title: aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data.
abstract: 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.
authors.affiliation: The Division of Neurophysiology, MRC National Institute for Medical Research, London NW7 1AA, UK.|The Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK.
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Niedworok
authors.affiliation: The Division of Neurophysiology, MRC National Institute for Medical Research, London NW7 1AA, UK.|The Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK.
authors.forename: Alexander P Y
authors.initials: AP
authors.lastname: Brown
authors.affiliation: Translational Imaging Group, Centre for Medical Image Computing, University College London, London WC1E 6BT, UK.
authors.forename: M
authors.identifier: 0000-0003-1284-2558
authors.initials: M
authors.lastname: Jorge Cardoso
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Pavel
authors.initials: P
authors.lastname: Osten
authors.affiliation: Translational Imaging Group, Centre for Medical Image Computing, University College London, London WC1E 6BT, UK.
authors.forename: Sebastien
authors.initials: S
authors.lastname: Ourselin
authors.affiliation: Translational Imaging Group, Centre for Medical Image Computing, University College London, London WC1E 6BT, UK.
authors.forename: Marc
authors.initials: M
authors.lastname: Modat
authors.affiliation: The Division of Neurophysiology, MRC National Institute for Medical Research, London NW7 1AA, UK.|The Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK.
authors.forename: Troy W
authors.initials: TW
authors.lastname: Margrie
mesh_terms: D000465:Algorithms; D000818:Animals; D001271:Atlases as Topic; D019985:Benchmarking; D001921:Brain / Q000033:anatomy & histology* / Q000000981:diagnostic imaging / Q000502:physiology; D063132:Connectome / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000706:statistics & numerical data*; D021621:Imaging, Three-Dimensional / Q000379:methods / Q000706:statistics & numerical data*; D008279:Magnetic Resonance Imaging / Q000379:methods / Q000706:statistics & numerical data*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D012984:Software