title: An assessment of methods for aligning two-dimensional microscope sections to create image volumes.
abstract: This study assessed five different methods for aligning microscope images of Nissl-stained sections of mouse brain to form three-dimensional image volumes. Methods exploiting both image content and information from un-sectioned tissue were investigated. The accuracy of reconstruction was estimated using fiducials with known physical properties, demonstrating that methods exploiting tissue content produced distorted image volumes while a method using artificial fiducials produced the most accurate and unbiased alignment. Methodological issues relating to methods of volume reconstruction are discussed and it is recommended that methods using information from un-sectioned tissue be used wherever possible.
authors.affiliation: Faculty of Medicine, Nursing and Health Sciences, Monash University, 246 Clayton Road, Clayton 3168, Australia. Richard.Beare@med.monash.edu.au
authors.forename: R
authors.initials: R
authors.lastname: Beare
authors.forename: K
authors.initials: K
authors.lastname: Richards
authors.forename: S
authors.initials: S
authors.lastname: Murphy
authors.forename: S
authors.initials: S
authors.lastname: Petrou
authors.forename: D
authors.initials: D
authors.lastname: Reutens
mesh_terms: D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D001921:Brain / Q000033:anatomy & histology; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D007150:Immunohistochemistry; D008297:Male; D051379:Mice; D008853:Microscopy / Q000379:methods*; D015203:Reproducibility of Results; D016610:Tissue Embedding; D016707:Tissue Fixation