AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data

TY - JOUR

T1 - AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data

AU - Niedworok, Christian J.

AU - Brown, Alexander P.Y.

AU - Jorge Cardoso, M.

AU - Osten, Pavel

AU - Ourselin, Sebastien

AU - Modat, Marc

AU - Margrie, Troy W.

PY - 2016/7/7

Y1 - 2016/7/7

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84977647212&partnerID=8YFLogxK

U2 - 10.1038/ncomms11879

DO - 10.1038/ncomms11879

M3 - Article

AN - SCOPUS:84977647212

SN - 2041-1723

VL - 7

JO - Nature Communications

JF - Nature Communications

M1 - 11879

ER -