in addition to having the microscope and cell counter, I think that you are going to need a very accurate way of making dilutions. There are way too many cells involved with brewing to go straight to a cell count. I'd imagine that you'd need to be able to do something like a 1:1,000,000,000 or more dilution. You don't want to do that in one step. Usually avoiding dilutions greater than 1:100 is ideal. You can accomplish large dilutions by doing "serial dilutions". Serial dilutions involve repeating the same dilution over and over again. So say you do a 1:100 dilution first. Then you mix that up well and do another 1:100 dilution. your second solution is now a 1:10,000. If you made a third 1:100 dilution, you'd be at 1:1,000,000.
Here's the thing, if you don't have the means of pipetting accurately, each 1:100 dilution is going to be off by a percentage. Each time you make that dilution for the serial dilution your percent accuracy is getting further from what you'd desire.
In our lab we had variable volume pipettors that cost about $200-$300 USD each. That way when I'd do a 1:100 dilution i can add 10uL (0.01mL) to 0.990mL with less than 0.1% error.
Here's a link to white labs for their procedure on counting cells.
http://www.whitelabs.com/beer/cell_count.html
