Related papers: The XPRESS Challenge: Xray Projectomic Reconstruct…

Deep convolutional neural networks are powerful tools for learning visual representations from images. However, designing efficient deep architectures to analyse volumetric medical images remains challenging. This work investigates…

For the past decade, convolutional networks have been used for 3D reconstruction of neurons from electron microscopic (EM) brain images. Recent years have seen great improvements in accuracy, as evidenced by submissions to the SNEMI3D…

Segmenting both bone surface and the corresponding acoustic shadow are fundamental tasks in ultrasound (US) guided orthopedic procedures. However, these tasks are challenging due to minimal and blurred bone surface response in US images,…

Automation of brain tumor segmentation in 3D magnetic resonance images (MRIs) is key to assess the diagnostic and treatment of the disease. In recent years, convolutional neural networks (CNNs) have shown improved results in the task.…

Developing automated and semi-automated solutions for reconstructing wiring diagrams of the brain from electron micrographs is important for advancing the field of connectomics. While the ultimate goal is to generate a graph of neuron…

Methods for resolving the 3D microstructure of the brain typically start by thinly slicing and staining the brain, and then imaging each individual section with visible light photons or electrons. In contrast, X-rays can be used to image…

Reconstructing a map of neuronal connectivity is a critical challenge in contemporary neuroscience. Recent advances in high-throughput serial section electron microscopy (EM) have produced massive 3D image volumes of nanoscale brain tissue…

Being able to adequately process and combine data arising from different sites is crucial in neuroimaging, but is difficult, owing to site, sequence and acquisition-parameter dependent biases. It is important therefore to design algorithms…

This paper explores the use of a soft ground-truth mask ("soft mask'') to train a Fully Convolutional Neural Network (FCNN) for segmentation of Multiple Sclerosis (MS) lesions. Detection and segmentation of MS lesions is a complex task…

Mammalian whole-brain connectomes are a foundational ingredient for holistic understanding of brains. Indeed, imaging connectomes at sufficient resolution to densely reconstruct cellular morphology and synapses represents a longstanding…

Convolutional Neural Networks (CNNs) and Vision Transformers (ViT) have been pivotal in biomedical image segmentation, yet their ability to manage long-range dependencies remains constrained by inherent locality and computational overhead.…

Morphology of mitochondria plays critical roles in mediating their physiological functions. Accurate segmentation of mitochondria from 3D electron microscopy (EM) images is essential to quantitative characterization of their morphology at…

Accurate segmentation of neural structures in Electron Microscopy (EM) images is paramount for neuroscience. However, this task is challenged by intricate morphologies, low signal-to-noise ratios, and scarce annotations, limiting the…

There are multiple scales of abstraction from which we can describe the same image, depending on whether we are focusing on fine-grained details or a more global attribute of the image. In brain mapping, learning to automatically parse…

Identifying complex neural circuitry from electron microscopic (EM) images may help unlock the mysteries of the brain. However, identifying this circuitry requires time-consuming, manual tracing (proofreading) due to the size and intricacy…

Precise 3D segmentation of infant brain tissues is an essential step towards comprehensive volumetric studies and quantitative analysis of early brain developement. However, computing such segmentations is very challenging, especially for…

We show dense voxel embeddings learned via deep metric learning can be employed to produce a highly accurate segmentation of neurons from 3D electron microscopy images. A "metric graph" on a set of edges between voxels is constructed from…

The morbidity of brain stroke increased rapidly in the past few years. To help specialists in lesion measurements and treatment planning, automatic segmentation methods are critically required for clinical practices. Recently, approaches…

Deep learning models are increasingly used for radiographic analysis, but their reliability is challenged by the stochastic noise inherent in clinical imaging. A systematic, cross-task understanding of how different noise types impact these…

Neuron reconstruction, one of the fundamental tasks in neuroscience, rebuilds neuronal morphology from 3D light microscope imaging data. It plays a critical role in analyzing the structure-function relationship of neurons in the nervous…