Extended Data Fig. 2: Registration workflow of pre- and post-MALDI microscopy images.

Pen marks are drawn with a black sharpie on the glass slide at the edges of the culturing area. These black pen marks are visible in both the pre- and post-MALDI microscopy images. Histogram-based thresholding is applied to both microscopy images to extract the penmarks areas followed by an edge detection that detects pixels on the edge of the pen marks. This generates more than 400.000 individual features for each microscopy image. A random subset of 5000 features from both pre- (in blue) and post-MALDI (in red) images are used as fiducials to estimate the coordinate transformation for image registration. The overlap of both pre- and post-MALDI fiducials is illustrated. The estimated coordinate transformation from post- to pre-MALDI is applied to the ablation mark coordinates (shown in green) in order to estimate their position in the pre-MALDI microscopy image.