Notes:
First:
Manual analysis of images can be a laborous and time consuming task.
With automatic acquisition you can create very big data sets without too much effort. This is fine because it allows you to do new kinds of experiments and observations. However to be useful the acquired data has to be analysed afterwards to get the answer to the question under examination.
Thus automatic analysis and the rationalization of manual analysis are needed.
Second:
The available tools are doing a great job for the tasks they were made for. However they are general purpose, providing solutions for most common tasks. They can´t take into account knowledge about your special experiment that might be essential for doing the required analysis.
If you need some functionallity not provided you can´t simply ask your informatique expert of choice to add it. You have to ask the producer and wait for a new release of the software.