Dear researchers
I have some doubts about biofilm roughness
Biofilm roughness provides a measure of how much the thickness of the biofilm varies, and is an indicator of biofilm heterogeneity.
so does increased biofilm roughness means the biofilm is patchy in some areas?
also what is the unit of measuring biofilm roughness?
Comstat does not provide an exact unit of measurement for biofilm roughness
BiofilmQ provides mentions the unit as (a.u.). So what is a.u. ??
Biofilm roughness refers to the surface irregularities and texture of a biofilm. It is typically quantified as the average deviation of the biofilm surface from a reference plane, often expressed in micrometers (µm) or nanometers (nm).
The biofilm with higher average roughness means more irregularities in the biofilm surface.
There are different methods for measuring biofilm roughness, including confocal laser scanning microscopy (CLSM), atomic force microscopy (AFM), and profilometry. CLSM and AFM are high-resolution imaging techniques that allow for the visualization and quantification of surface features at the micro and nanoscale, respectively. Profilometry is a non-destructive method that measures surface topography by scanning a stylus over the biofilm surface, generating a profile of surface features.
In general, the unit of measurement used for biofilm roughness will depend on the specific method used to quantify it, as well as the resolution and sensitivity of the measurement instrument.
The answer is with ChatGPT help.
Thanks Dr for the help.
I asked my professor for help..below was his response.
most biofilms are irregular because they need water channels between the stacks
Read the attached paper to get a better grasp on the topic.
au = arbitrary units
Schlafer S, Meyer RL. Confocal microscopy imaging of the biofilm matrix. J Microbiol Methods. 2017 Jul;138:50-59.
Thank you Dr for Sharing.
More details about the arbitrary units is here
Arbitrary units (AU) is a relative unit of measurement used in BiofilmQ software to express the roughness of biofilm surfaces. The AU is not a physical unit of measurement like micrometers or nanometers, but rather a dimensionless value that represents the degree of surface roughness relative to a reference surface.
In BiofilmQ, the roughness value of a biofilm is determined by the height values of the pixels that make up the biofilm surface, and the roughness value is then normalized to a reference surface. The reference surface is typically chosen to be the substrate or the glass slide on which the biofilm is grown. The normalized roughness value is expressed in arbitrary units (AU) and is directly proportional to the degree of surface roughness.
The use of arbitrary units allows for a standardized comparison of roughness values between different biofilms, even if the biofilms were grown under different experimental conditions or imaged using different imaging modalities. However, it is important to note that the exact numerical value of roughness in AU may not be directly comparable between studies or software programs that use different reference surfaces or normalization methods.
Depends of thickens and hardness and size of probe I using AFM or light profilometry. The unit is linear in most cases [um] or [nm].
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