SIMPLI output files

Output files generated by the automated image processing software SIMPLI (https://github.com/ciccalab/SIMPLI - https://doi.org/10.1038/s41467-022-28470-x).<b>area_measurements: </b>quantification of total pixel area in the ROI positive for each marker used. These quantification was used to determine the total deposition of amyloid-b and pTau (Fig. S4.B-I), as well as synapses markers (NTNG2 and Synaprophysin; Fig. S3.A) and myelin (PLP1; Fig. S6.E).<b>clustered_cells: </b>list of all nuclei segmented in all ROIs (rows). Mean signal instensity per marker analysed is indicated in the "Intensity_MeanIntensity_" columns. This quantification was used for nuclei clustering by Seurat integrated in SIMPLI (cluster # to which each cell was assiged is indicated in the "res_0.9_ids" column, which indicate the clustering resolution; Fig. S2.A). X and Y location of segmented nuclei in the ROI is also indicated in the "Location_Center_X" and "Location_Center_Y" columns, which was used to determine nuclei distribution in each cortical layer (Fig. 2.D; Fig. 3. B,D,F; Fig. S6.H). The quantification of mean signal instensity in the "Intensity_MeanIntensity_Ab" and "Intensity_MeanIntensity_pTau" columns was used to quantify intracellular signal for amyloid-b and pTau respectively (Fig. 4).<b>all_cells-clusters: </b>same as clustered_cells.csv file but with the correct format to be used for spatial interactions analyses using the imcRtools package built by the Bodenmiller group. Spatial interactions were quantified between neuronal and glial populations (Fig. 5.e and Fig. S6.f,g).<br><br>