Tg(Aldh1l1-EGFP)OFC789Gsat/Mmucd transgenic mice were used to visualize astrocytes in all in vivo engulfment assays. Pups were anaesthetized with isoflurane and 5 mg/kg LPS was injected i.p. at postnatal day 3. Twenty hours later 1 μl of cholera toxin-β subunit (CTB) conjugated with Alexa594 (Invitrogen, 1 mg/ml in normal saline) was injected into the contralateral eye. After 24 h mice were sacrificed and half had the dorsal LGN dissected out for microfluidic qPCR analysis, while the remainder were perfused with PBS followed by 4% paraformaldehyde at 70% cardiac output and brains were dissected, post-fixed overnight for 4 °C and transferred to 15% and 30% sucrose for 24 h each at 4 °C. Brains were sectioned at 50 μm and floating coronal sections containing dLGN were mounted on slide glasses and used for analysis of the dLGN. For each dLGN, two fields (the tip and medial portions of dLGN that contain both contra- and ipsilateral projections) were imaged using Zeiss LSM510 inverted confocal microscopy to obtain 50–70 consecutive optical sections with 0.3 μm interval thickness. ImageJ was used to remove outliers (radius
