I am interested in studying biofilm formation as a function of multiple variables, and would like to go beyond spectrophotometric/colorimetric/microplate readings and to analyze biofilm structures microscopically as well. Unfortunately, fluorescent microscopy and confocal laser scanning microscopy, tools that are routinely used by well-funded research groups for this purpose, are currently not at my disposal.
To this end, I am considering to utilize traditional staining (e.g., crystal violet) of these structures followed by simple light microscopy. May I ask for recommendations on objectively/quantitatively analyzing the images that can be generated this way (perhaps through a specific software)? Thank you!