Oocytes and embryos are often characterised using fluorescent staining or immunohistochemistry, typically Mitotracker reagents or FITC-conjugated antibodies combined with nuclear stains such as DAPI.  Succesful analysis relies largely on the acquisition of high quality images with sufficient resolution and a good signal to noise ratio.  High-end microscopy hardware, including the objective lens, still produce images that are subject to illumination and blur based problems, and these make the identification and analysis of regions of interest (ROI) innacurate and difficult.  To date, correction of such problems has been cumbersome and time-consuming for the average researcher, often requiring expensive software packages which are used to generate predominately subjective data.  To circumvent this we have developed a software system, specifically designed for follicles, but applicable to oocytes, embryos and other cell types, that automatically and objectively processes and analyses fluorescent images.  Using background image subtraction, flat-form correction, deconvolution, and image segmentation, our software system accurately removes the problems of autofluorescence, uneven illumination and blur, while providing statistical information and analysis about ROI intensity, size and distribution from which biological inferences can be made.  The software also has scope for multiple image comparison and overlay, image classification by size or intensity features, and feature recognition of 'unknown' images for image classification or analysis.  Comparison of our software's accuracy with more traditional techniques using other image processing software (Image J & Photoshop) has shown that our software is more accurate in identifying ROI outline through image processing and has significantly more available information, including intensity profiles for fluorescence distribution and computed difference images for quantitative analysis of stain colocalisation.  Our software also reduces labour time from hours to minutes.  This type of dedicated software could be a significant advance for fluorescence and light microscopy imaging of follicles, gametes and embryos.