The large advantage in confocal is thin "depth-of-field" so I am not sure
why you would want to counter it.  You computer should not be memory
limited - this sort of disaster only occurred on very early turnkey
systems.  As far as number of steps in the Z-axis, what is the size of a
bacterial cell?  This is the primary factor in deciding what the minimum
step size should be.  As far as time goes, unless your "event" or "feature"
has time-dependent characteristics, a general rule-of-thumb with most
measuring devices is "the more information, the better".  This means have
patience, let the device collect your data in the manner you know will give
best resolution, get a cup of coffee or chat up the new colleague  while
you wait.
Rob Palmer
CEB/UT

>I was happy to see this thread develop.  I am also just moving into the
>confocal stages of a microbial ecology project (also utilizing ssu rRNA
>probes).
>None of the previous replies has mentioned the depth of field trade off one
>suffers when increasing magnification. I am under the impression that
>because 63x objective provides greater depth of field one can afford fewer
>steps along the z-axis. I assume this saves time in imaging and analysis
>and, obviously, memory.
>Do these assumptions hold or is my confocal inexperience showing?
>
>Kevin Brent Smith
>University of Louisville Biology Dept.
>