Movie S1 - Automated Transmission-Mode Scanning Electron Microscopy (tSEM) for Large Volume Analysis at Nanoscale Resolution

Serial tSEM images aligned with elastic alignment tool. Here 201 serial section images were acquired from the rat dentate gyrus on tSEM at 16,384×16,384 pixels (2 nm/pixel), and aligned as described in Methods using Fiji/TrakEM2 software. The aligned images were then cropped to 12,830×6,861 pixels (25.66 µm×13.72 µm) and down-sampled to 1,920×799 pixels in Fiji/TrakEM2. The image histograms were adjusted using Fiji with the “Enhance Local Contrast (CLAHE)” plugin (http://fiji.sc/wiki/index.php/Enhance_Local_Contrast_(CLAHE)) before this movie (7 frames/sec) was generated. This movie demonstrates the effectiveness of the elastic alignment tool, where the presence of various section artifacts (e.g., folds and staining artifacts) does not affect the alignment of artifact-free regions across large serial tSEM images.
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