The main objective of this project is the development and application of an image acquisition system for identification of pathogenic microorganisms in real-time mode (or almost real-time). The system comprises an optical system and digital sensor aimed to images acquisition in the visible, ultraviolet and near infrared bands with the expected quality that will be able to feed an automatic image classification framework. The project includes the development of image processing and analyses tools for image enhancement and fine tuning of the acquisition kit, the definition of the image database and related metadata and also the development of a framework for image labelling and dataset creation for enabling supervised learning algorithms.