Synapses in transmission electron micrographs

<p>This dataset contains 13 transmission electron micrographs of Schaffer collateral and mossy fiber synapses in organotypic hippocampal slices.<br>The data was published as part of the study [1]. It has been re-used for [2] to evaluate automated synaptic vesicle segmentation.<br>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&rsquo;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 &ldquo;Sharpeye&rdquo; (Tr&ouml;ndle, Moorenweis, Germany).<br>The data is organized in two different subfolders, "train_unlabeled", which was used for domain adaptation training and "test", which was used for evaluation.<br>Each folder contains the micrographs and, if present, corresponding annotation in hdf5 files.<br>The hdf5 files contain the following internal datasets:<br>- raw: The electron micrograph.<br>- labels/vesicles: The vesicle annotations, annotated in IMOD and export as instance masks (only for the files in "test")<br>- labels/mask: A mask annotation that marks the areas with annotated vesicles (only for ths files in "test")</p> <p>[1] Maus et al., Ultrastructural Correlates of Presynaptic Functional Heterogeneity in Hippocampal Synapses, Cell Reports, 2020, DOI: 10.1016/j.celrep.2020.02.083<br>[2] Muth, Moschref et al., 2024, Preprint to be published</p>