This dataset provides samples (and suggested annotations plus results) to test and check the workflow for the continuous measurement of snGFR with volume modelling a z-stack of a proximal tubulus [1]. A detailed description of the algorithm used for this analysis is linked to the GitHub release of "cont-3D-snGFR" of the AG Hugo, Experimental Nephrology in the Department of Internal Medicine of the University Clinic Carl Gustav Carus at the Technische Universtität Dresden. [1] Kessel, F., Kröger, H. & Hugo, C. Continuous analysis of single nephron GFR. doi:10.5281/zenodo.4059549 (2020). Dataset1.lif contains additional sample files of 15 time series with their corresponding z-stacks. This dataset is published in the NEUBIAS gateway of F1000Research as extended data connected to the manuscript: Kessel F, Kröger H, Gerlach M et al. A new analysis approach for single nephron GFR in intravital microscopy of mice [version 1; peer review: awaiting peer review]. F1000Research 2020, 9:1372 (https://doi.org/10.12688/f1000research.26888.1)