AlignEM-SWiFT: Graphical Interface for Aligning Electron Micrographs Using Signal Whitening Fourier Transforms

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Yancey, J. G.
Bartol, T. M.
Wetzel, A.
Carson, J.
Mendenhall, J. M.
Thiyagarajan, V.
Kuwajima, M.
Harris, K. M.
Sejnowski, T. J.

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We have built an intuitive graphical user interface for aligning serial section electron micrographs (ssEM) using Signal Whitening Fourier Transforms (SWiFT). AlignEM-SWiFT is a graphical extension of SWiFT-IR, a proven suite of image registration programs developed by computer scientist Arthur Wetzel at the Pittsburgh Supercomputing Center. The SWiFT-IR approach achieves high precision image matching but requires specific mathematical understanding that limits its accessibility. AlignEM-SWiFT circumvents shell scripting by generalizing low-level computer instructions and forging useful high-level abstractions. It is able to generate scale image hierarchies, compute affine transforms, generate aligned images using multi-image rendering, generate model images using remodeling, and create alignments with a global 3D coordinate system. Exported alignments comply with the Next- generation File Formats (NGFF) specification. An embedded Neuroglancer viewer enables instantaneous volumetric rendering of exported alignments inside the application window. The control panel adjusts to user needs based on a checkpoint mechanism for tracking project completeness. It also has a terminal- like output display for monitoring running processes. Users new to EM alignment will benefit from on- board documentation, descriptive warning dialogs, and instructive tooltips. Advanced controls and debugging features are available in the menubar. We are developing support for user-defined alignment scenarios or ""recipes"" comprised of interchangeable alignment modules or ""ingredients"". While AlignEM-SWiFT is currently deployed and available to the community via the Workbench at the Texas Advanced Computing Center (TACC), the work presented here is germane to the latest version which is just days away from being deployed to TACC. This software is part of an effort to integrate with other open-source EM technologies being developed at TACC. Our integrated 3DEM analysis platform will include tools for segmentation, annotation, reconstruction, and tomography.


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