Fig. 1

Schematic representation of the main analysis workflow proposed described in MATISSE. The Cartesian coordinates of all reads found in the section analyzed is used to create the initial Matisse object. Several functionalities including KDE plots, colocalization analysis, gene quantification and gradient identification and analysis can be applied using this object as an input. Data can also be segmented, based on the cell boundaries, the location of individual spots or using a grid equally distributed along the section. Its output, stored in a second Matisse object, can be used for cell typing and clustering the data, among others