Article
Neurosciences
Zifei Liang, Tanzil Mahmud Arefin, Choong H. Lee, Jiangyang Zhang
Summary: Diffusion MRI (dMRI) tractography is the only non-invasive tool for mapping macroscopic structural connectivity. This study demonstrated that a deep learning network trained on mesoscopic tract-tracing data can improve the estimation of fiber orientation distributions (FODs) in mouse brain dMRI data, leading to enhanced specificity in tractography results without compromising sensitivity.
Article
Neurosciences
Raimo A. Salo, Ilya Belevich, Eija Jokitalo, Olli Grohn, Alejandra Sierra
Summary: Validation and interpretation of diffusion magnetic resonance imaging (dMRI) require a detailed understanding of microstructure. This study used SBEM to image rat brain volumes and compared different parameterizations with dMRI methods NODDI and CSD. SBEM combined with 3D-ST analysis provides enhanced capability for interpreting dMRI signals in complex tissue microstructure.
Article
Radiology, Nuclear Medicine & Medical Imaging
Scott Trinkle, Sean Foxley, Narayanan Kasthuri, Patrick La Riviere
Summary: Synchrotron X-ray microCT was used to validate diffusion MRI in a whole mouse brain, showing good agreement in fiber orientations and tract pathways between the two modalities. The microCT data allowed for spatial registration with diffusion MRI, simplifying comparisons and demonstrating the potential for future multi-scale validation studies.
MAGNETIC RESONANCE IN MEDICINE
(2021)
Review
Multidisciplinary Sciences
Markus Axer, Katrin Amunts
Summary: A comprehensive understanding of the interconnectedness of neurons and brain regions is crucial for studying brain function and dysfunction. Neuroimaging, including diffusion magnetic resonance imaging and tractography, has revolutionized the study of brain connectivity. New methods, such as machine learning and simulation, can help fill in missing experimental data. Future research requires the development of high-resolution templates and directionality concepts in order to represent different solutions of tractography and their accuracy estimates.
Article
Neurosciences
Arnaud Attye, Felix Renard, Monica Baciu, Elise Roger, Laurent Lamalle, Patrick Dehail, Helene Cassoudesalle, Fernando Calamante
Summary: Deep learning-based convolutional neural networks have shown efficiency in fast segmentation of major brain fascicles structures based on diffusion-weighted imaging. TractLearn is introduced as a unified framework for quantitative analysis of brain fascicles, enabling mapping between high-dimensional image domain and reduced latent space using geodesic learning.
Review
Clinical Neurology
Chris W. J. van der Weijden, Emma Biondetti, Ingomar W. Gutmann, Hildebrand Dijkstra, Rory McKerchar, Daniele de Paula Faria, Erik F. J. de Vries, Jan F. Meilof, Rudi A. J. O. Dierckx, Valentin H. Prevost, Alexander Rauscher
Summary: Myelin is a protective sheath made of phospholipid bilayer and water that wraps around axons. Non-invasive quantitative myelin imaging methods are needed for evaluating myelin damage, assessing the efficacy of remyelination therapies, and monitoring brain maturation in children. Different MRI and PET techniques have been developed for myelin imaging based on various biophysical principles. This review provides an overview of these techniques, including image acquisition, data analysis, and validation status, and concludes that quantitative susceptibility mapping, inhomogeneous magnetization transfer for MRI, and C-11-MeDAS for PET are the most promising techniques.
Article
Neurosciences
C. Leuze, M. Goubran, M. Barakovic, M. Aswendt, Q. Tian, B. Hsueh, A. Crow, E. M. M. Weber, G. K. Steinberg, M. Zeineh, E. D. Plowey, A. Daducci, G. Innocenti, J-P Thiran, K. Deisseroth, J. A. McNab
Summary: Diffusion MRI is a non-invasive method for mapping brain fiber orientations, and when combined with CLARITY tissue clearing, it offers new insights and opportunities for accurate estimation of neuronal fiber and vasculature orientations. Through the comparison of dMRI and CLARITY results, advancements towards robust multi-modal MRI-CLARITY comparisons are being made.
Review
Physics, Applied
Nikolaus Weiskopf, Luke J. Edwards, Gunther Helms, Siawoosh Mohammadi, Evgeniya Kirilina
Summary: Quantitative magnetic resonance imaging and in vivo histology aim to characterize tissue microstructure of living brain, providing deeper understanding of MRI tissue contrast and more accurate image parameters as compared to traditional histology methods.
NATURE REVIEWS PHYSICS
(2021)
Article
Neurosciences
Davood Karimi, Lana Vasung, Camilo Jaimes, Fedel Machado-Rivas, Simon K. Warfield, Ali Gholipour
Summary: This study proposed a data-driven method to improve the accuracy and robustness of white matter fiber orientation distribution function (fODF) estimation, demonstrating effectiveness through training with simulated and real data. In phantom and real data experiments, the method showed higher accuracy compared to other competing methods, particularly in under sampled diffusion measurements. Additionally, expert ratings indicated significantly better reconstruction of various brain tracts using the proposed method.
Article
Neurosciences
Fang-Cheng Yeh, Andrei Irimia, Dhiego Chaves de Almeida Bastos, Alexandra J. Golby
Summary: This review discusses the challenges of anatomical accuracy in fiber tracking, explores the impact of different white matter pathways on tracking methods, and summarizes the pros and cons of commonly-used techniques. Additionally, it introduces the progress in clinical applications of tractography in patients with brain tumors and traumatic brain injury, highlighting current limitations and future directions for development.
Article
Neurosciences
Robert Jones, Chiara Maffei, Jean Augustinack, Bruce Fischl, Hui Wang, Berkin Bilgic, Anastasia Yendiki
Summary: The study evaluates the application of compressed sensing techniques in diffusion spectrum imaging, finding that CS-DSI can be used to accurately reconstruct the EAP with high fidelity and approximate fully sampled DSI data in a shorter acquisition time. However, the study notes that the signal-to-noise ratio affects the accuracy of CS-DSI, and increasing the CS acceleration factor beyond a certain point may impact the accuracy of the reconstruction methods.
Article
Neurosciences
Daniel Z. L. Kor, Saad Jbabdi, Istvan N. Huszar, Jeroen Mollink, Benjamin C. Tendler, Sean Foxley, Chaoyue Wang, Connor Scott, Adele Smart, Olaf Ansorge, Menuka Pallebage-Gamarallage, Karla L. Miller, Amy F. D. Howard
Summary: This study introduces an automated pipeline for extracting quantitative histological measures from immunohistochemical stains and correlating them with MRI parameters. The pipeline is reproducible, robust to artifacts and can be applied to multiple stains. Partial correlation results suggest caution in interpreting simple correlations between MRI and histological measures due to potential co-localization of other tissue features.
Article
Multidisciplinary Sciences
Philippe Poulin, Guillaume Theaud, Francois Rheault, Etienne St-Onge, Arnaud Bore, Emmanuelle Renauld, Louis de Beaumont, Samuel Guay, Pierre-Marc Jodoin, Maxime Descoteaux
Summary: TractoInferno is the largest open-source multi-site tractography database in the world, aimed at providing standardized training datasets and evaluation protocols for machine learning tractography approaches. It includes 284 samples from different sites, covering a wide range of data and algorithms for research and evaluation.
Article
Neurosciences
Yifan Lv, Zili Kang, Tianle Han, Mengshen He, Ruhai Du, Tuo Zhang, Tianming Liu, Bao Ge
Summary: In this study, the relationship between fiber length and geodesic distance in the brain was explored. The results showed that cortical regions tend to choose the shortest path for connection, even when intra-cortical routes are longer than potential extrinsic fiber routes.
Article
Neurosciences
Henry F. J. Tregidgo, Sonja Soskic, Juri Althonayan, Chiara Maffei, Koen Van Leemput, Polina Golland, Ricardo Insausti, Garikoitz Lerma-Usabiaga, Cesar Caballero-Gaudes, Pedro M. Paz-Alonso, Anastasia Yendiki, Daniel C. Alexander, Martina Bocchetta, Jonathan D. Rohrer, Juan Eugenio Iglesias
Summary: The human thalamus plays a crucial role in various brain functions and is linked to several neurological disorders. Current neuroimaging studies focus on the volume and connectivity of specific nuclei within the thalamus rather than studying the entire structure. However, accurately identifying these nuclei based on standard in vivo structural MRI is challenging due to limited image contrast. This study presents a Bayesian segmentation algorithm that combines prior information and likelihood models from both structural and diffusion MRI to improve thalamic segmentation.
Article
Computer Science, Interdisciplinary Applications
Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek J. Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, J. B. Poline, Prasun K. Roy, Stephen C. Strother, Tong Boon Tang, Paul Tiesinga, Thomas Wachtler, Daniel K. Wojcik, Maryann E. Martone
Summary: There is a great need for coordination around standards and best practices in neuroscience to address challenges in data science. Developing community standards and gaining their adoption is difficult, as the current landscape is characterized by a lack of robust, validated standards and a plethora of underdeveloped and underutilized standards and best practices. An independent organization, the International Neuroinformatics Coordinating Facility (INCF), is dedicated to promoting data sharing in neuroscience and has implemented procedures for evaluating and endorsing community standards and best practices.
Correction
Computer Science, Interdisciplinary Applications
Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek J. Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, J. B. Poline, Prasun K. Roy, Stephen C. Strother, Tong Boon Tang, Paul Tiesinga, Thomas Wachtler, Daniel K. Wojcik, Maryann E. Martone
Review
Neurosciences
Damian O. Eke, Amy Bernard, Jan G. Bjaalie, Ricardo Chavarriaga, Takashi Hanakawa, Anthony J. Hannan, Sean L. Hill, Maryann E. Martone, Agnes McMahon, Oliver Ruebel, Sharon Crook, Edda Thiels, Franco Pestilli
Summary: With the increase in neuroscience projects on an international scale, there is a need to consider different ethical principles, laws, regulations, and policies for data sharing. This article proposes principles and operational considerations for navigating data governance in neuroscience at an international level and highlights the gaps, challenges, and opportunities in the global brain data ecosystem.
Article
Developmental Biology
Chiara Tocco, Martin Ovsthus, Jan G. Bjaalie, Trygve B. Leergaard, Michele Studer
Summary: This study reveals that the expression of Nr2f1 gene in the cortical region directly affects the topographic mapping from the cortex to the pontine nuclei. Using transgenic mice and various techniques, the researchers identified that Nr2f1 expression in postmitotic neurons is crucial for controlling somatosensory topographic projections, while its expression in progenitor cells influences the ratio of different fiber types.
Article
Multidisciplinary Sciences
Malin Sandstrom, Mathew Abrams, Jan G. Bjaalie, Mona Hicks, David N. Kennedy, Arvind Kumar, Jean-Baptiste Poline, Prasun K. Roy, Paul Tiesinga, Thomas Wachtler, Wojtek J. Goscinski
Summary: Repositories and science gateways are vital resources for the neuroscience community, but users struggle to find the most suitable services. INCF has developed recommendations and criteria for selecting, establishing, and running repositories or scientific gateways with a FAIR perspective.
Article
Substance Abuse
Ingeborg Bolstad, Helge Toft, Lars Lien, Jenny Skumsnes Moe, Benjamin Rolland, Jorgen G. Bramness
Summary: Insomnia is common among patients with AUD and can have negative impacts on their quality of life and cognitive functioning. This study aimed to examine the prevalence and development of self-perceived insomnia among inpatients in treatment for AUD, and identified factors such as sex, depression, and physical activity associated with insomnia.
Article
Substance Abuse
Ingeborg Bolstad, Lars Lien, Jenny Skumsnes Moe, Sumita Pandey, Helge Toft, Jorgen G. Bramness
Summary: This study compared the level of circulating cytokines in different groups of patients with alcohol use disorder, including non-tobacco users, smokers, users of Swedish snus, and dual tobacco users. The findings suggest that nicotine has anti-inflammatory effects in patients with alcohol use disorder, but its other adverse effects limit its potential as a therapeutic option.
ALCOHOL-CLINICAL AND EXPERIMENTAL RESEARCH
(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
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
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
Heidi Kleven, Thomas H. Gillespie, Lyuba Zehl, Timo Dickscheid, Jan G. Bjaalie, Maryann E. Martone, Trygve B. Leergaard
Summary: Brain atlases are crucial for accurate anatomical description of neuroscience data, but the lack of standardized description hinders their use in analytic tools and data registration. To address this issue, we developed an Atlas Ontology Model (AtOM) that provides a standardized framework for communication and use of brain atlases. By applying AtOM to different species' brain atlases, we demonstrate its potential in facilitating data integration and complying with FAIR guiding principles.