Gammapy: high level data analysis for extragalactic science cases with the Cherenkov Telescope Array

Mapping Intimacies ◽

10.22323/1.301.0601 ◽

2017 ◽

Author(s):

Julien Lefaucheur ◽

Catherine Boisson ◽

Zeljka Bosnkak ◽

Matteo Cerruti ◽

Christoph Deil ◽

...

Keyword(s):

Data Analysis ◽

Telescope Array ◽

Cherenkov Telescope ◽

Level Data ◽

High Level

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Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain

Frontiers in Neuroanatomy ◽

10.3389/fnana.2021.787601 ◽

2022 ◽

Vol 15 ◽

Author(s):

Kyra T. Newmaster ◽

Fae A. Kronman ◽

Yuan-ting Wu ◽

Yongsoo Kim

Keyword(s):

Data Analysis ◽

Mouse Brain ◽

Neuronal Cell ◽

Cell Types ◽

Developmental Time ◽

Cell Type ◽

Level Data ◽

Primary Model ◽

Resolution Mapping ◽

High Level

The brain is composed of diverse neuronal and non-neuronal cell types with complex regional connectivity patterns that create the anatomical infrastructure underlying cognition. Remarkable advances in neuroscience techniques enable labeling and imaging of these individual cell types and their interactions throughout intact mammalian brains at a cellular resolution allowing neuroscientists to examine microscopic details in macroscopic brain circuits. Nevertheless, implementing these tools is fraught with many technical and analytical challenges with a need for high-level data analysis. Here we review key technical considerations for implementing a brain mapping pipeline using the mouse brain as a primary model system. Specifically, we provide practical details for choosing methods including cell type specific labeling, sample preparation (e.g., tissue clearing), microscopy modalities, image processing, and data analysis (e.g., image registration to standard atlases). We also highlight the need to develop better 3D atlases with standardized anatomical labels and nomenclature across species and developmental time points to extend the mapping to other species including humans and to facilitate data sharing, confederation, and integrative analysis. In summary, this review provides key elements and currently available resources to consider while developing and implementing high-resolution mapping methods.

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