Review
Multidisciplinary Sciences
Trygve B. Leergaard, Jan G. Bjaalie
Summary: Understanding neural connections in the brain is crucial for studying normal brain function, aging, and disease. Researchers use experimental techniques to map connections in rodent models but face challenges in comparing and integrating results. Three-dimensional brain atlases provide a new opportunity for accumulating and reinterpreting research findings.
Article
Multidisciplinary Sciences
Harry Carey, Michael Pegios, Lewis Martin, Chris Saleeba, Anita J. Turner, Nicholas A. Everett, Ingvild E. Bjerke, Maja A. Puchades, Jan G. Bjaalie, Simon Mcmullan
Summary: Registration of data to a common frame of reference is crucial in analyzing and integrating diverse neuroscientific data. The traditional methods for registration are time-consuming and rely on expertise. However, using the neural network DeepSlice, we were able to significantly improve the speed while maintaining the accuracy of registering mouse brain histological images to the Allen Brain Common Coordinate Framework.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Fabian Schadt, Ina Israel, Alexandra Beez, Kastriot Alushi, Judith Weiland, Ralf-Ingo Ernestus, Thomas Westermaier, Samuel Samnick, Nadine Lilla
Summary: Little is known about changes in brain metabolism following SAH, possibly leading towards secondary brain damage. Despite sustained progress in the last decade, analysis of in vivo acquired data still remains challenging. This [F-18]FDG-PET study provides important insights into glucose metabolism alterations following SAH-for the first time in different brain regions and up to day 7 during course of disease.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Camilla H. Blixhavn, Finn-Mogens S. Haug, Heidi Kleven, Maja A. Puchades, Jan G. Bjaalie, Trygve B. Leergaard
Summary: The Timm's sulphide silver method can be used as a neuromorphological marker to stain zincergic terminal fields. In addition to visualizing zincergic terminal fields, the method also labels transition metals in neuronal perikarya and glial cells. We have established a comprehensive repository of microscopic images of rat brain sections stained with Timm's method to provide a benchmark reference for experimental investigations of zinc-related phenomena.
Article
Engineering, Multidisciplinary
Tian -fan Zhang, Zhe Li, Qi Yuan, You-ning Wang
Summary: Image classification aims to understand the attributes and features of each object in the scene by assigning them to predefined categories, and further explores the potential features and internal connections of the data. However, accurately classifying sparse data, especially small objects in images, is a challenge. This paper presents a spatial distance-based spatial clustering algorithm to address the issue of feature sparsity and imbalance in image data.
ALEXANDRIA ENGINEERING JOURNAL
(2022)
Article
Neurosciences
Sang-Jin Im, Ji-Yeon Suh, Jae-Hyuk Shim, Hyeon-Man Baek
Summary: Preclinical studies using rodents have been popular among neuroscience researchers for their close reflection of human biology. While MRI technology has been utilized to accurately identify brain regions in rodents, the analysis methods in this field are not as well-developed compared to those for human subjects. This study introduces a deterministic tractographic analysis pipeline for detailed structural segmentation and connectivity analysis of the rat brain, which has been preliminarily tested on normal and stroke rat models.
Article
Computer Science, Artificial Intelligence
Matthew Sinclair, Andreas Schuh, Karl Hahn, Kersten Petersen, Ying Bai, James Batten, Michiel Schaap, Ben Glocker
Summary: This paper proposes a framework called Atlas-ISTN, which simultaneously learns segmentation and registration and constructs a population-derived atlas. The framework addresses the issue of noise in target images and improves the model's predictive performance. Experimental results on synthetic data and medical images demonstrate that the framework outperforms baseline models.
MEDICAL IMAGE ANALYSIS
(2022)
Article
Biochemical Research Methods
Heidi Kleven, Ingvild E. Bjerke, Francisco Clasca, Henk J. Groenewegen, Jan G. Bjaalie, Trygve B. Leergaard
Summary: This paper presents an updated rat brain atlas, which provides annotations of 222 structures and detailed maps of various brain regions, supporting the interpretation and analysis of experimental rat brain data.
Article
Neurosciences
Liangjun Chen, Zhengwang Wu, Dan Hu, Ya Wang, Fenqiang Zhao, Tao Zhong, Weili Lin, Li Wang, Gang Li
Summary: This paper constructs a four-dimensional brain atlas based on infant brain MR images, which has a high spatiotemporal resolution and preserves more structural details. It greatly improves the accuracy of neurodevelopmental analysis during infancy.
Article
Neurosciences
G. Allan Johnson, Rick Laoprasert, Robert J. Anderson, Gary Cofer, James Cook, Forrest Pratson, Leonard E. White
Summary: A multi-contrast, multi-dimensional atlas of the Wistar rat was created using magnetic resonance histology (MRH), providing microscopic spatial resolution and improved visualization of fiber architecture, orientation distribution, and crossing fibers. The use of multi-gradient echo images and compressed sensing for multiple specimens enhanced contrast and aided in anatomical delineation, offering potential for automated label registration in MR histology and preclinical imaging.
Review
Medicine, Research & Experimental
Enrico Capobianco, Marco Dominietto
Summary: This review discusses the potential applications of using multimodal imaging, radiomic data processing, and brain atlases in GBM studies, as well as the development of inference tools that can be generalized to other cancers. The focus is on building radiomic models from multimodal imaging data and translating suitably processed information into more accurate patient stratifications and evaluations of treatment efficacy using machine learning and other computational tools.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Tianhao Zhang, Binbin Nie, Hua Liu, Baoci Shan
Summary: This study proposes a PET-only spatial normalization method based on adaptive probabilistic brain atlas, which can accurately normalize brain PET images of different radiotracers without MR images. Compared with the template-based method, the atlas-based method shows higher consistency with the gold standard in quantitative analysis.
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2022)
Article
Multidisciplinary Sciences
Ingvild E. Bjerke, Sharon C. Yates, Arthur Laja, Menno P. Witter, Maja A. Puchades, Jan G. Bjaalie, Trygve B. Leergaard
Summary: Calcium-binding proteins parvalbumin and calbindin are expressed in neuronal populations regulating brain networks involved in spatial navigation, memory processes, and social interactions. Through semi-automated image analysis, it was found that these neurons distribute in complementary patterns across the mouse brain, with parvalbumin neurons dominating in sensorimotor processing and navigation areas, and calbindin neurons prevailing in behavioral state regions. Additionally, the distribution of parvalbumin neurons in the hippocampal region of the rat and mouse brain follows similar principles.
Article
Neurosciences
G. Bertonati, M. B. Amadeo, C. Campus, M. Gori
Summary: The human brain relies on the visual cortices to solve spatial tasks. The way spatial information is represented depends on the reference frames used. This study explores how different spatial representations affect the recruitment of visual areas during multisensory spatial tasks. Results show that spatial tasks specifically modulate occipital event-related potentials (ERPs), suggesting that different spatial representations are supported by separate neurophysiological mechanisms.
HUMAN BRAIN MAPPING
(2023)
Article
Engineering, Multidisciplinary
Xiaofeng Yin, Jiuxu Deng, Bo Chen, Bo Jin, Xinyi Gu, Zhidan Qi, Kunpeng Leng, Baoguo Jiang
Summary: This study developed a novel minimally invasive orthogonal recording method to observe the overall evoked cortical potential in the rat brain, obtaining reproducible and visualized temporal-spatial progress of excitations in the rat brain for the first time. The results suggest that the brain's response to peripheral stimulation has precise and reproducible temporal-spatial properties.
