Quantifying the Effects of Antimicrobials on <em>In vitro</em> Biofilm Architecture using COMSTAT Software

Caffeic Acid Phenethyl Ester (CAPE) Inhibits Cross-Kingdom Biofilm Formation of Streptococcus mutans and Candida albicans

“…Double-channel scanning was performed with the green channel (at an excitation wavelength of 488 nm) and the red channel (at an excitation wavelength of 561 nm) ( 52 ). Three points were randomly selected for the inspection of every specimen, the quantified statistical results of fluorescence intensity and the biofilm thickness of the three-dimensional reconstruction images were assessed using ImageJ COMSTAT software ( 53 , 54 ).…”

“…Double-channel scanning inspections were performed with the green channel (at an excitation wavelength of 488 nm) and the red channel (at an excitation wavelength of 561 nm). Three random points were selected for the investigation of each sample, and the quantified fluorescence intensity was assessed with ImageJ COMSTAT software ( 53 ).…”

Pseudomonas aeruginosa aggregation and Psl expression in sputum is associated with antibiotic eradication failure in children with cystic fibrosis

“…Quantification of biovolume intensity and Psl antibody binding within P. aeruginosa biofilms was calculated, as previously described herein, using Volocity. To measure P. aeruginosa aggregation, surface-to-biovolume ratio was quantified using Comstat2 software as a plugin to ImageJ, as previously described 33 .…”

“…Pseudomonas aeruginosa biofilm growth in glass slide chamber and imaging. Pseudomonas aeruginosa isolates recovered from the sputum specimens were grown as biofilms using a Nunc Lab-Tek II, 8-chambered cover glass slide (Thermo Fisher Scientific, Mississauga, ON), previously described 33 . In brief, P. aeruginosa was grown in LB (optimal for growing biofilms in the glass slide chamber) for 24 h at 37 °C with shaking (225 rpm).…”

How to study biofilms: technological advancements in clinical biofilm research

“…Although CLSM uses fluorescence to visualise samples, it is different from fluorescence microscopy due to the pinpoint laser which improves resolution and the scanning of the laser through the sample on the x, y and z planes which provides z -stack images which can be reconstructed using open-source software such as COMSTAT2 ( Vorregaard, 2008 ; Samarian et al., 2014 ) and BiofilmQ ( Hartmann et al., 2021 ) . The information obtained from z -stack image analysis can provide information on biofilm depth, biomass, and surface area which is useful to compare biofilm characteristics when exposed to different molecules, along with live/dead staining ( Figures 2A, B ) which can show the distribution of bacterial viability within the biofilm ( Bridier et al., 2010 ; Morris et al., 2020 ; Cleaver et al., 2021 ). Specific dyes and probes can be used, such as FM 1-43, fluorescent in situ hybridisation (FISH) probes ( Thurnheer et al., 2004 ; Malic et al., 2009 ; Lebeer et al., 2011 ), and carboxy-SNARF ( Corsini et al., 2021 ) for the monitoring of pH within the biofilm.…”