Synapses in transmission electron micrographs

This dataset contains 13 transmission electron micrographs of Schaffer collateral and mossy fiber synapses in organotypic hippocampal slices.The data was published as part of the study [1]. It has been re-used for [2] to evaluate automated synaptic vesicle segmentation.For this data, organotypic slices were prepared from the hippocampi of neonatal mice using the interface protocol and vitrified after 28 day in vitro in culture medium supplemented with 20% (w/v) bovine serum albumin using an HPM100 (Leica) high-pressure freezing device. Automated freeze-substitution and epoxy embedding was performed as previously described (Imig and Cooper, 2017)57. Ultrastructural analysis was performed on 60 nm-thick sections postcontrasted with 1% aqueous uranyl acetate and Reynold’s lead citrate. Electron micrographs were acquired at 20 000 x magnification (pixel size = 0.592 nm) with an 80 kV LEO 912-Omega transmission electron microscope (Zeiss) equipped with a slow scan dual-speed CCD camera “Sharpeye” (Tröndle, Moorenweis, Germany).The data is organized in two different subfolders, "train_unlabeled", which was used for domain adaptation training and "test", which was used for evaluation.Each folder contains the micrographs and, if present, corresponding annotation in hdf5 files.The hdf5 files contain the following internal datasets:- raw: The electron micrograph.- labels/vesicles: The vesicle annotations, annotated in IMOD and export as instance masks (only for the files in "test")- labels/mask: A mask annotation that marks the areas with annotated vesicles (only for ths files in "test")

[1] Maus et al., Ultrastructural Correlates of Presynaptic Functional Heterogeneity in Hippocampal Synapses, Cell Reports, 2020, DOI: 10.1016/j.celrep.2020.02.083[2] Muth, Moschref et al., 2024, Preprint to be published