ArticleNeuroinformatics2012
Common atlas format and 3D brain atlas reconstructor: infrastructure for constructing 3D brain atlases.
Article in Neuroinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed.
- Article
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- Claustrum and dorsal endopiriform cortex complex cell-identity is determined by Nurr1 and regulates hallucinogenic-like states in mice.Nature communications · 2024Article
- In search of the locus coeruleus: guidelines for identifying anatomical boundaries and electrophysiological properties of the blue spot in mice, fish, finches, and beyond.Journal of neurophysiology · 2024Review
- Establishing a 3-Tesla Magnetic Resonance Imaging Method for Assessing Diffuse Axonal Brain Injury in Rats.International journal of molecular sciences · 2024Article
- Review
- Germinal matrix hemorrhage induces immune responses, brain injury, and motor impairment in neonatal rats.Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism · 2023Article
- Olfactory modulation of the medial prefrontal cortex circuitry: Implications for social cognition.Seminars in cell & developmental biology · 2022Review
- Constructing the rodent stereotaxic brain atlas: a survey.Science China. Life sciences · 2022Review
- Remote Corticospinal Tract Degeneration After Cortical Stroke in Rats May Not Preclude Spontaneous Sensorimotor Recovery.Neurorehabilitation and neural repair · 2021Article
- Open access resource for cellular-resolution analyses of corticocortical connectivity in the marmoset monkey.Nature communications · 2020Article
- Distinct structure-function relationships across cortical regions and connectivity scales in the rat brain.Scientific reports · 2020Article
- Secondary Degeneration of White Matter After Focal Sensorimotor Cortical Ischemic Stroke in Rats.Frontiers in neuroscience · 2020Article
- Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images.Frontiers in neuroinformatics · 2020Article
- Electrical Source Imaging in Freely Moving Rats: Evaluation of a 12-Electrode Cortical Electroencephalography System.Frontiers in neuroinformatics · 2020Article
- Long-term in vivo microscopy of CAR T cell dynamics during eradication of CNS lymphoma in mice.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Opening the "Black Box": Functions of the Frontal Lobes and Their Implications for Sociology.Frontiers in sociology · 2019Review
- Predictive encoding of motor behavior in the supplementary motor area is disrupted in parkinsonism.Journal of neurophysiology · 2018Article
- Diffusion MRI-based cortical connectome reconstruction: dependency on tractography procedures and neuroanatomical characteristics.Brain structure & function · 2018Article
- Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template.The Journal of comparative neurology · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the challenges of modern neuroscience is integrating voluminous data of diferent modalities derived from a variety of specimens. This task requires a common spatial framework that can be provided by brain atlases. The first atlases were limited to two-dimentional presentation of structural data. Recently, attempts at creating 3D atlases have been made to offer navigation within non-standard anatomical planes and improve capability of localization of different types of data within the brain volume. The 3D atlases available so far have been created using frameworks which make it difficult for other researchers to replicate the results. To facilitate reproducible research and data sharing in the field we propose an SVG-based Common Atlas Format (CAF) to store 2D atlas delineations or other compatible data and 3D Brain Atlas Reconstructor (3dBAR), software dedicated to automated reconstruction of three-dimensional brain structures from 2D atlas data. The basic functionality is provided by (1) a set of parsers which translate various atlases from a number of formats into the CAF, and (2) a module generating 3D models from CAF datasets. The whole reconstruction process is reproducible and can easily be configured, tracked and reviewed, which facilitates fixing errors. Manual corrections can be made when automatic reconstruction is not sufficient. The software was designed to simplify interoperability with other neuroinformatics tools by using open file formats. The content can easily be exchanged at any stage of data processing. The framework allows for the addition of new public or proprietary content.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.