NeuroFly: A framework for whole-brain single neuron reconstruction

Neurons, with their elongated, tree-like dendritic and axonal structures, enable efficient signal integration and long-range communication across brain regions. By reconstructing individual neurons' morphology, we can gain valuable insights into brain connectivity, revealing the structure basis of cognition, movement, and perception. Despite the accumulation of extensive 3D microscopic imaging data, progress has been considerably hindered by the absence of automated tools to streamline this process. Here we introduce NeuroFly, a validated framework for large-scale automatic single neuron reconstruction. This framework breaks down the process into three distinct stages: segmentation, connection, and proofreading. In the segmentation stage, we perform automatic segmentation followed by skeletonization to generate over-segmented neuronal fragments without branches. During the connection stage, we use a 3D image-based path following approach to extend each fragment and connect it with other fragments of the same neuron. Finally, human annotators are required only to proofread the few unresolved positions. The first two stages of our process are clearly defined computer vision problems, and we have trained robust baseline models to solve them. We validated NeuroFly's efficiency using in-house datasets that include a variety of challenging scenarios, such as dense arborizations, weak axons, images with contamination. We will release the datasets along with a suite of visualization and annotation tools for better reproducibility. Our goal is to foster collaboration among researchers to address the neuron reconstruction challenge, ultimately accelerating advancements in neuroscience research. The dataset and code are available at https://github.com/beanli161514/neurofly

Rethinking Scale Imbalance in Semi-supervised Object Detection for Aerial Images

This paper focuses on the scale imbalance problem of semi-supervised object detection(SSOD) in aerial images. Compared to natural images, objects in aerial images show smaller sizes and larger quantities per image, increasing the difficulty of manual annotation. Meanwhile, the advanced SSOD technique can train superior detectors by leveraging limited labeled data and massive unlabeled data, saving annotation costs. However, as an understudied task in aerial images, SSOD suffers from a drastic performance drop when facing a large proportion of small objects. By analyzing the predictions between small and large objects, we identify three imbalance issues caused by the scale bias, i.e., pseudo-label imbalance, label assignment imbalance, and negative learning imbalance. To tackle these issues, we propose a novel Scale-discriminative Semi-Supervised Object Detection (S^3OD) learning pipeline for aerial images. In our S^3OD, three key components, Size-aware Adaptive Thresholding (SAT), Size-rebalanced Label Assignment (SLA), and Teacher-guided Negative Learning (TNL), are proposed to warrant scale unbiased learning. Specifically, SAT adaptively selects appropriate thresholds to filter pseudo-labels for objects at different scales. SLA balances positive samples of objects at different scales through resampling and reweighting. TNL alleviates the imbalance in negative samples by leveraging information generated by a teacher model. Extensive experiments conducted on the DOTA-v1.5 benchmark demonstrate the superiority of our proposed methods over state-of-the-art competitors. Codes will be released soon.

High-Resolution Cloud Removal with Multi-Modal and Multi-Resolution Data Fusion: A New Baseline and Benchmark

In this paper, we introduce Planet-CR, a benchmark dataset for high-resolution cloud removal with multi-modal and multi-resolution data fusion. Planet-CR is the first public dataset for cloud removal to feature globally sampled high resolution optical observations, in combination with paired radar measurements as well as pixel-level land cover annotations. It provides solid basis for exhaustive evaluation in terms of generating visually pleasing textures and semantically meaningful structures. With this dataset, we consider the problem of cloud removal in high resolution optical remote sensing imagery by integrating multi-modal and multi-resolution information. Existing multi-modal data fusion based methods, which assume the image pairs are aligned pixel-to-pixel, are hence not appropriate for this problem. To this end, we design a new baseline named Align-CR to perform the low-resolution SAR image guided high-resolution optical image cloud removal. It implicitly aligns the multi-modal and multi-resolution data during the reconstruction process to promote the cloud removal performance. The experimental results demonstrate that the proposed Align-CR method gives the best performance in both visual recovery quality and semantic recovery quality. The project is available at https://github.com/zhu-xlab/Planet-CR, and hope this will inspire future research.

Exploring the Potential of SAR Data for Cloud Removal in Optical Satellite Imagery

The challenge of the cloud removal task can be alleviated with the aid of Synthetic Aperture Radar (SAR) images that can penetrate cloud cover. However, the large domain gap between optical and SAR images as well as the severe speckle noise of SAR images may cause significant interference in SAR-based cloud removal, resulting in performance degeneration. In this paper, we propose a novel global-local fusion based cloud removal (GLF-CR) algorithm to leverage the complementary information embedded in SAR images. Exploiting the power of SAR information to promote cloud removal entails two aspects. The first, global fusion, guides the relationship among all local optical windows to maintain the structure of the recovered region consistent with the remaining cloud-free regions. The second, local fusion, transfers complementary information embedded in the SAR image that corresponds to cloudy areas to generate reliable texture details of the missing regions, and uses dynamic filtering to alleviate the performance degradation caused by speckle noise. Extensive evaluation demonstrates that the proposed algorithm can yield high quality cloud-free images and performs favorably against state-of-the-art cloud removal algorithms.

Motion Deblurring with Real Events

In this paper, we propose an end-to-end learning framework for event-based motion deblurring in a self-supervised manner, where real-world events are exploited to alleviate the performance degradation caused by data inconsistency. To achieve this end, optical flows are predicted from events, with which the blurry consistency and photometric consistency are exploited to enable self-supervision on the deblurring network with real-world data. Furthermore, a piece-wise linear motion model is proposed to take into account motion non-linearities and thus leads to an accurate model for the physical formation of motion blurs in the real-world scenario. Extensive evaluation on both synthetic and real motion blur datasets demonstrates that the proposed algorithm bridges the gap between simulated and real-world motion blurs and shows remarkable performance for event-based motion deblurring in real-world scenarios.

Matching Neuromorphic Events and Color Images via Adversarial Learning

The event camera has appealing properties: high dynamic range, low latency, low power consumption and low memory usage, and thus provides complementariness to conventional frame-based cameras. It only captures the dynamics of a scene and is able to capture almost "continuous" motion. However, different from frame-based camera that reflects the whole appearance as scenes are, the event camera casts away the detailed characteristics of objects, such as texture and color. To take advantages of both modalities, the event camera and frame-based camera are combined together for various machine vision tasks. Then the cross-modal matching between neuromorphic events and color images plays a vital and essential role. In this paper, we propose the Event-Based Image Retrieval (EBIR) problem to exploit the cross-modal matching task. Given an event stream depicting a particular object as query, the aim is to retrieve color images containing the same object. This problem is challenging because there exists a large modality gap between neuromorphic events and color images. We address the EBIR problem by proposing neuromorphic Events-Color image Feature Learning (ECFL). Particularly, the adversarial learning is employed to jointly model neuromorphic events and color images into a common embedding space. We also contribute to the community N-UKbench and EC180 dataset to promote the development of EBIR problem. Extensive experiments on our datasets show that the proposed method is superior in learning effective modality-invariant representation to link two different modalities.

Continuous Dropout

Dropout has been proven to be an effective algorithm for training robust deep networks because of its ability to prevent overfitting by avoiding the co-adaptation of feature detectors. Current explanations of dropout include bagging, naive Bayes, regularization, and sex in evolution. According to the activation patterns of neurons in the human brain, when faced with different situations, the firing rates of neurons are random and continuous, not binary as current dropout does. Inspired by this phenomenon, we extend the traditional binary dropout to continuous dropout. On the one hand, continuous dropout is considerably closer to the activation characteristics of neurons in the human brain than traditional binary dropout. On the other hand, we demonstrate that continuous dropout has the property of avoiding the co-adaptation of feature detectors, which suggests that we can extract more independent feature detectors for model averaging in the test stage. We introduce the proposed continuous dropout to a feedforward neural network and comprehensively compare it with binary dropout, adaptive dropout, and DropConnect on MNIST, CIFAR-10, SVHN, NORB, and ILSVRC-12. Thorough experiments demonstrate that our method performs better in preventing the co-adaptation of feature detectors and improves test performance. The code is available at: https://github.com/jasonustc/caffe-multigpu/tree/dropout.