Biofilm-Quantification

MATLAB Code for 3D volume quantification of bacterial biofilms

Code requires bioformats MATLAB Toolbox and MATLAB version R2021a or higher.

The script is designed to quantify Biofilm volumes. The biofilms should be stained with the common live cell/dead cell staining kit, i.e, Syto 9 and propidium iodide, respectively. Code assumes that the biofilms are tiffs and stored as z-stacks.

Note: Dye labeling and fluorescence with Syto9 and propidium iodide vary by strain,concentrations used, and environmental conditions. It is the responsibility of the domain researcher and analysist to determine labeling concentrations for their dyes and validate results using other methods.

Briefly, the code expects users to have 16-bit images, tif format, with two channels interleaved. The code will deinterleave the PI and Syto9 channels from the multidimensional tiff stack and perform Otsu’s method on each channel to determine a threshold. The thresholds determined are used to display the volume using MATLABs labelvolshow and to compute the number of voxels in the deinterleaved channels, this is, PI and Syto 9, respectively.