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- Hansson, Kristin, et al.
(författare)
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RipleyGUI : software for analyzing spatial patterns in 3D cell distributions
- 2013
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Ingår i: Frontiers in Neuroinformatics. - : Frontiers Media SA. - 1662-5196. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- The true revolution in the age of digital neuroanatomy is the ability to extensively quantify anatomical structures and thus investigate structure-function relationships in great detail. To facilitate the quantification of neuronal cell patterns we have developed RipleyGUI, a MATLAB-based software that can be used to detect patterns in the 3D distribution of cells. RipleyGUI uses Ripley's K-function to analyze spatial distributions. In addition the software contains statistical tools to determine quantitative statistical differences, and tools for spatial transformations that are useful for analyzing non-stationary point patterns. The software has a graphical user interface making it easy to use without programming experience, and an extensive user manual explaining the basic concepts underlying the different statistical tools used to analyze spatial point patterns. The described analysis tool can be used for determining the spatial organization of neurons that is important for a detailed study of structure function relationships. For example, neocortex that can be subdivided into six layers based on cell density and cell types can also be analyzed in terms of organizational principles distinguishing the layers.
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- MacNicol, Eilidh, et al.
(författare)
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Age-Specific Adult Rat Brain MRI Templates and Tissue Probability Maps
- 2022
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Ingår i: Frontiers in Neuroinformatics. - : Frontiers Media SA. - 1662-5196. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Age-specific resources in human MRI mitigate processing biases that arise from structural changes across the lifespan. There are fewer age-specific resources for preclinical imaging, and they only represent developmental periods rather than adulthood. Since rats recapitulate many facets of human aging, it was hypothesized that brain volume and each tissue's relative contribution to total brain volume would change with age in the adult rat. Data from a longitudinal study of rats at 3, 5, 11, and 17 months old were used to test this hypothesis. Tissue volume was estimated from high resolution structural images using a priori information from tissue probability maps. However, existing tissue probability maps generated inaccurate gray matter probabilities in subcortical structures, particularly the thalamus. To address this issue, gray matter, white matter, and CSF tissue probability maps were generated by combining anatomical and signal intensity information. The effects of age on volumetric estimations were then assessed with mixed-effects models. Results showed that herein estimation of gray matter volumes better matched histological evidence, as compared to existing resources. All tissue volumes increased with age, and the tissue proportions relative to total brain volume varied across adulthood. Consequently, a set of rat brain templates and tissue probability maps from across the adult lifespan is released to expand the preclinical MRI community's fundamental resources.
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- Poline, JB, et al.
(författare)
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Data sharing in neuroimaging research
- 2012
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Ingår i: Frontiers in neuroinformatics. - : Frontiers Media SA. - 1662-5196. ; 6, s. 9-
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Tidskriftsartikel (refereegranskat)
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- Zwiers, MP, et al.
(författare)
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BIDScoin: A User-Friendly Application to Convert Source Data to Brain Imaging Data Structure
- 2022
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Ingår i: Frontiers in neuroinformatics. - : Frontiers Media SA. - 1662-5196. ; 15, s. 770608-
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Tidskriftsartikel (refereegranskat)abstract
- Analyses of brain function and anatomy using shared neuroimaging data is an important development, and have acquired the potential to be scaled up with the specification of a new Brain Imaging Data Structure (BIDS) standard. To date, a variety of software tools help researchers in converting their source data to BIDS but often require programming skills or are tailored to specific institutes, data sets, or data formats. In this paper, we introduce BIDScoin, a cross-platform, flexible, and user-friendly converter that provides a graphical user interface (GUI) to help users finding their way in BIDS standard. BIDScoin does not require programming skills to be set up and used and supports plugins to extend their functionality. In this paper, we show its design and demonstrate how it can be applied to a downloadable tutorial data set. BIDScoin is distributed as free and open-source software to foster the community-driven effort to promote and facilitate the use of BIDS standard.
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