Cell were counted using Visiopharm stereological software45. Fluorescence intensity measurements (FIM) were performed using Zen 2.0 Blue Imaging software in randomly selected Regions of Interest (ROIs) within organoid regions listed in the figure legends. All images acquired were in the linear range of the camera. Images of sections from control and schizophrenia organoids were acquired under identical illumination conditions and identical camera gain, offset, and exposure times. Background images (outside the tissue sections) were taken and subtracted from the images of stained sections. The total area of each ROI image was recorded, as well as the number of thresholded pixels and their integrated intensity. Each channel was converted into the eight-bit grayscale and the mean intensity was calculated. Statistical analysis was performed using t-test in MiniTab software and data is presented as mean ± Standard Error of the Mean (SEM). For detailed protocols see Supplementary Methods.
