Robust methods to create ex vivo minimum deformation atlases for brain mapping

Janke, Andrew L.; Ullmann, Jeremy F.P.

doi:10.1016/j.ymeth.2015.01.005

Cited by 63 publications

(42 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The second‐level data processing included co‐registration, spatial smoothing, and group analysis (Supplementary Figure 1B). Nonlinear transformation (using ‘fnirt’ in FSL) was used to co‐register the distortion‐corrected EPI to the individual FSE image and then to a study‐specific template created based on 8 untreated YAC128 and 8 wild‐type mice in the Australian Mouse Brain Mapping Consortium (AMBMC) atlas space (http://www.imaging.org.au/AMBMC/) . Gaussian smoothing with full width at half maximum of 0.424 mm was applied.…”

Section: Methodsmentioning

confidence: 99%

Connectomic imaging reveals Huntington‐related pathological and pharmaceutical effects in a mouse model

et al. 2018

View full text Add to dashboard Cite

Recent studies suggest that neurodegenerative diseases could affect brain structure and function in disease‐specific network patterns; however, how spontaneous activity affects structural covariance network (SC) is not clear. We hypothesized that hyper‐excitability in Huntington disease (HD) disrupts the coordinated structural and functional connectivity, and treatment with memantine helps to reduce excitotoxicity and normalize the connectivity. MRI was conducted to measure somatosensory activation, resting‐state functional‐connectivity (rsFC), SC, amplitude of low frequency fluctuation (ALFF) and ALFF covariance (ALFFC) in the YAC128 mouse model of HD. We found somatosensory activation was unchanged but the subcortical ALFF was increased in HD mice, indicating subcortical but not cortical hyperactivity. The reduced sensorimotor rsFC but spared hippocampal and default mode networks in the HD mice was consistent with the more pronounced impairment in motor function compared with cognitive performance. The disease suppressed SC globally and reduced ALFFC in the basal ganglia network as well as its anti‐correlation with the default mode network. By comparing these connectivity measures, we found that the originally coupled rsFC‐SC relationship was impaired whereas SC‐ALFFC correlation was increased by HD, suggesting disease facilitated covariation of brain volume and activity amplitude but not neural synchrony. The comparison with mono‐synaptic axonal projection supports the hypothesis that rsFC, but not SC or ALFFC, is highly dependent on structural connectivity under healthy conditions. Treatment with memantine had a strong effect on normalizing the SC and reducing ALFF while slightly increasing other connectivity measures and restoring the rsFC‐SC coupling, which is consistent with its effect on alleviating hyper‐excitability and improving the coordinated neural growth. These results indicate that HD affects the cerebral structure–function relationship which could be partially reverted by NMDA antagonism. These connectivity measures provide unique insights into pathological and pharmaceutical effects in brain circuitry, and could be translatable biomarkers for evaluating drug effect and refining its efficacy.

show abstract

Section: Methodsmentioning

confidence: 99%

Connectomic imaging reveals Huntington‐related pathological and pharmaceutical effects in a mouse model

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Other population based templates relied on a comparable (Hikishima et al, 2011) or smaller (Risser et al, 2019) numbers of individuals of similar sex and age, but did not incorporate histological validation of the area boundaries. Further, the morphological averaging was performed with a higher number of iterations (20) than recommended (Janke et al, 2015), which allowed to better emphasize cytoarchitectonic features and transitions between individual brain structures. Thus, the present atlas likely provides a good representation of the average morphology and variability of the cortex among young adult, captive-born marmosets.…”

Section: Methodological Considerationsmentioning

confidence: 99%

“…The resulting image (Fig. 2C) is not biased towards any of the individual histological volumes (Avants and Gee, 2004), and, by taking advantage of the subpixel accuracy of the morphological averaging (Janke et al, 2015), has a higher spatial resolution than the input 3D images. The same set of transformations was applied to the segmentations of the input brain hemispheres (Fig.…”

Section: Average Template Constructionmentioning

confidence: 99%

Histology-based average template of the marmoset cortex with probabilistic localization of cytoarchitectural areas

Majka

Bednarek

Chan

et al. 2020

Preprint

View full text Add to dashboard Cite

Highlights• A 3D template of the marmoset cortex representing the average of 20 individuals.• The template is based on Nissl stain and preserves information about cortical layers.• Probabilistic mapping of areas, cortical thickness, and layer intensity profiles.• Includes spatial transformations to other marmoset brain atlases. AbbreviationsFor a list of areas and their abbreviations see Table S2. AbstractThe rapid adoption of marmosets in neuroscience has created a demand for three dimensional (3D) atlases of the brain of this species to facilitate data integration in a common reference space. We report on a new open access template of the marmoset cortex (the Nencki-Monash, or NM template), representing a morphological average of 20 brains of young adult individuals, obtained by 3D reconstructions generated from Nissl-stained serial sections. The method used to generate the tem plate takes into account morphological features of the individual brains, as well as the borders of clearly defined cytoarchitectural areas. This has resulted in a resource which allows direct estimates of the most likely coordinates of each cortical area, as well as quantification of the margins of error involved in assigning voxels to areas, and preserves quantitative information about the laminar structure of the cortex. We provide spatial transformations between the NM and other available marmoset brain templates, thus enabling integration with magnetic resonance imaging (MRI) and tracer-based connectivity data. The NM template combines some of the main advantages of histology-based atlases (e.g. information about the cytoarchitectural structure) with features more commonly associated with MRI-based templates (isotropic nature of the dataset, and probabilistic analyses). The underlying workflow may be found useful in the future development of brain atlases that incorporate information about the variability of areas in species for which it may be impractical to ensure homogeneity of the sample in terms of age, sex and genetic background.

show abstract

“…Continuing in the area of 3D atlasing, Janke and Ullman present Robust methods to create ex-vivo minimum deformation atlases for brain mapping [4], affirming that highly detailed ex-vivo 3D atlases of average structure are of critical importance to neuroscience and its current push to understand the global microstructure of the brain. They observe that multiple single slice histology sections can no longer provide sufficient detail of inter-slice microstructure and lack out of plane resolution, proposing instead two ex-vivo methods: High-field lMRI with the addition of contrast media that allows intact whole brain microstructure imaging with an isotropic resolution of 15 lm in mouse, and blockface imaging to image an entire brain in a rigorous fashion with an out of plane resolution of 10 lm.…”

mentioning

confidence: 96%

“…An exciting part of this work is the use of a specialized TissueCyte 1000 serial two-photon (STP) tomography system, which couples high-speed two-photon microscopy with automated blockface vibratome sectioning [3]. By imaging the blockface, STP tomography essentially eliminates tissue distortions that occur in conventional section-based histological methods, a method that many projects are using (see Janke and Ullman this volume [4]) yielding a series of highly conformed, inherently pre-aligned images amenable to more precise 3D spatial mapping. This methodology enables a new high resolution common coordinate framework for the brain that all Allen Institute data can be mapped to.…”

mentioning

confidence: 99%