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

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Protocol publication

[…] To test whether the range of z-sections chosen by the human raters had a significant influence on the Dice scores of raters, we reanalysed a subset of the manual segmentations, choosing a window of three and seven consecutive z-sections for each structure in each brain. All segmentations that were not performed in this window were then discarded for this analysis. The position of the window was chosen on each brain and structure to contain the maximum possible number of human segmentations. New STAPLE consensus segmentations were generated for the z-limited analysis. [...] To illustrate the position of the analysed structures and sections, 3D models were generated from the Allen Mouse Brain 3D voxel data using Fiji/ImageJ to generate mesh models and blender ( to remesh, smooth and render them. […]

Pipeline specifications

Software tools STAPLE, ImageJ
Applications Laser scanning microscopy, Microscopic phenotype analysis
Organisms Mus musculus, Rattus norvegicus, Homo sapiens