Hybridization probes were incubated at concentrations of 100 nM each in hybridization buffer (1M NaTCA, 5mM EDTA, 50mM Tris pH7.4, 0.2mg.mL Heparin in DEPC water) for two hours at 37ºC and 100% humidity. The sections were then incubated with ligase buffer and phosphorylated common bridge and connector circle oligos at 10 nM for 60 minutes and then with ligase buffer, T4 ligase, and ligase buffer for two hours under the same conditions. DNA amplification was then accomplished using Phi-29 polymerase (Lucigen-30221) in polymerase buffer at the same conditions overnight. After the reaction was complete, slides were washed with label buffer (2X SCC/20% Formamide in DEPC water) and then incubated with 100nM Tye705 label probe in label probe buffer for one hour in the same conditions. Immunofluorescent co-staining and imaging were obtained and analyzed as follows. Negative controls of secondary antibody alone and reactions performed with identically labeled probes for the bacteria Bacillus subtilis gene mgsA were imaged and used for thresholding for quantitative image analysis. All probes were ordered from Integrated DNA Technologies, target probes were ordered with standard desalting and all probes were stored as 100μM stocks.