Fig. 1: Study design and QUINT workflow overview.
From: Detecting the effect of genetic diversity on brain composition in an Alzheimer’s disease mouse model
a Regional cell and amyloid-beta composition were quantified using the expanded QUINT workflow. (1) Raw images were processed to meet size requirements. (2) Brain sections were registered to the Allen Mouse Brain Atlas CCFv3 2015 in QuickNII and refined using VisuAlign. Hemibrain masks were created in QNLMask (3) Ilastik pixel classification was used to segment the images for the features-of-interest for each stain and converted to RGB format in FIJI. (4) Post-registration quality control assessment was performed using the QCAlign tool. (5) The output of the segmentation, registration, and mask creation steps were combined using Nutil to determine the percent stain-positive coverage per region area. b Immunohistochemistry was completed for an experimental cohort of 40 mice from the AD-BXD mouse model of AD (see Supplementary Table 1). Adapted from Neuner et al., 20199,90. Created with BioRender.com. c Representative images of brain sections of 6 m and 14 m mice were sectioned and stained for thionine, NeuN, GFAP, Iba1, and AB1-42. The red scale bar on each image represents 1000 µm. d Representative images from each step in the QUINT workflow. B6 C57BL/6J, Ntg Nontransgenic.
