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The 3D characterization of microstructures is crucial for understanding and designing functional materials. However, the scanning electron microscope (SEM), widely used in scientific research, captures only 2D electron intensity…

Accurately registering in-vivo two-photon and ex-vivo fluorescence micro-optical sectioning tomography images of individual neurons is critical for structure-function analysis in neuroscience. This task is profoundly challenging due to a…

Volumetric medical image segmentation is pivotal in enhancing disease diagnosis, treatment planning, and advancing medical research. While existing volumetric foundation models for medical image segmentation, such as SAM-Med3D and SegVol,…

Foundation segmentation models such as SAM and SAM-2 perform well on natural images but struggle with brain MRIs where structures like the caudate and thalamus lack sharp boundaries and have low contrast. Rather than fine tune these models…

Neuroanatomical segmentation in magnetic resonance imaging (MRI) of the brain is a prerequisite for volume, thickness and shape measurements. This work introduces a new highly accurate and versatile method based on 3D convolutional neural…

Efforts to automate the reconstruction of neural circuits from 3D electron microscopic (EM) brain images are critical for the field of connectomics. An important computation for reconstruction is the detection of neuronal boundaries. Images…

In the past five years, the use of generative and foundational AI systems has greatly improved the decoding of brain activity. Visual perception, in particular, can now be decoded from functional Magnetic Resonance Imaging (fMRI) with…

Motivation: 3D neuron segmentation is a key step for the neuron digital reconstruction, which is essential for exploring brain circuits and understanding brain functions. However, the fine line-shaped nerve fibers of neuron could spread in…

This paper presents a new ambient light normalization framework, DINOLight, that integrates the self-supervised model DINOv2's image understanding capability into the restoration process as a visual prior. Ambient light normalization aims…

Unsupervised domain adaptation (UDA) is vital for alleviating the workload of labeling 3D point cloud data and mitigating the absence of labels when facing a newly defined domain. Various methods of utilizing images to enhance the…

Maps of brain microarchitecture are important for understanding neurological function and behavior, including alterations caused by chronic conditions such as neurodegenerative disease. Techniques such as knife-edge scanning microscopy…

Medical image segmentation is crucial for clinical decision-making, but the scarcity of annotated data presents significant challenges. Few-shot segmentation (FSS) methods show promise but often require training on the target domain and…

Domain shift presents a significant challenge in applying Deep Learning to the segmentation of 3D medical images from sources like Magnetic Resonance Imaging (MRI) and Computed Tomography (CT). Although numerous Domain Adaptation methods…

We present Neural Kernel Fields: a novel method for reconstructing implicit 3D shapes based on a learned kernel ridge regression. Our technique achieves state-of-the-art results when reconstructing 3D objects and large scenes from sparse…

Deep learning affords enormous opportunities to augment the armamentarium of biomedical imaging, albeit its design and implementation have potential flaws. Fundamentally, most deep learning models are driven entirely by data without…

The neuron reconstruction from raw Optical Microscopy (OM) image stacks is the basis of neuroscience. Manual annotation and semi-automatic neuron tracing algorithms are time-consuming and inefficient. Existing deep learning neuron…

We propose a segmentation framework that uses deep neural networks and introduce two innovations. First, we describe a biophysics-based domain adaptation method. Second, we propose an automatic method to segment white and gray matter, and…

AI-enhanced segmentation of neuronal boundaries in electron microscopy (EM) images is crucial for automatic and accurate neuroinformatics studies. To enhance the limited generalization ability of typical deep learning frameworks for medical…

There is substantial interest in developing artificial intelligence systems to support radiologists across tasks ranging from segmentation to report generation. Existing computed tomography (CT) foundation models have largely focused on…

Analysis and visualization of 3D microscopy images pose challenges due to anisotropic axial resolution, demanding volumetric super-resolution along the axial direction. While training a learning-based 3D super-resolution model seems to be a…