Source 1primary paper2023Nature
Toolkit/Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3)
Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3)
Also known as: Allen CCFv3
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
The web research summary states that the anchor study explicitly uses Allen CCFv3 for spatial registration.
Usefulness & Problems
No literature-backed usefulness or problem-fit explainer has been materialized for this record yet.
Published Workflows
Objective: Construct a whole-mouse-brain atlas that is both molecularly defined and spatially resolved.
Why it works: The workflow combines a spatial transcriptomics assay with whole-brain transcriptomic taxonomy and a common coordinate framework so molecularly defined cell types can be placed into anatomical space.
integration of spatial transcriptomics with whole-brain scRNA-seqregistration into a common anatomical coordinate frameworkMERFISHwhole-brain scRNA-seq integrationAllen CCFv3 spatial registration
Stages
- 1.Spatial transcriptomic atlas generation by MERFISH(functional_characterization)
This stage provides the spatially resolved measurements needed for the whole-brain atlas.
Selection: Generate spatially resolved molecular measurements across the whole mouse brain.
- 2.Integration with whole-brain scRNA-seq taxonomy(secondary_characterization)
This stage links spatial measurements to transcriptomic cell-type definitions.
Selection: Integrate spatial measurements with whole-brain scRNA-seq to assign molecularly defined cell identities.
- 3.Registration into Allen CCFv3 space(confirmatory_validation)
This stage places the atlas into a shared anatomical reference space for spatial interpretation.
Selection: Map atlas outputs into a common anatomical coordinate framework.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Techniques
Computational DesignTarget processes
No target processes tagged yet.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
The whole-mouse-brain spatial cell atlas was built with MERFISH and integrated with whole-brain scRNA-seq.
The anchor paper is a 2023 Nature primary paper describing a whole-mouse-brain spatial cell atlas built with MERFISH and integrated with whole-brain scRNA-seq
This paper reports a molecularly defined and spatially resolved cell atlas of the whole mouse brain.
Molecularly defined and spatially resolved cell atlas of the whole mouse brain
The atlas yields more than 5,000 transcriptomic clusters mapped into Allen CCFv3 space.
yielding >5,000 transcriptomic clusters mapped into Allen CCFv3 space
transcriptomic clusters mapped 5000 clusters
Approval Evidence
1 source1 linked approval claimfirst-pass slug allen-mouse-brain-common-coordinate-framework-version-3-ccfv3
The web research summary states that the anchor study explicitly uses Allen CCFv3 for spatial registration.
Source:
resource scalesupports
The atlas yields more than 5,000 transcriptomic clusters mapped into Allen CCFv3 space.
yielding >5,000 transcriptomic clusters mapped into Allen CCFv3 space
Source:
Comparisons
No literature-backed comparison notes have been materialized for this record yet.
Ranked Citations
- 1.