The framework also provides algorithms for bidirectional transformation of results obtained using either MR or LSFM (iDISCO cleared) mouse brain imaging while the coordinate system enables users to easily assign in vivo coordinates across the different brain templates....
common coordinate framework (CCFv3) serves as a 3D reference atlas to overcome many limitations of 2D atlases described above and to provide standardized spatial context to integrate data from different studies for the adult mouse brain15. Recent brain mapping tools, such as mBrainAligner22,23and ...
Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin-Paxinos (FP) and the common coordinate framewor
5 the mouse brain in stereotaxic coordinates is the most widely used and cited atlas of the mouse brain in print. it provides researchers and students with both accurate stereotaxic coordinates for laboratory use, and detailed delineations and indexing of structures for reference. the compact 3rd ...
The Mouse Brain in Stereotaxic Coordinates is the most widely used and cited atlas of the mouse brain in print. It provides researchers and students with both accurate stereotaxic coordinates for laboratory use, and detailed delineations and indexing of structures for reference. The accompanying DVD ...
Standard 2D mouse brain reference atlases, e.g., the Allen Reference Atlas (ARA) (Dong, 2008) and the Mouse Brain in Stereotaxic Coordinates (MBSC) (Paxinos and Franklin, 2001, Paxinos and Franklin, 2012), continue to serve important roles, but a digital 3D reference atlas is preferred for...
BrainAtlas,agenome-scaleatlasofgeneexpressioninthemousebrain(Lein,Hawrylyczetal.2007),with adaptationsincluding:1)additionofayellowcounterstaintoenhanceanalysisoftheISH;2)changesintissue embeddingprocessesforembryonictissue;3)adjustedproteinaseKconcentrationsoptimizedforeachage; ...
The Mouse Brain in Stereotaxic Coordinates is the most widely used and cited atlas of the mouse brain in print. It provides researchers and students with both accurate stereotaxic coordinates for laboratory use, and detailed delineations and indexing of structures for reference. The Compact 3rd editio...
By contrast to more conventional histopathological screens that often rely on qualitative assessment, we used a quantitative approach where each section had to pass well-defined stereotaxic coordinates defined according to the Mouse Brain Atlas54 before image analysis. To do this, we recorded how ...
We present an online platform, Allen Brain Cell Atlas, to visualize the mouse whole-brain cell-type atlas along with the single-cell RNA-sequencing and MERFISH datasets. We systematically analysed the neuronal and non-neuronal cell types across the brain and identified a high degree of ...