GlioTrace example dataset

Description This dataset contains example region of interest (ROIs) stacks from time-lapse brain-slice data on migrating glioblastoma cells. Each .npz file stores the two channels (GFP and Lectin-594) as two separate NumPy arrays. Each array has the format height x width x time. The example dataset is divided into two subfolders, corresponding to data from two separate mice. Experimental metadata for the example data can be found in the separate Excel sheet. Dataset contents - `Example_data.zip` - main dataset file - `metadata.csv` - experimental metadata Data collection Live PDCX brain slices were imaged using a high-content confocal microscopy system. Whole-slice time-lapse Z-stack images were acquired at 10× magnification, using 9 × 9 tiled fields and 10-µm Z-steps, with imaging intervals of up to 2 hours for up to 5 days. Tumor cells were visualized through GFP fluorescence, while vascular and microglial/macrophage structures were visualized using the tissue-penetrant fluorescent conjugate TL-DyLight 594. Data processing The acquired images were tiled, registered and stabilized before selection of ROIs of the size 500 x 500 px. The selected ROIs were subsequently stabilized again to facilitate tracking. Related publication Mangukiya, Skeppås et al. Reconstructing the single-cell spatiotemporal dynamics of glioblastoma invasion. Nature Communications, 2026. Citation Please cite this dataset as: Mangukiya, H., Skeppås, M., et al. (2026). Reconstructing the single-cell spatiotemporal dynamics of glioblastoma invasion: GlioTrace example dataset. Zenodo. 10.5281/zenodo.21981544 Contact Madeleine Skeppås, [e-mail]