In biological applications and systems where even the smallest details have a meaning, CCD cameras are mostly preferred and they hold most of the market share despite their high costs. In this paper, we propose a custom-designed CMOS camera to compete with the default CCD camera of an inverted microscope for fluorescence imaging. The custom-designed camera includes a commercially available mid-performance CMOS image sensor and a Field-Programmable Gate Array (FPGA) based hardware platform (FPGA4U). The high cost CCD camera of the microscope is replaced by the custom-designed CMOS camera and the two are quantitatively compared for a specific application where an Estrogen Reception (ER) expression in breast cancer diagnostic samples that emits light at 665nm has been imaged by both cameras. The gray-scale images collected by both cameras show a very similar intensity distribution. In addition, normalized white pixels after thresholding resulted in 4.96% for CCD and 3.38% for CMOS. The results and images after thresholding show that depending on the application even a mid-performance CMOS camera can provide enough image quality when the target is localization of fluorescent stained biological details. Therefore the cost of the cameras can be drastically reduced while benefiting from the inherent advantages of CMOS devices plus adding more features and flexibility to the camera systems with FPGAs.