You can use SEM. Basic staining methods can also be applied.

Thanks Sir, But I am looking for quantitative methods to measure the aggregation/co-aggregation between bacteria and filamentous fungi. Methods are available on bacteria-yeast aggregation, but not on bacteria-filamentous fungi

Thanks for your input. Regards

Or you can use FISH/other fluorescent staining and stain the biofilm, followed by fluorescence microscopy and image analysis. If you type something like "biofilm fungi bacteria fluorescence" into pubmed you will see a lot of these studies.

Thanks Sir for your suggestion

Thanks Sir for your suggestion