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Papers Published

1. Johnson, GA; Ali-Sharief, A; Badea, A; Brandenburg, J; Cofer, G; Fubara, B; Gewalt, S; Hedlund, LW; Upchurch, L, High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology., Neuroimage, vol. 37 no. 1 (August, 2007), pp. 82-89 [17574443], [doi] .
   (last updated on 2025/02/12)

   Abstract:
   The Mouse Biomedical Informatics Research Network (MBIRN) has been established to integrate imaging studies of the mouse brain ranging from three-dimensional (3D) studies of the whole brain to focused regions at a sub-cellular scale. Magnetic resonance (MR) histology provides the entry point for many morphologic comparisons of the whole brain. We describe a standardized protocol that allows acquisition of 3D MR histology (43-microm resolution) images of the fixed, stained mouse brain with acquisition times <30 min. A higher resolution protocol with isotropic spatial resolution of 21.5 microm can be executed in 2 h. A third acquisition protocol provides an alternative image contrast (at 43-microm isotropic resolution), which is exploited in a statistically driven algorithm that segments 33 of the most critical structures in the brain. The entire process, from specimen perfusion, fixation and staining, image acquisition and reconstruction, post-processing, segmentation, archiving, and analysis, is integrated through a structured workflow. This yields a searchable database for archive and query of the very large (1.2 GB) images acquired with this standardized protocol. These methods have been applied to a collection of both male and female adult murine brains ranging over 4 strains and 6 neurologic knockout models. These collection and acquisition methods are now available to the neuroscience community as a standard web-deliverable service.

   Keywords:
   Animals • Brain • Databases as Topic • Dominance, Cerebral • Image Enhancement • Image Processing, Computer-Assisted • Imaging, Three-Dimensional • Magnetic Resonance Imaging • Mice • Mice, Inbred C57BL • Phenotype* • Sensitivity and Specificity • Software* • anatomy & histology* • methods* • physiology