A three-dimensional MRI atlas of the zebra finch brain in stereotaxic coordinates

Poirier, Colline; Vellema, Michiel; Verhoye, Marleen; Meir, Vincent Van; Wild, J. Martin; Balthazart, Jacques; Linden, Annemie Van der

doi:10.1016/j.neuroimage.2008.01.069

Cited by 58 publications

(76 citation statements)

References 27 publications

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“…Traditional atlases are often based on drawings of histological brain sections, and are dependent on the interests of the researcher constructing the atlas both in sectioning orientation as well as delineation of brain structures. 3D imaging techniques such as MRI however, give us the opportunity to examine the brain from a 3-dimensional, whole-brain point of view (Ma et al, 2005;Poirier et al, 2008;Saleem and Logothetis, 2007;Van Essen, 2005). Here we presented the first 3-dimensional MRI-based atlas of the canary brain, a model system often used for neurobiological and behavioral studies.…”

Section: Discussionmentioning

confidence: 99%

“…Together with our previously published 3D brain atlas of the zebra finch (Poirier et al, 2008), we now have two detailed, easily adaptable brain atlases for two commonly studied species of songbird that should appeal to scientists from different disciplines working on the function, physiology and anatomy of the songbird brain.…”

Section: Discussionmentioning

confidence: 99%

“…Brain atlases play an essential role in providing the necessary anatomical information, but traditional atlases are mostly based on drawings of brain sections, resulting in only a limited 2-dimensional perspective on the brain. Advances in Magnetic Resonance Imaging however, make it possible to create detailed and flexible 3-dimensional models of the brain (Johnson et al, 1997;Ma et al, 2005;Poirier et al, 2008;Van Essen, 2005). Since digital 3D atlases are independent of previously specified sectioning angles, they can overcome the restricted viewpoint of traditional atlases and provide a complete insight into the sometimes complex anatomy of the brain and the spatial relationship between brain areas.…”

Section: Introductionmentioning

confidence: 99%

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A customizable 3-dimensional digital atlas of the canary brain in multiple modalities

et al. 2011

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A customizable 3-dimensional digital atlas of the canary brain in multiple modalities

et al. 2011

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“…One of such adaptation efforts is to construct the animal brain template in order to use the existing analytic tools for human studies. In the past several years, several animal brain MRI templates have been constructed for mice [Lin et al, 2003; Sawiak et al, 2009], baboons [Black et al, 2001b], macaque [Alexander et al, 2008; Black et al, 2001a], zebra finch [Poirier et al, 2008], and Sprague-Dawley (SD) rats [Schwarz et al, 2006; Schweinhardt et al, 2003]. …”

Section: Introductionmentioning

confidence: 99%

A rat brain MRI template with digital stereotaxic atlas of fine anatomical delineations in paxinos space and its automated application in voxel‐wise analysis

Nie

Chen

Zhao

et al. 2012

Human Brain Mapping

106

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This study constructs a rat brain T2-weighted magnetic resonance imaging template including olfactory bulb and a compatible digital atlas. The atlas contains 624 carefully delineated brain structures based on the newest (2005) edition of rat brain atlas by Paxinos and Watson. An automated procedure, as an SPM toolbox, was introduced for spatially normalizing individual rat brains, conducting statistical analysis and visually localizing the results in the Atlas coordinate space. The brain template/atlas and the procedure were evaluated using functional images between rats with the right side middle cerebral artery occlusion (MCAO) and normal controls. The result shows that the brain region with significant signal decline in the MCAO rats was consistent with the occlusion position.

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“…Vice versa, Webbased atlases allow scientists from different laboratories to add data to a common standardized neuroanatomical framework, where imaging, gene expression, and physiological data can be linked to the anatomical structures. Digital brain atlases are already available for human (Kikinis et al, 1996), mouse Mackenzie-Graham et al, 2007), zebra finch (Poirier et al, 2008), and several insect species (Drosophila, Rein et al, 2002;honey bee, Brandt et al, 2005;locust, Kurylas et al, 2008;cockroach, Chiang et al, 2001).…”

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confidence: 99%

Average shape standard atlas for the adult Drosophila ventral nerve cord

Boerner

Duch

2010

J of Comparative Neurology

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Neuroanatomy benefits from quantification of neural structures, i.e., neurons, circuits, and brain parts, within a common reference system. Recent improvements in imaging techniques and increased computational power have made the creation of Web-based databases possible, which serve as common platforms for incorporating anatomical data. This study establishes a standard average shape atlas for the ventral nerve cord (VNC) of Drosophila melanogaster. This atlas allows for the registration of morphological, developmental, and genetic data into one quantitative 3D reference system. The standard is based on an average adult Drosophila VNC neuropil as labeled in 24 whole-mount preparations with the commercially available antibody (nc82) recognizing the Drosophila Bruchpilot protein (Brp). For the standardization procedure no expert knowledge of brain anatomy is required and global thresholding as well as straightforward affine and elastic registration procedures minimize user interactions. Successful registration is demonstrated for tracts and commissures, gene expression patterns, and geometric reconstructions of individual neurons. Any structure that is counterstained with anti-Brp can be registered into the standard, allowing for fast comparison of data from different experiments and different laboratories. In addition, standard transformations can be applied to gray scale image data, so that any confocal image stack that is colabeled with anti-Brp can be analyzed within standardized 3D reference coordinates. This allows for the creation of putative neural connectivity maps and the comparison of expression patterns derived from different preparations. The standard and protocols for histological methods, segmentation, and registration procedures will be made available on the Web.

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A three-dimensional MRI atlas of the zebra finch brain in stereotaxic coordinates

Cited by 58 publications

References 27 publications

A customizable 3-dimensional digital atlas of the canary brain in multiple modalities

A customizable 3-dimensional digital atlas of the canary brain in multiple modalities

A rat brain MRI template with digital stereotaxic atlas of fine anatomical delineations in paxinos space and its automated application in voxel‐wise analysis

Average shape standard atlas for the adult Drosophila ventral nerve cord

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