Bacterial cells are typically one thousandth the volume of mammalian cells, which places them near the edge of instrument detection. At this size it can be challenging to differentiate viable cells from debris of similar size

here's a trivial example of why the "standard" geometric mean  is not a good estimate of central tendency when you have values near  zero.

o improve accuracy, Sony hasintroduced the Weighted Least Square Method (WLSM) al-gorithm. In WLSM, the square value of residuals are individu-ally weighted

Additionally, make sure to use both forward and side scatter on log scale when measuring microparticles or microbiological samples like bacteria. These types of particles generate dim scatter signals that are close to the cytometer’s noise, so it’s often necessary to visualize signal on a log scale in order to separate the signal from scatter noise.

Side scatter measurement provides information about the internal complexity (i.e. granularity) of a cell. The interface between the laser and intracellular structures causes the light to refract or reflect. Cellular components that increase side scatter include granules and the nucleus (1). 

FSC intensity is proportional to the diameter of the cell, and is primarily due to light diffraction around the cell.

openCyto package is designed to facilitate the application of automated gating methods in a sequential way to mimic the construction of a manual gating scheme.

Flow Cytometry Analysis with R: the flowCore package

R (flowBeads

flow cytometry data were analyzed in R using the flowCore Bioconductor package (

flow cytometry using the red fluorescent nucleic acid dye SYTO17 as a counterstain to improve detection of cells with a low GFP signal

relative granulocity/internal complexity (Side Scatter - SSC)

relative size (Forward Scatter - FSC)