Open-source resources and technologies developed in the group.

The Spa-RQ tool package was designed for spatial phenotyping on stained serial sections. It contains two independent software domains: ‘Spa-R' for image registration and 'Spa-Q' for DAB co-stained signal quantification. Spa-R can be used to register pairs or batches of input images of a variety of formats, including TIFF, JPEG and PNG. Spa-Q measures the areas of two individual DAB signals, and determines the area of their overlap (OL) in multiple annotated regions. Spa-RQ is available open source, compatible with both Windows and Mac systems.


Journal of Visualized Experiments article on tumour tissue slice explants

Organotypic primary tissue explant cultures, which include precision-cut slices, represent the three-dimensional tissue architecture as well as the multicellular interactions of native tissue. In this video article, we show how to generate murine lung tumour slices and culture them in a rotating incubation unit. We also demonstrate how slices should be systematically analysed to depict the intra-tumour heterogeneity of expressed biomarkers.