Zen black

tagPAINT images were processed using Zeiss Zen Black software. The position of bound imaging strands in the acquisition was determined by Gaussian fitting, using a peak mask radius size of 6 pixels and a signal to noise ratio cut-off of 8. The localization data were then drift corrected using the point patterns generated from the localization of gold nanorod fiducials within the field of view using the Zeiss Zen Black software drift correction. The point pattern data were then convolved with a Gaussian kernel using the ThunderSTORM plugin in Fiji, with a pixel size of 9.7 nm. The median precision values were extracted from the distribution of precision values (electronic supplementary material, figure S2) given in the output of the Zen processing.

BMDM (2 × 10⁵) were plated on glass coverslips in 24-well plates and treated with 1 μg/ml of C. trachomatis LPS or 1 μg/ml E. coli LPS and or were untreated as a control. At 5 min posttreatment, cells were fixed in 2% paraformaldehyde (PFA) for 10 min at room temperature and blocked for 1 h in a 1× PBS solution containing 0.3% Triton X-100 and 100 mg/ml goat serum at room temperature. Cells were immunostained with 1× PBS-1% BSA-0.3% Triton solution containing anti-CD14 antibody. Primary antibody rat anti-mouse CD14 (4C1) was used at a 1:200 dilution. Secondary antibodies were used at 1:400 (Alexa Fluor 555 goat anti-rat). Coverslips were stained with DAPI at 1:1,000 in PBS for 5 min and mounted using Prolong Gold. High-resolution images were captured using a Zeiss 880 laser scanning microscope with an Airyscan detector. Intensity histograms measuring signal intensity of blue-channel DAPI and red-channel anti-CD14 were produced by tracing a histogram line through representative cell populations and processed in Zen Black (Carl Zeiss Imaging). Z-stack projections were imaged at an interval of 0.2 μm. All images were processed in Zen Blue and Zen Black (Carl Zeiss Imaging).

Coronal slices were serially collected and analyzed from the OB (+4 mm from Bregma) to the cortical amygdala (−0.5 mm from bregma). To evaluate cell density for each imaged slice, immunopositive somatas were manually counted for each subdivision and the surface of subdivision was measured (Zeiss Zen Black, Zeiss). Counting was blind to the genotype in SOM-Cre, PV-Cre and VIP-Cre mice. Values for each subregion are averaged across sections for each mouse and used to calculate the mean cell density (averaged number of cells per mm²) and mean proportion of cells (% of cells counted in each subdivision relative to the total number of cells labeled in the respective brain). One out of every four slices were used for GFP counting in Fig. 2c. One out of every six slices were used for GFP/SOM colocalization in Fig. 2g.