A scalable and modular automated pipeline for stitching of large electron microscopy datasets

Serial-section electron microscopy (ssEM) is the method of choice for studying macroscopic biological samples at extremely high resolution in three dimensions. In the nervous system, nanometer-scale images are necessary to reconstruct dense neural wiring diagrams in the brain, so -called . The data...

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Bibliographic Details
Published in:	eLife Vol. 11
Main Authors:	Mahalingam, Gayathri, Torres, Russel, Kapner, Daniel, Trautman, Eric T, Fliss, Tim, Seshamani, Shamishtaa, Perlman, Eric, Young, Rob, Kinn, Samuel, Buchanan, JoAnn, Takeno, Marc M, Yin, Wenjing, Bumbarger, Daniel J, Gwinn, Ryder P, Nyhus, Julie, Lein, Ed, Smith, Steven J, Reid, R Clay, Khairy, Khaled A, Saalfeld, Stephan, Collman, Forrest, Macarico da Costa, Nuno
Format:	Journal Article
Language:	English
Published:	England eLife Sciences Publications, Ltd 26-07-2022 eLife Sciences Publications Ltd
Subjects:	Algorithms Animals Brain Cell Biology connectomics Drosophila melanogaster Humans image alignment image processing Image Processing, Computer-Assisted - methods image stitching large-scale microscopy Mice Microscopy, Electron Neuroscience Software Tools and Resources image processing mouse connectomics cell biology image stitching neuroscience large-scale microscopy image alignment human
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Summary:	Serial-section electron microscopy (ssEM) is the method of choice for studying macroscopic biological samples at extremely high resolution in three dimensions. In the nervous system, nanometer-scale images are necessary to reconstruct dense neural wiring diagrams in the brain, so -called . The data that can comprise of up to 10 individual EM images must be assembled into a volume, requiring seamless 2D registration from physical section followed by 3D alignment of the stitched sections. The high throughput of ssEM necessitates 2D stitching to be done at the pace of imaging, which currently produces tens of terabytes per day. To achieve this, we present a modular volume assembly software pipeline (Assembly Stitching and Alignment Pipeline) that is scalable to datasets containing petabytes of data and parallelized to work in a distributed computational environment. The pipeline is built on top of the Trautman and Saalfeld (2019) services used in the volume assembly of the brain of adult (Zheng et al. 2018). It achieves high throughput by operating only on image meta-data and transformations. ASAP is modular, allowing for easy incorporation of new algorithms without significant changes in the workflow. The entire software pipeline includes a complete set of tools for stitching, automated quality control, 3D section alignment, and final rendering of the assembled volume to disk. ASAP has been deployed for continuous stitching of several large-scale datasets of the mouse visual cortex and human brain samples including one cubic millimeter of mouse visual cortex (Yin et al. 2020); Microns Consortium et al. (2021) at speeds that exceed imaging. The pipeline also has multi-channel processing capabilities and can be applied to fluorescence and multi-modal datasets like array tomography.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors contributed equally to this work.
ISSN:	2050-084X 2050-084X
DOI:	10.7554/eLife.76534