Multimodal imaging of the dynamic brain tumor microenvironment during glioblastoma progression and in response to treatment

• The deposited data have been generated by intravital imaging of glioma-bearing mice, which allows one to longitudinally track different cell types during tumor progression and response to therapy. • Raw and processed data are divided into two folders, based on the cell lineage-tracing model used (either CX3CR1 or FLT3 lineage-tracing model). • Each folder contains the raw imaging data and an R script folder. • The raw imaging data consist of “Statistics”, parameters extracted after analysis with Imaris (.csv files).

Each subfolder represents a specific timepoint for a unique imaging position in one individual mouse. Note that each segmented component (microglia (MG), second harmonic generation (SHG, measuring collagen), and tumor cells) have their own individual subfolder. • The R script folder contains 3 files: the source file containing custom functions for processing and visualization; the processing file which combines imaging- and metadata, and transforms this into a single experimental object in R; and the output file which presents the analyses and visualizations of the data.