High Resolution Three-Dimensional Mapping in the Intact Nervous System

The brain is composed of multiple cellular components, and their extensive interaction in macroscope 3D space, as an integrated computational unit. To understand governing principles of the brain, it is critical to study microscopic details (e.g., neuronal processes, vasculature systems) in a global scale. This need creates both technical and conceptual challenges. Recently emerging mesoscale mapping methods offer potential solutions to examine cellular details in the whole brain. For example, light sheet fluorescent microscopy imaging with tissue clearing methods, paves a new way to rapidly acquire microscopic details in intact 3D biological samples. However, their broad applications and adaptations are still rapidly developing. In addition, the resulting large-scale data present other challenges such as signal detection and further image analysis in a standard atlas framework. Moreover, meso-scale brain mapping projects fueled by recent effort (e.g., BRAIN initiative, Human Brain Project) need data confederation strategies to incorporate findings from multiple sources. In this topic collection, we call for papers covering broad topics related to meso-scale brain mapping in multiple species (e.g., mice, non-human primates) including sample preparation, imaging methods, data analysis modules, neuroinformatics, digital atlasing, and data coordination. The communication of progresses in these synergistic and collaborative topics will foster the development of this rapidly evolving and highly impactful field.

Themes of interest include but are not limited to the following:
- Mouse brain mapping
- Different ages (development, adult, and aging)
- Various cell types (neurons, glia, vasculature)
- Brain connectivity
- Tissue clearing and LSFM imaging
- Neuroinformatics
- Digital atlasing
- Data integration and confederation
- Multispecies: mouse, rat, non-human primate, human

Excluded
- Other organs (not related to nervous system)
- Conventional neuroimaging (e.g., MRI)
- Macro-scale electrophysiology
- Electron microscopy