Extended Data Fig. 4: Details of the SpaceM processing.

The SpaceM processing is composed of two parts: filtering ablation marks and normalizing metabolite intensities across single cells. First, for each cell, its touching ablation marks are filtered based on their area, their sampling proportions (proportion of the ablation mark area sampling any cell) and their sampling specificity (the proportion of their sampling area shared with the cell of interest). Ablation marks sampling predominantly extracellular areas or too many cells at the same time are filtered out (as illustrated here for the ablation mark II and III). Second, for a given metabolite, its intensity in a cell is calculated as a weighted mean of the metabolite intensities from the filtered ablation marks sampling that cell. The intensities are divided by the sampling proportion to account for differences in amount of sampled cellular material between ablation marks. To increase the contribution of ablation marks which sample the cell of interest more than other ablation marks, their intensities are weighted by the sampling specificity. ‘area(a)’ stands for the area of an ablation mark a; ‘sampling area(a)’ stands for the intracellular area of ablation mark ‘a’; ‘area(c)’ stands for the area of a cell ‘c’; all areas are computed in microscopy pixels.