Segmentation of the mouse hippocampal formation in magnetic resonance images

Richards, Kay; Watson, Charles; Buckley, Rachel F.; Kurniawan, Nyoman D.; Yang, Zhengyi; Keller, Marianne; Beare, Richard; Bartlett, Perry F.; Egan, Gary F.; Galloway, Graham J.; Paxinos, George; Petrou, Steven; Reutens, David C.

doi:10.1016/j.neuroimage.2011.06.025

Cited by 97 publications

(76 citation statements)

References 37 publications

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“…Six ROIs were selected based on anatomical relevance, the cingulate cortex, primary somatosensory cortex (barrel field), insular cortex, caudate-putamen, and hippocampus were based on the AMBMC atlas (Richards et al, 2011, Ullmann et al, 2013, Ullmann et al, 2014 and the thalamus was based on . Data extracted from left and right ROIs were combined for analysis ( Figure 1).…”

Section: Roi Analysismentioning

confidence: 99%

Altered regional connectivity reflecting effects of different anaesthesia protocols in the mouse brain

Grandjean

Bosshard

et al. 2017

NeuroImage

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Altered regional connectivity reflecting effects of different anaesthesia protocols in the mouse brain, NeuroImage, http://dx.doi.org/10.1016/j.neuroimage. 2017.01.074 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. AbstractStudies in mice using resting-state functional magnetic resonance imaging (rs-fMRI) have provided opportunities to investigate the effects of pharmacological manipulations on brain function and map the phenotypes of mouse models of human brain disorders. Mouse rs-fMRI is typically performed under anaesthesia, which induces both regional suppression of brain activity and disruption of large-scale neural networks. Previous comparative studies using rodents investigating various drug effects on long-distance functional connectivity (FC) have reported agent-specific FC patterns, however, effects of regional suppression are sparsely explored. Here we examined changes in regional connectivity under six different anaesthesia conditions using mouse rs-fMRI with the goal of refining the framework of understanding the brain activation under anaesthesia at a local level. Regional homogeneity (ReHo) was used to map local synchronization in the brain, followed by analysis of several brain areas based on ReHo maps. The results revealed high local coherence in most brain areas. The primary somatosensory cortex and caudate-putamen showed agent-specific properties. Lower local coherence in the cingulate cortex was observed under medetomidine, particularly when compared to the combination of medetomidine and isoflurane. The thalamus was associated with retained local coherence across anaesthetic levels and multiple nuclei. These results show that anaesthesia induced by the investigated anaesthetics through different molecular targets promote agent-specific regional connectivity. In addition, ReHo is a data-driven method with minimum user interaction, easy to use and fast to compute. Given that examination of the brain at a local level is widely applied in human rs-fMRI studies, our results show its sensitivity to extract information on varied neuronal activity under six different regimens relevant to mouse functional imaging. These results, therefore, will inform future rsfMRI studies on mice and the type of anaesthetic agent used, and will help to bridge observations between this burgeoning research field and ongoing human research across analytical scales.

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Section: Roi Analysismentioning

confidence: 99%

Altered regional connectivity reflecting effects of different anaesthesia protocols in the mouse brain

Grandjean

Bosshard

et al. 2017

NeuroImage

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“…Although initially developed for imaging humans, MRI has become a key platform for imaging small animals and is now routinely performed on mice (Richards et al 2011;Ullmann et al 2012), rats (Petiet et al 2007), and zebrafish (Ullmann et al 2010b;Kabli et al 2009;Ullmann et al 2010a). However, MRI becomes increasingly challenging as the size of the animal decreases.…”

Section: Introductionmentioning

confidence: 99%

Enhanced characterization of the zebrafish brain as revealed by super-resolution track-density imaging

et al. 2013

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Abstract:In this study we explored the use of super-resolution track density imaging (TDI) for neuroanatomical characterization of the adult zebrafish brain. We compared the quality of image contrast and resolution obtained with T 2 * magnetic resonance imaging (MRI), diffusion tensor based imaging (DTI), TDI, and histology. The anatomical structures visualized in 5 µm TDI maps corresponded with histology. Moreover the super-resolution property and the local-directional information provided by directionally-encoded color TDI facilitated delineation of a larger number of brain regions, commissures and small white matter tracks when compared to conventional MRI and DTI. In total, we were able to visualize 17 structures that were previously unidentifiable using MR microimaging, such as the four layers of the optic tectum. This study demonstrates the use of TDI for characterization of the adult zebrafish brain as a pivotal tool for future phenotypic examination of transgenic models of neurological diseases.

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“…The previous papers in the series dealt with the hippocampus (Richards et al, 2011), the cerebellum (Ullmann et al, 2012), the basal ganglia (Ullmann et al, 2014), and the cerebral cortex (Ullmann et al, 2013). The present paper offers a detailed description of the major parts of the mouse diencephalon in high-resolution MR images.…”

Section: Discussionmentioning

confidence: 93%

“…The FSL atlas package used by our consortium includes labels for the segmentation of the mouse diencephalon, as well as the previous AMBMC atlases including the basal ganglia (Ullmann et al, 2014), cerebellum (Ullmann et al, 2012), cerebral cortex (Ullmann et al, 2013), and hippocampus (Richards et al, 2011). Additionally, a symmetric average mouse brain MRI model is included in the package that should be used for image registrations (Janke and Ullmann, 2015).…”

Section: The Pretectal Nuclei (Prosomere 1)mentioning

confidence: 99%