Connectomics, a subfield of neuroscience, aims to map and analyze synapse-level wiring diagrams of the nervous system. While recent advances in deep learning have accelerated automated neuron and synapse segmentation, reconstructing accurate connectomes still demands extensive human proofreading to correct segmentation errors. We present SynAnno, an interactive tool designed to streamline and enhance the proofreading of synaptic annotations in large-scale connectomics datasets. SynAnno integrates into existing neuroscience workflows by enabling guided, neuron-centric proofreading. To address the challenges posed by the complex spatial branching of neurons, it introduces a structured workflow with an optimized traversal path and a 3D mini-map for tracking progress. In addition, SynAnno incorporates fine-tuned machine learning models to assist with error detection and correction, reducing the manual burden and increasing proofreading efficiency. We evaluate SynAnno through a user and case study involving seven neuroscience experts. Results show that SynAnno significantly accelerates synapse proofreading while reducing cognitive load and annotation errors through structured guidance and visualization support. The source code and interactive demo are available at: https://github.com/PytorchConnectomics/SynAnno.

Multi-modality (MM) image fusion aims to render fused images that maintain the merits of different modalities, e.g., functional highlight and detailed textures. To tackle the challenge in modeling cross-modality features and decomposing desirable modality-specific and modality-shared features, we propose a novel Correlation-Driven feature Decomposition Fusion (CDDFuse) network. Firstly, CDDFuse uses Restormer blocks to extract cross-modality shallow features. We then introduce a dual-branch Transformer-CNN feature extractor with Lite Transformer (LT) blocks leveraging long-range attention to handle low-frequency global features and Invertible Neural Networks (INN) blocks focusing on extracting high-frequency local information. A correlation-driven loss is further proposed to make the low-frequency features correlated while the high-frequency features uncorrelated based on the embedded information. Then, the LT-based global fusion and INN-based local fusion layers output the fused image. Extensive experiments demonstrate that our CDDFuse achieves promising results in multiple fusion tasks, including infrared-visible image fusion and medical image fusion. We also show that CDDFuse can boost the performance in downstream infrared-visible semantic segmentation and object detection in a unified benchmark. The code is available at https://github.om/haozixiang1228/MMIF-CDDFuse.

Multimodal representation learning for images with paired raw texts can improve the usability and generality of the learned semantic concepts while significantly reducing annotation costs. In this paper, we explore the design space of loss functions in visual-linguistic pretraining frameworks and propose a novel Relaxed Contrastive (ReCo) objective, which act as a drop-in replacement of the widely used InfoNCE loss. The key insight of ReCo is to allow a relaxed negative space by not penalizing unpaired multimodal samples (i.e., negative pairs) that are already orthogonal or negatively correlated. Unlike the widely-used InfoNCE, which keeps repelling negative pairs as long as they are not anti-correlated, ReCo by design embraces more diversity and flexibility of the learned embeddings. We conduct exten-sive experiments using ReCo with state-of-the-art models by pretraining on the MIMIC-CXR dataset that consists of chest radiographs and free-text radiology reports, and eval-uating on the CheXpert dataset for multimodal retrieval and disease classification. Our ReCo achieves an absolute improvement of 2.9% over the InfoNCE baseline on the CheXpert Retrieval dataset in average retrieval precision and re-ports better or comparable performance in the linear evaluation and finetuning for classification. We further show that ReCo outperforms InfoNCE on the Flickr30K dataset by 1.7% in retrieval Recall@1, demonstrating the generalizability of our approach to natural images.

Unpaired image-to-image translation (UNIT) aims to map images between two visual domains without paired training data. However, given a UNIT model trained on certain domains, it is difficult for current methods to incorporate new domains because they often need to train the full model on both existing and new domains. To address this problem, we propose a new domain-scalable UNIT method, termed as latent space anchoring, which can be efficiently extended to new visual domains and does not need to fine-tune encoders and decoders of existing domains. Our method anchors images of different domains to the same latent space of frozen GANs by learning lightweight encoder and regressor models to reconstruct single-domain images. In the inference phase, the learned encoders and decoders of different domains can be arbitrarily combined to translate images between any two domains without fine-tuning. Experiments on various datasets show that the proposed method achieves superior performance on both standard and domain-scalable UNIT tasks in comparison with the state-of-the-art methods.

3D instance segmentation for unlabeled imaging modalities is a challenging but essential task as collecting expert annotation can be expensive and time-consuming. Existing works segment a new modality by either deploying pre-trained models optimized on diverse training data or sequentially conducting image translation and segmentation with two relatively independent networks. In this work, we propose a novel Cyclic Segmentation Generative Adversarial Network (CySGAN) that conducts image translation and instance segmentation simultaneously using a unified network with weight sharing. Since the image translation layer can be removed at inference time, our proposed model does not introduce additional computational cost upon a standard segmentation model. For optimizing CySGAN, besides the CycleGAN losses for image translation and supervised losses for the annotated source domain, we also utilize self-supervised and segmentation-based adversarial objectives to enhance the model performance by leveraging unlabeled target domain images. We benchmark our approach on the task of 3D neuronal nuclei segmentation with annotated electron microscopy (EM) images and unlabeled expansion microscopy (ExM) data. The proposed CySGAN outperforms pre-trained generalist models, feature-level domain adaptation models, and the baselines that conduct image translation and segmentation sequentially. Our implementation and the newly collected, densely annotated ExM zebrafish brain nuclei dataset, named NucExM, are publicly available at https://connectomics-bazaar.github.io/proj/CySGAN/index.html.

In this paper, we present the results of the MitoEM challenge on mitochondria 3D instance segmentation from electron microscopy images, organized in conjunction with the IEEE-ISBI 2021 conference. Our benchmark dataset consists of two large-scale 3D volumes, one from human and one from rat cortex tissue, which are 1,986 times larger than previously used datasets. At the time of paper submission, 257 participants had registered for the challenge, 14 teams had submitted their results, and six teams participated in the challenge workshop. Here, we present eight top-performing approaches from the challenge participants, along with our own baseline strategies. Posterior to the challenge, annotation errors in the ground truth were corrected without altering the final ranking. Additionally, we present a retrospective evaluation of the scoring system which revealed that: 1) challenge metric was permissive with the false positive predictions; and 2) size-based grouping of instances did not correctly categorize mitochondria of interest. Thus, we propose a new scoring system that better reflects the correctness of the segmentation results. Although several of the top methods are compared favorably to our own baselines, substantial errors remain unsolved for mitochondria with challenging morphologies. Thus, the challenge remains open for submission and automatic evaluation, with all volumes available for download.

Many video understanding tasks require analyzing multishot videos, but existing datasets for video object segmentation (VOS) only consider single-shot videos. To address this challenge, we collected a new dataset-YouMVaS-of 200 popular YouTube videos spanning ten genres, where each video is on average five minutes long and with 75 shots. We selected recurring actors and annotated 431K segmentation masks at a frame rate of six, exceeding previous datasets in average video duration, object variation, and narrative structure complexity. We incorporated good practices of model architecture design, memory management, and multi-shot tracking into an existing video segmentation method to build competitive baseline methods. Through error analysis, we found that these baselines still fail to cope with cross-shot appearance variation on our YouMVOS dataset. Thus, our dataset poses new challenges in multi-shot segmentation towards better video analysis. Data, code, and pre-trained models are available at https://donglaiw.github.io/proj/youMVOS

Evaluation practices for image super-resolution (SR) use a single-value metric, the PSNR or SSIM, to determine model performance. This provides little insight into the source of errors and model behavior. Therefore, it is beneficial to move beyond the conventional approach and reconceptualize evaluation with interpretability as our main priority. We focus on a thorough error analysis from a variety of perspectives. Our key contribution is to leverage a texture classifier, which enables us to assign patches with semantic labels, to identify the source of SR errors both globally and locally. We then use this to determine (a) the semantic alignment of SR datasets, (b) how SR models perform on each label, (c) to what extent high-resolution (HR) and SR patches semantically correspond, and more. Through these different angles, we are able to highlight potential pitfalls and blindspots. Our overall investigation highlights numerous unexpected insights. We hope this work serves as an initial step for debugging blackbox SR networks.

Guided depth super-resolution (GDSR) is an essential topic in multi-modal image processing, which reconstructs high-resolution (HR) depth maps from low-resolution ones collected with suboptimal conditions with the help of HR RGB images of the same scene. To solve the challenges in interpreting the working mechanism, extracting cross-modal features and RGB texture over-transferred, we propose a novel Discrete Cosine Transform Network (DCTNet) to alleviate the problems from three aspects. First, the Discrete Cosine Transform (DCT) module reconstructs the multi-channel HR depth features by using DCT to solve the channel-wise optimization problem derived from the image domain. Second, we introduce a semi-coupled feature extraction module that uses shared convolutional kernels to extract common information and private kernels to extract modality-specific information. Third, we employ an edge attention mechanism to highlight the contours informative for guided upsampling. Extensive quantitative and qualitative evaluations demonstrate the effectiveness of our DCTNet, which outperforms previous state-of-the-art methods with a relatively small number of parameters. The code is available at https://github.com/Zhaozixiang1228/GDSR-DCTNet.

Deep convolutional neural networks (CNNs) have pushed forward the frontier of super-resolution (SR) research. However, current CNN models exhibit a major flaw: they are biased towards learning low-frequency signals. This bias becomes more problematic for the image SR task which targets reconstructing all fine details and image textures. To tackle this challenge, we propose to improve the learning of high-frequency features both locally and globally and introduce two novel architectural units to existing SR models. Specifically, we propose a dynamic highpass filtering (HPF) module that locally applies adaptive filter weights for each spatial location and channel group to preserve high-frequency signals. We also propose a matrix multi-spectral channel attention (MMCA) module that predicts the attention map of features decomposed in the frequency domain. This module operates in a global context to adaptively recalibrate feature responses at different frequencies. Extensive qualitative and quantitative results demonstrate that our proposed modules achieve better accuracy and visual improvements against state-of-the-art methods on several benchmark datasets.

Segmenting 3D cell nuclei from microscopy image volumes is critical for biological and clinical analysis, enabling the study of cellular expression patterns and cell lineages. However, current datasets for neuronal nuclei usually contain volumes smaller than $10^{\text{-}3}\ mm^3$ with fewer than 500 instances per volume, unable to reveal the complexity in large brain regions and restrict the investigation of neuronal structures. In this paper, we have pushed the task forward to the sub-cubic millimeter scale and curated the NucMM dataset with two fully annotated volumes: one $0.1\ mm^3$ electron microscopy (EM) volume containing nearly the entire zebrafish brain with around 170,000 nuclei; and one $0.25\ mm^3$ micro-CT (uCT) volume containing part of a mouse visual cortex with about 7,000 nuclei. With two imaging modalities and significantly increased volume size and instance numbers, we discover a great diversity of neuronal nuclei in appearance and density, introducing new challenges to the field. We also perform a statistical analysis to illustrate those challenges quantitatively. To tackle the challenges, we propose a novel hybrid-representation learning model that combines the merits of foreground mask, contour map, and signed distance transform to produce high-quality 3D masks. The benchmark comparisons on the NucMM dataset show that our proposed method significantly outperforms state-of-the-art nuclei segmentation approaches. Code and data are available at https://connectomics-bazaar.github.io/proj/nucMM/index.html.