Invited Speaker
Full spectrum flow cytometry enables high-dimensional characterisation of cellular phenotypes in complex biological systems by capturing the entire emission profile of fluorochromes. An important feature is its capacity to detect and remove cellular autofluorescence, a variable background signal that limits sensitivity and resolution. Despite the recognised success of full-spectrum flow cytometry in high-dimensional immunophenotyping, its broader application remains limited. Here, we present a generalisable workflow that integrates instrument customisation with autofluorescence removal to improve signal resolution. Using this workflow, we successfully characterised a niche-labelling mouse model that is otherwise impossible to resolve using conventional flow cytometry. In addition, this approach allows simultaneous detection of high- and low-intensity signals and accurate identification of cellular populations. This workflow also highlights the importance of coordinated instrument customisation and autofluorescence removal in full-spectrum flow cytometry, enabling its broad application in complex biological systems.