Yes, you can calculate using the formula cfu/ml = (no. of colonies x dilution factor) / volume of culture plate for each individual replicates and then find an average.
in the microbiological control, for each dilution you use 2 dishes agar to minimize the error wich is considered as average, and then for the calculation you apply the following formula n ufc/ml or g = sum of colonies of all dishes containing between 30 and 300 / (n1 + 0.1n2) × v × d or you can use also the formula: n ufc/ml= number of colonies/d×v.
You first calculate the average (assuming the numbers relate to the same conditions) and then take the log of the average (e.g. for a logarithmic growth curve.
We calculate the CFU/dilution factor/organ weigth (individually) and after that, we calculate the average by group and applicate the logaritm of the average if necessary. When the CFU count is low we do not use log.
In some case is better to express CFU/organ. For example, in spleen when the organ weight can be affected by the lymphocyte proliferation. But the organ weigth is obligatory when the mass of the specimen is imprecise (for example skin, muscle, etc).
ST -- Hi. In our lab, we use three agar plate for each time point or sample (depending on the experiment), then calculate cfu/ml for each replicate separately and finally take the average of all the replicates with standard error.