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Whole brain segmentation on structural magnetic resonance imaging (MRI) is essential for understanding neuroanatomical-functional relationships. Traditionally, multi-atlas segmentation has been regarded as the standard method for whole…
We present a numerically efficient method to reconstruct a disordered network of thin biopolymers, such as collagen gels, from three-dimensional (3D) image stacks recorded with a confocal microscope. Our method is based on a template…
Magnetic resonance imaging (MRI) has great potential to improve prostate cancer diagnosis. It can spare men with a normal exam from undergoing invasive biopsy while making biopsies more accurate in men with lesions suspicious for cancer.…
Three-dimensional (3D) ultrasound imaging can overcome the limitations of conventional two dimensional (2D) ultrasound imaging in structural observation and measurement. However, conducting volumetric ultrasound imaging for large-sized…
The root is an important organ of a plant since it is responsible for water and nutrient uptake. Analyzing and modelling variabilities in the geometry and topology of roots can help in assessing the plant's health, understanding its growth…
Accurate estimation of plant skeletal structures (e.g., branching structures) from images is essential for smart agriculture and plant science. Unlike human skeletons with fixed topology, plant skeleton estimation presents a unique…
While multislice electron ptychography can provide thermal-vibration limited resolution and 3D information, it relies on the proper selection of many intertwined experimental and computational parameters. Here, we outline a theoretical…
Planning of radiotherapy involves accurate segmentation of a large number of organs at risk, i.e. organs for which irradiation doses should be minimized to avoid important side effects of the therapy. We propose a deep learning method for…
A detailed analysis of ptychography for 3D phase reconstructions of thick specimens is performed. We introduce multi-focus ptychography, which incorporates a 4D-STEM defocus series to enhance the quality of 3D reconstructions along the beam…
Tracking of plant cells in images obtained by microscope is a challenging problem due to biological phenomena such as large number of cells, non-uniform growth of different layers of the tightly packed plant cells and cell division.…
Automatic 3D reconstruction of glia morphology is a powerful tool necessary for investigating the role of microglia in neurological disorders in the central nervous system. Current glia skeleton reconstruction techniques fail to capture an…
Accurately localizing and identifying vertebrae from CT images is crucial for various clinical applications. However, most existing efforts are performed on 3D with cropping patch operation, suffering from the large computation costs and…
Reconstructing deformable endoscopic tissues is crucial for achieving robot-assisted surgery. However, 3D Gaussian Splatting-based approaches encounter challenges in achieving consistent tissue surface reconstruction, while existing…
The goal of MRI reconstruction is to restore a high fidelity image from partially observed measurements. This partial view naturally induces reconstruction uncertainty that can only be reduced by acquiring additional measurements. In this…
We address 2D floorplan reconstruction from 3D scans. Existing approaches typically employ heuristically designed multi-stage pipelines. Instead, we formulate floorplan reconstruction as a single-stage structured prediction task: find a…
This work focuses on the 3D reconstruction of non-rigid objects based on monocular RGB video sequences. Concretely, we aim at building high-fidelity models for generic object categories and casually captured scenes. To this end, we do not…
Registration of histological serial sections is a challenging task. Serial sections exhibit distortions and damage from sectioning. Missing information on how the tissue looked before cutting makes a realistic validation of 2D registrations…
High-resolution non-invasive 3D study of intact spine and spinal cord morphology on the level of complex vascular and neuronal organization is a crucial issue for the development of treatments for the injuries and pathologies of central…
X-ray angiography is widely used in cardiac interventions to visualize coronary vessels, assess integrity, detect stenoses and guide treatment. We propose a framework for reconstructing 3D vessel trees from biplanar X-ray images which are…
Patient-specific bone models are essential for designing surgical guides and preoperative planning, as they enable the visualization of intricate anatomical structures. However, traditional CT-based approaches for creating bone models are…