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Dynamic imaging is essential for analyzing various biological systems and behaviors but faces two main challenges: data incompleteness and computational burden. For many imaging systems, high frame rates and short acquisition times require…
The 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses…
Unrolled neural networks have recently achieved state-of-the-art accelerated MRI reconstruction. These networks unroll iterative optimization algorithms by alternating between physics-based consistency and neural-network based…
Histology has long been a foundational technique for studying anatomical structures through tissue slicing. Advances in computational methods now enable three dimensional (3D) reconstruction of organs from histology images, enhancing the…
Structural reconstruction of plant roots from MRI is challenging, because of low resolution and low signal-to-noise ratio of the 3D measurements which may lead to disconnectivities and wrongly connected roots. We propose a two-stage…
Computer-generated holography (CGH) is a promising method that modulates user-defined waveforms with digital holograms. An efficient and fast pipeline framework is proposed to synthesize CGH using initial point cloud and MRI data. This…
Surface analysis of the cortex is ubiquitous in human neuroimaging with MRI, e.g., for cortical registration, parcellation, or thickness estimation. The convoluted cortical geometry requires isotropic scans (e.g., 1mm MPRAGEs) and good…
Gliomas are the most common primary brain tumors, evolving from the cerebral supportive cells. For clinical follow-up, the evaluation of the preoperative tumor volume is essential. Volumetric assessment of tumor volume with manual…
3D reconstruction of the fiber connectivity of the rat brain at microscopic scale enables gaining detailed insight about the complex structural organization of the brain. We introduce a new method for registration and 3D reconstruction of…
Magnetic Resonance Imaging (MRI) is a technology for non-invasive imaging of anatomical features in detail. It can help in functional analysis of organs of a specimen but it is very costly. In this work, methods for (i) virtual…
We propose an automatic 3D segmentation algorithm for multiphoton microscopy images of microglia. Our method is capable of segmenting tubular and blob-like structures from noisy images. Current segmentation techniques and software fail to…
The skeleton is an essential shape characteristic providing a compact representation of the studied shape. Its computation on the image grid raises many issues. Due to the effects of discretization, the required properties of the skeleton -…
Magnetic resonance imaging (MRI) is one of the noninvasive imaging modalities that can produce high-quality images. However, the scan procedure is relatively slow, which causes patient discomfort and motion artifacts in images. Accelerating…
Phase recovery from intensity-only measurements forms the heart of coherent imaging techniques and holography. Here we demonstrate that a neural network can learn to perform phase recovery and holographic image reconstruction after…
3D stylization, the application of specific styles to three-dimensional objects, offers substantial commercial potential by enabling the creation of uniquely styled 3D objects tailored to diverse scenes. Recent advancements in artificial…
We propose an holographic microscopy reconstruction method, which propagates the hologram, in the object half space, in the vicinity of the object. The calibration yields reconstructions with an undistorted reconstruction grid i.e. with…
Multiscale shape skeletonization on pixel adjacency graphs is an advanced intriguing research subject in the field of image processing, computer vision and data mining. The previous works in this area almost focused on the graph vertices.…
Automated quality assessment of structural brain MRI is an important prerequisite for reliable neuroimaging analysis, but yet remains challenging due to motion artifacts and poor generalization across acquisition sites. Existing approaches…
Ptychography is an emerging imaging technique that is able to provide wavelength-limited spatial resolution from specimen with extended lateral dimensions. As a scanning microscopy method, a typical two-dimensional image requires a number…
In 3-D reconstruction problems, the image data obtained from cryo electron microscopy is the projection of many heterogeneous instances of the object under study (e.g., a virus). When the object is heterogeneous but has an overall symmetry,…