Fig. 1

Annotation Regions. The average fluorescent intensity and percent positivity of GFAP were quantified in representative sections of the cortical gyrus (yellow box in A, field of view in B–F) and sulcus (not highlighted) using a modified version of the Area Quantification FL analysis algorithm in HALO. Annotations were generated by switching to the brightfield view and using the magnetic pen tool to delineate the grey-white matter border in the dapi and autofluorescence channels (B, black). The pen tool was then used to outline a 2 mm portion of the grey-white border (C, yellow), and a 200 µm GWMI annotation was produced using the marginal partitioning tool (D, yellow). A 2 mm line was then drawn at the cortical surface and the marginal partitioning tool was used to generate a 200 µm subpial annotation (E, yellow arrow head). The brush tool was used to annotate the cortical grey matter spanning between the subpial and GWMI annotations (E, white arrow head). Composite image showing all annotations with the GFAP channel in darkfield view (F). Green = GFAP, blue = DAPI. Scale bars: A = 5 mm, B–F = 1 mm