FriendlyClearMap: an optimized toolkit for mouse brain mapping and analysis.

ABSTRACT:

Background

Tissue clearing is currently revolutionizing neuroanatomy by enabling organ-level imaging with cellular resolution. However, currently available tools for data analysis require a significant time investment for training and adaptation to each laboratory's use case, which limits productivity. Here, we present FriendlyClearMap, an integrated toolset that makes ClearMap1 and ClearMap2's CellMap pipeline easier to use, extends its functions, and provides Docker Images from which it can be run with minimal time investment. We also provide detailed tutorials for each step of the pipeline.

Findings

For more precise alignment, we add a landmark-based atlas registration to ClearMap's functions as well as include young mouse reference atlases for developmental studies. We p

SUBMITTER: Negwer M 

PROVIDER: S-EPMC10205001 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature