ArticleGigaScience2022
FriendlyClearMap: an optimized toolkit for mouse brain mapping and analysis.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- The ANTsX ecosystem for mapping the mouse brain.Nature communications · 2025Article
- Modular strategies for spatial mapping of diverse cell type data of the mouse brain.Research square · 2025Article
- ClearFinder: a Python GUI for annotating cells in cleared mouse brain.BMC bioinformatics · 2025Article
- An arginine-rich nuclear localization signal (ArgiNLS) strategy for streamlined image segmentation of single cells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Virtual reality-empowered deep-learning analysis of brain cells.Nature methods · 2024Article
- An arginine-rich nuclear localization signal (ArgiNLS) strategy for streamlined image segmentation of single-cells.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
9 authors.
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Abstract
backgroundTissue 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.
findingsFor 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 provide an alternative cell segmentation method besides ClearMap's threshold-based approach: Ilastik's Pixel Classification, importing segmentations from commercial image analysis packages and even manual annotations. Finally, we integrate BrainRender, a recently released visualization tool for advanced 3-dimensional visualization of the annotated cells.
conclusionsAs a proof of principle, we use FriendlyClearMap to quantify the distribution of the 3 main GABAergic interneuron subclasses (parvalbumin+ [PV+], somatostatin+, and vasoactive intestinal peptide+) in the mouse forebrain and midbrain. For PV+ neurons, we provide an additional dataset with adolescent vs. adult PV+ neuron density, showcasing the use for developmental studies. When combined with the analysis pipeline outlined above, our toolkit improves on the state-of-the-art packages by extending their function and making them easier to deploy at scale.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.