Supplementary datasets for the paper Calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization. Two deskewed and deconvolved lattice light-sheet datasets (100 frames each) from the live-cell experiments are available, a control embryo dataset (01-07-2016_TimeLapse4_DMSO_21hrs_Calcein_FM464) and a VEGFR inhibited dataset (24-06-2016_Timelapse1_Axtinib_150_19hrs_Calcein_FM464). These datasets were used for collecting size and motion statistics. The control embryo dataset is available in raw microscope output without deskew or deconvolution applied (Raw_01-07-2016_TimeLapse4_DMSO_21hrs_Calcein_FM464). Four confocal datasets from the cytoskeletal remodeling experiments are also included, phalloidin stained images, control (Phalloidin PMC DMSO 5 zoom4s) and VEGFR inhibited (Phalloidin PMC Axt 18 zoom4); and myosinIIP stained images, control (Myosin PMC 30h DMSO new slid 4a zoom4) and VEGFR inhibited (Phalloidin PMC Axt 18 zoom4). Source code and instructions for the analysis tools used for both the lattice light-sheet and confocal data is available at: https://git-bioimage.coe.drexel.edu/opensource/llsm-calcium-vesicles-lever Code for the deconvolution and deskew algorithms is available from the Janelia research center at: https://www.janelia.org/open-science/lattice-light-deconvolution-software-cudadeconv