually, the learned intra- and inter-class cues are integrated from coarse to fine, rendering sufficient information interaction and fusion between multi-scale features. Quantitative and qualitative experiments demonstrate that the superiority of our model compared with other representative methods. The I2CNet achieves accuracy of 94.14% and Jaccard of 85.25% on blastocyst public dataset.

Automatic classification of retinal arteries and veins plays an important role in assisting clinicians to diagnosis cardiovascular and eye-related diseases. However, due to the high degree of anatomical variation across the population, and the presence of inconsistent labels by the subjective judgment of annotators in available training data, most of existing methods generally suffer from blood vessel discontinuity and arteriovenous confusion, the artery/vein (A/V) classification task still faces great challenges. In this work, we propose a multi-scale interactive network with A/V discriminator for retinal artery and vein recognition, which can reduce the arteriovenous confusion and alleviate the disturbance of noisy label. A multi-scale interaction (MI) module is designed in encoder for realizing the cross-space multi-scale features interaction of fundus images, effectively integrate high-level and low-level context information. In particular, we also design an ingenious A/V discriminator (AVD) that utilizes the independent and shared information between arteries and veins, and combine with topology loss, to further strengthen the learning ability of model to resolve the arteriovenous confusion. In addition, we adopt a sample re-weighting (SW) strategy to effectively alleviate the disturbance from data labeling errors. The proposed model is verified on three publicly available fundus image datasets (AV-DRIVE, HRF, LES-AV) and a private dataset. We achieve the accuracy of 97.47%, 96.91%, 97.79%, and 98.18% respectively on these four datasets. Extensive experimental results demonstrate that our method achieves competitive performance compared with state-of-the-art methods for A/V classification. To address the problem of training data scarcity, we publicly release 100 fundus images with A/V annotations to promote relevant research in the community.

Diabetic retinopathy (DR) is a leading cause of permanent blindness among the working-age people. Automatic DR grading can help ophthalmologists make timely treatment for patients. However, the existing grading methods are usually trained with high resolution (HR) fundus images, such that the grading performance decreases a lot given low resolution (LR) images, which are common in clinic. In this paper, we mainly focus on DR grading with LR fundus images. According to our analysis on the DR task, we find that: 1) image super-resolution (ISR) can boost the performance of both DR grading and lesion segmentation; 2) the lesion segmentation regions of fundus images are highly consistent with pathological regions for DR grading. Based on our findings, we propose a convolutional neural network (CNN)-based method for joint learning of multi-level tasks for DR grading, called DeepMT-DR, which can simultaneously handle the low-level task of ISR, the mid-level task of lesion segmentation and the high-level task of disease severity classification on LR fundus images. Moreover, a novel task-aware loss is developed to encourage ISR to focus on the pathological regions for its subsequent tasks: lesion segmentation and DR grading. Extensive experimental results show that our DeepMT-DR method significantly outperforms other state-of-the-art methods for DR grading over three datasets. In addition, our method achieves comparable performance in two auxiliary tasks of ISR and lesion segmentation.

Recent years have witnessed the growing interest in disease severity grading, especially for ocular diseases based on fundus images. The existing grading methods are usually trained with high resolution (HR) images. However, the grading performance decreases a lot given low resolution (LR) images, which are common in practice. In this paper, we mainly focus on diabetic retinopathy (DR) grading with LR fundus images. According to our analysis on the DR task, we find that: 1) image super-resolution (ISR) can boost the performance of DR grading and lesion segmentation; 2) the lesion segmentation regions of fundus images are highly consistent with pathological regions for DR grading. Thus, we propose a deep multi-task learning based DR grading (DeepMT-DR) method for LR fundus images, which simultaneously handles the auxiliary tasks of ISR and lesion segmentation. Specifically, based on our findings, we propose a hierarchical deep learning structure that simultaneously processes the low-level task of ISR, the mid-level task of lesion segmentation and the high-level task of DR grading. Moreover, a novel task-aware loss is developed to encourage ISR to focus on the pathological regions for its subsequent tasks: lesion segmentation and DR grading. Extensive experimental results show that our DeepMT-DR method significantly outperforms other state-of-the-art methods for DR grading over two public datasets. In addition, our method achieves comparable performance in two auxiliary tasks of ISR and lesion segmentation.

Consistency training has proven to be an advanced semi-supervised framework and achieved promising results in medical image segmentation tasks through enforcing an invariance of the predictions over different views of the inputs. However, with the iterative updating of model parameters, the models would tend to reach a coupled state and eventually lose the ability to exploit unlabeled data. To address the issue, we present a novel semi-supervised segmentation model based on parameter decoupling strategy to encourage consistent predictions from diverse views. Specifically, we first adopt a two-branch network to simultaneously produce predictions for each image. During the training process, we decouple the two prediction branch parameters by quadratic cosine distance to construct different views in latent space. Based on this, the feature extractor is constrained to encourage the consistency of probability maps generated by classifiers under diversified features. In the overall training process, the parameters of feature extractor and classifiers are updated alternately by consistency regularization operation and decoupling operation to gradually improve the generalization performance of the model. Our method has achieved a competitive result over the state-of-the-art semi-supervised methods on the Atrial Segmentation Challenge dataset, demonstrating the effectiveness of our framework. Code is available at https://github.com/BX0903/PDC.

The novel Coronavirus disease (COVID-19) is a highly contagious virus and has spread all over the world, posing an extremely serious threat to all countries. Automatic lung infection segmentation from computed tomography (CT) plays an important role in the quantitative analysis of COVID-19. However, the major challenge lies in the inadequacy of annotated COVID-19 datasets. Currently, there are several public non-COVID lung lesion segmentation datasets, providing the potential for generalizing useful information to the related COVID-19 segmentation task. In this paper, we propose a novel relation-driven collaborative learning model to exploit shared knowledge from non-COVID lesions for annotation-efficient COVID-19 CT lung infection segmentation. The model consists of a general encoder to capture general lung lesion features based on multiple non-COVID lesions, and a target encoder to focus on task-specific features based on COVID-19 infections. We develop a collaborative learning scheme to regularize feature-level relation consistency of given input and encourage the model to learn more general and discriminative representation of COVID-19 infections. Extensive experiments demonstrate that trained with limited COVID-19 data, exploiting shared knowledge from non-COVID lesions can further improve state-of-the-art performance with up to 3.0% in dice similarity coefficient and 4.2% in normalized surface dice. In addition, experimental results on large scale 2D dataset with CT slices show that our method significantly outperforms cutting-edge segmentation methods metrics. Our method promotes new insights into annotation-efficient deep learning and illustrates strong potential for real-world applications in the global fight against COVID-19 in the absence of sufficient high-quality annotations.

Absence seizures are characterized by sudden loss of consciousness and interruption of ongoing motor activities for a brief period of time lasting few to several seconds and up to half a minute. Due to their brevity and subtle clinical manifestations absence seizures are easily missed by inexperienced observers. Accurate evaluation of their high frequency of recurrence can be a challenge even for experienced observers. We present a novel method for detecting and analyzing absence seizures acquired from electroencephalogram (EEG) recordings in patients with absence seizures. Six patients were included in this study; two seizure free, of a total recording time of 26 hours, and four experiencing over 100 seizures within 14.5 hours of total recordings. Our algorithm detected only one false positive finding in the first seizure free patients and 148 of 186 continuous uninterrupted 3Hz spike and wave discharge (SWD) epochs in the rest of the patients. Out of the total 38 missed SWD epochs 28 were ≤ 2.1 sec in duration. The remaining epochs included interrupted 3Hz SWDs. Our proposed algorithm offers an efficient automatic detection scheme that can be used in diagnostic and therapeutic evaluations in patients with absence seizures.