Investigating cellular diversity in a novel Alzheimer’s disease mouse model using the optimized QUINT workflow (v1)

This study includes 40 mice (20 at 6 months(m), 20 at 14 months(m); 2 males and 38 females). Of the mice, 29 are from 14 AD-BXD strains, 2 are the C57B1/6J founder strain, 6 are the F1 B6/DBA/2J (D2) 5XFAD founder strain, and 3 are nontransgenic (Ntg)-BXD. Hemibrains were sent to Neuroscience Associates (NSA Inc., Knoxville, TN, USA) to be embedded, processed, and stained simultaneously in blocks of 40. The brains were freeze sectioned coronally at 40 μm intervals (not including the hypothalamus and cerebellum). Hemibrains were serially stained for thionine, NeuN, Iba1, GFAP, and AB1-42. Images were taken with 20x objective. Cropped and down-sampled images from NSA were processed using the QUINT workflow. Ilastik pixel classification was used to establish cell detection parameters for each stain. Brain sections were registered to the Allen Mouse Brain Atlas CCFv3 (2015) using the QuickNII software and refined using VisuAlign. Post-registration quality control assessment was performed using the novel QCAlign tool. Segmentation and registration steps were combined using Nutil Quantifier to output regional percent stain-positive coverage per region area, hereafter referred to as stain load. Regional changes in cell composition were assessed between animals.