Microscopic analysis forms an integral part of many scientific studies. It is a task which requires great expertise and care. However, it can often be an extremely repetitive and labourious task. In some cases many hundreds of slides may need to be analysed, a process that will require each slide to be meticulously examined. Machine vision tools could be used to help assist in just such repetitive and tedious tasks. However, many machine vision solutions involve a lengthy data acquisition phase and in many cases result in systems that are highly specialised and not easily adaptable. In this paper, we describe a framework that applies flexible machine vision techniques to microscope analysis and utilises active learning to help overcome the data acquisition and adaptability problems. In particular we investigate the potential of various aspects of our proposed framework on a particular real world microscopic task, the recognition of parasite eggs.