A recent published chapter co-authored by Charles Ellis, a third-year SoCoBio DTP student at the University of Southampton, presents methodological approaches to delineate / analyse lysosomes and other intracellular trafficking vesicles using three open-access programmes (Fiji, CellProfiler and Icy). These semi-automated workflows are described in a step-by-step manner to help users produce results rapidly from 2D and 3D fluorescence datasets. The chapter also describes the advantages and limitations of each approach / programme, whilst providing notated insights into the design and purpose of each step.

These approaches were designed in collaboration with Dr. David S. Chatelet (Biomedical Imaging Unit, University of Southampton & University Hospital Southampton) and Dr. J. Arjuna Ratnayaka (University of Southampton).

See the chapter online here: https://link.springer.com/protocol/10.1007/7651_2025_657