ACMEtool3
The ACMEtool3 (Automated Cell Measuring and Enumeration Tool) is a program that does image analysis in multiple channels. It was developed to analyze aquatic bacterial cells, concentrated on filter membranes and stained, usually with DAPI (4',6-diamidino-2-phenylindole) and FISH (fluorescent in-situ hybridization). It can also be used for simple cell counting, or more complex experiments, such as microautoradiograpy combined with FISH, or geneFISH. It can yield cell volumes, and signal intensities, and it was also applied on other objects than bacteria, i.e. erythrocytes and worm tissue. The program requires 8 bit grayscale images that follow a specific naming scheme, explained in the tutorial. It was specifically designed to be an easy and highly flexible tool to rapidly evaluate thousands of images in high throughput.
The program is available for free for any non-commercial purpose. However, it is a time-limited beta version. The program will expire after the beta phase, there will be a free version afterwards. The program requires a validation. A hardware ID will be transmitted to a validation server at each start. The usage of the software is at the user's own risk. There is no warranty whatsoever, and there is no guarantee that the obtained results are correct. Bug reports or feature requests are most welcome. For any question, contact: mzeder@technobiology.ch.
The program can be downloaded 
here.
There are two short video tutorials:
The first explains the basic concept and
the second shows you how to use the program.
A set of example images can be downloaded here.