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

Niedworok, C. J., Brown, A. P., Jorge Cardoso, M., Osten, P., Ourselin, S., Modat, M., Margrie, T. W. (July 2016) aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nat Commun, 7. p. 11879. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

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DOI: 10.1038/ncomms11879


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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > computers > computer software
Investigative techniques and equipment > microscopy > flourescence microscopy
Investigative techniques and equipment > Whole Brain Circuit Mapping
CSHL Authors:
Communities: CSHL labs > Osten lab
Depositing User: Matt Covey
Date: 7 July 2016
Date Deposited: 08 Jul 2016 20:33
Last Modified: 10 Sep 2019 17:02
PMCID: PMC4941048
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