aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data
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Christian J Niedworok Alexander PY Brown M Jorge Cardoso Pavel Osten Sebastien Ourselin Marc Modat Troy W MargrieAbstract
The validation of automated image registration and segmentation is crucial for accurate and reliable mapping of brain connectivity and function in three-dimensional (3D) data sets. While validation standards are necessarily high and routinely met in the clinical arena, they have to date been lacking for high-resolution microscopy data sets obtained from the rodent brain. Here we present a tool for optimized automated mouse atlas propagation (aMAP) based on clinical registration software (NiftyReg) for anatomical segmentation of high-resolution 3D fluorescence images of the adult mouse brain. We empirically evaluate aMAP as a method for registration and subsequent segmentation by validating it against the performance of expert human raters. This study therefore establishes a benchmark standard for mapping the molecular function and cellular connectivity of the rodent brain.
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Journal Nature Communications
Volume 7
Pages 11879
Available online
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Publisher website (DOI) 10.1038/ncomms11879
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Europe PubMed Central 27384127
Pubmed 27384127
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