Extraction of Parvalbumin positive cells from an Allen mouse brain in situ hybridisation experiment

Aim of project: To assign coordinates and quantify parvalbumin positive cells extracted from a series of brain section images obtained from the Allen Brain ISH repository. Study design: The image series was exported from the Allen Mouse Brain Atlas Data Portal, http://mouse.brain-map.org/experiment/show/75457579 (© 2004 Allen Institute for Brain Science. Allen Mouse Brain Atlas. Available from: mouse.brain-map.org). The series included images of 20 sagittal mouse brain sections from the left hemisphere labelled for parvalbumin by in situ hybridisation (Specimen 06-0419, Probe RP_060523_03_E07; Image credit: Allen Institute). Positive cells were identified by segmentation with the ilastik software. The section images were registered to reference atlas space with the QuickNII software and custom atlas maps were exported. Extracted features were quantified, localised and assigned coordinates with the Nutil software. Study output: 20 segmentation images 20 customised atlas maps 20 atlas maps with superimposed colour coded features A .json file with coordinates for visualising the parvalbumin positive cells in atlas space (Allen mouse brain Common Coordinate framework version 3). 2 reports (.docx) with quantifications per atlas region (1 report is for the whole brain, the other per section). Reference: Allen Mouse Brain Atlas. Lein, E.S. et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain, Nature 445: 168-176. doi:10.1038/nature05453.