TissUUmaps is a tool, but started out as a research project within the Wählby lab at the Dept. of IT, Uppsala University, Sweden, in 2015. Or to be completely true, it started in 2011, when Carolina Wählby was working at the Broad Institute, and was contacted by former collaborator Mats Nilsson at Stockholm University, who had invented a method to sequence mRNA directly in tissue sections, and needed computational tools to decode the image data. This led to a joint publication on in situ sequencing in Nature Methods in 2013, and a collaboration that is still ongoing.
Originally, the project was called TissueMaps, but to avoid confusion with other tools, we re-named it TissUUmaps, emphasizing out loyalty to ‘UU’, Uppsala University.
Apart from the TissUUmaps tool, the project as such has also generated several methods for pre- and post-processing of data from in situ sequencing experiments. We also work with learning-based methods to explore tissue morphology, with application in digital pathology. This research is presented in our publications, listed below.