18 papers · ranked by Valyu relevance
Patrick Kaifosh, Jeffrey D. Zaremba, Nathan B. Danielson, Attila Losonczy
'Attila Losonczy'] Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python…
Jixiong Su, Shoupei Liu, Shasha Yang, Yanfeng Zhu + 7 more
Three-photon microscopy (3PM) has extended optical imaging beyond the reach of two-photon microscopy (2PM), but its practical depth remains far below theoretical predictions because of low photon efficiency and severe noise contamination. Here we present an integrated hardware and software solution that addresses these…
Yi-An A. Chen, Lars Kasper, Clement T. Chow, Alexandre Boutet + 5 more
Accurate registration of regions of interest (ROIs) from standard atlases to participants’ native spaces is a critical step in fMRI studies, as it directly affects the reliability of sampled BOLD signals. While T1-weighted (T1w) image-based ROI registration is well validated and widely adopted in cortical fMRI, its…
Shiqi Huang, Tingfa Xu, Ziyi Shen, Shaheer Ullah Saeed + 3 more
'Dean C. Barratt' 'Yipeng Hu'] This paper describes a new spatial correspondence representation based on paired regions-of-interest (ROIs), for medical image registration. The distinct properties of the proposed ROI-based correspondence are discussed, in the context of potential benefits in clinical applications…
Yi-An A. Chen, Lars Kasper, Clement T. Chow, Yu Kuo + 6 more
Accurate registration of regions of interest (ROIs) from standard atlases to participants’ native spaces is a critical step in fMRI studies, as it directly affects the reliability of sampled BOLD signals. While T1-weighted (T1w) image-based ROI registration is well validated and widely adopted in cortical fMRI, its…
Shiqi Huang, Tingfa Xu, Wen Yan, Dean Barratt + 1 more
Establishing pixel/voxel-level or region-level correspondences is the core challenge in image registration. The latter, also known as region-based correspondence representation, leverages paired regions of interest (ROIs) to enable regional matching while preserving fine-grained capability at pixel/voxel level.…
Shiqi Huang, Tingfa Xu, Ziyi Shen, Shaheer Ullah Saeed + 3 more
'Dean C. Barratt' 'Yipeng Hu'] Abstract. The goal of image registration is to establish spatial correspondence between two or more images, traditionally through dense displacement fields (DDFs) or parametric transformations (e.g., rigid, affine, and splines). Rethinking the existing paradigms of achieving alignment via…
Rosalia Tatano, Benjamin Berkels, Thomas M. Deserno
Region of interest (ROI) alignment in medical images plays a crucial role in diagnostics, procedure planning, treatment, and follow-up. Frequently, a model is represented as triangulated mesh while the patient data is provided from CAT scanners as pixel or voxel data. Previously, we presented a 2D method for…
Kohki Konishi, Guilherme Neves, Matthew Russell, Masafumi Mimura + 2 more
Electron microscopy is essential for the quantitative study of synaptic ultrastructure. At present, the correlation of functional and structural properties of the same synapse is extremely challenging. We introduce a novel integrated workflow designed to simplify sample navigation across spatial scales, allowing the…
Kohki Konishi, Guilherme Neves, Matthew Russell, Masafumi Mimura + 2 more
Volume Correlative Light and Electron Microscopy (vCLEM) is a powerful method for assessing the ultrastructure of molecularly defined subcellular domains. A central challenge in vCLEM has been the efficient navigation of Regions of Interest (ROIs) across multimodal and multiscale imaging datasets. We developed two key…
Changjin Sun, Fei Tong, Junjie Luo, Yuting Wang + 9 more
Rapid localization of ROI (Region of Interest) for tomographic medical images (TMIs) is an important foundation for efficient image reading, computer-aided education, and well-informed rights of patients. However, due to the multimodality of clinical TMIs, the complexity of anatomy, and the deformation of organs caused…
Xuetong Zhai, Hendrik Santosa, Theodore J. Huppert
Significance: Functional near-infrared spectroscopy (fNIRS) uses surface-placed light sources and detectors to record underlying changes in the brain due to fluctuations in hemoglobin levels and oxygenation. Since these measurements are recorded from the surface of the scalp, the mapping from underlying…
M Paknezhad, Sheng Yang Michael Loh, Yukti Choudhury, Valerie Koh Cui Koh + 10 more
'Valerie Koh Cui Koh' 'TimothyTay Kwang Yong' 'Hui Shan Tan' 'Ravindran Kanesvaran' 'Puay Hoon Tan' 'John Yuen Shyi Peng' 'Weimiao Yu' 'Yongcheng Benjamin Tan' 'Yong Zhen Loy' 'Min‐Han Tan' 'Hwee Kuan Lee'] Motivation High resolution 2D whole slide imaging provides rich information about the tissue structure. This…
Tim‐Oliver Sauer, Oliver J. Ott, Godehard Lahmer, Rainer Fietkau + 1 more
4.1.1#### Phantom study The differences between individual DOFs in the phantom study are not interpreted as easily. It is conceivable that they originate from systematic inaccuracies either of the surface scanner, or the position of the Hexapod couch. The latter was taken as the reference in this study, although it is…
Nicholas Hardcastle, Wolfgang A Tomé, Donald M Cannon, Charlotte L Brouwer + 12 more
'Charlotte L Brouwer' 'Paul WH Wittendorp' 'Nesrin Dogan' 'Matthias Guckenberger' 'Stéphane Allaire' 'Yogish Mallya' 'Prashant Kumar' 'Markus Oechsner' 'Anne Richter' 'Shiyu Song' 'Michael Myers' 'Bülent Polat' 'Karl Bzdusek'] Background Adaptive Radiotherapy aims to identify anatomical deviations during a radiotherapy…
Gregory A. Landrum, Jessica Braun, Paul Katzberger, Marc T. Lehner + 1 more
Here, we present lwreg, a lightweight, yet flexible chemical registration system supporting the capture of both two-dimensional molecular structures (topologies) and three-dimensional conformers. lwreg is open source, with a simple Python API and is designed to be easily integrated into computational workflows. In…
Timothy L. Kline
In a wide variety of fields, analysis of images involves defining a region and measuring its inherent properties. Such measurements include a region's surface area, curvature, volume, average gray and/or color scale, and so on. Furthermore, the subsequent subdivision of these regions is sometimes performed. These…
Jeaphianne van Rijn, Antreas Afantitis, Mustafa Culha, Maria Dusinska + 10 more
Data management of nanomaterials and nanosafety data needs to operate under the FAIR (findability, accessibility, interoperability, and reusability) principles and this requires a unique, global identifier per nanomaterial. Existing identifiers may not always be applicable, or sufficient to definitively identify the…