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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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.
| 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 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/32957 |
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