Fig. 1
Impact of MALDI-MSI on tissue and spatial transcriptomics data quality using control mouse brain tissue and GBM-derived cells. (A) DAPI-based cell segmentation (nucleus + 5 µm) control versus MALDI-MSI regions. Maximum-intensity projections of DAPI fluorescence in control (left) and MALDI-MSI (right) measured mouse brain. White outlines indicate cell boundaries defined by DAPI segmentation with a 5 µm radial expansion. The MALDI spot grid appears as a regular array of fluorescent micro-dots on the MALDI-MSI measured section but does not interfere with nuclear detection or boundary detection. Scale bar: 50 µm. (B) Scanning electron micrograph of a GBM-derived cell on ITO after MALDI-MSI showing superficial surface modification. Boxplots compare (C) total transcript counts per cell and (D) number of detected transcripts per area (mm2) between MALDI-MSI measured and non-MALDI-MSI measured (Control) mouse brain sections (≥ 40,000 cells per section). For the transcripts per area, 5 anatomical similar regions of 1mm2 were analysed on both tissues. Statistical significance was assessed by paired student T-test (** p < 0.005; * p < 0.05).
