Abstract: A method and a system for analyzing a fluid sample for a biological activity. The method includes, providing a filter unit including a membrane having a front face and a rear face, passing the fluid sample through the filter membrane from its front face, applying the filter unit in a container, adding a medium into the container, and performing a scanning and image analyzing procedure of the filter membrane using at least one selected scanning wavelength. The scanning is an optical 3D scanning and includes acquiring a plurality of images along at least one scanning path.