Actually in my experience automated cell counter work not bad and could give some additional information about size distributuion etc. but a bit more expensive. In experienced hands manual counting works good with very broad range of cell concentrations, take a comparable time, less sample volume, pipeting, moving in lab. Viability estimation also possible and all operations could be done in steril area.
If your lab has no problem with money then you can use pipetors with integrated cell counter. It will bring all cons in one solution. An alternative option if you are using cell for flow cytometry then just add FlowCount beads to calculate concentration.
I've attached below comparison of cell counting by all discussed methods. So manual counting sometimes could underestimate cell concentration.
Cell counting using Trypan Blue is a very common way to evaluate cell viability, however other methods such as MTT assays are also reliable. To be noted, in my experience, the MTT assays always have an upper limit for the plate reading, which depends on how long you plan to record the cell proliferation. You have to perform a pilot study to determine the doubling time of your cells, and how many cells you need to seed in a well, etc. If possible, you can evaluate the cell numbers using these two ways simultaneously.
In my humble opinion, if you are planning to work with the same cell line for exteded time, it is better to count manually. While counting you will get used to the healthy cellular morphology and get familiar with your cells. It is easier to point out if something went wrong with them. But it is only my preference.
Hi Delilah, in a nutshell: Statistics makes the difference. An automated counter takes several thousand cells into account, some instruments also simultaneously quantify debris, dead cells and aggreagates (e. g. CASY). Key is the precision you need, the time counting should take, and the information content you want.
However, I can only speak for CASY - below is some further reading.