ClusterAlign: A fiducial tracking and tilt series alignment tool for thick sample tomography

Abstract Thick specimens, as encountered in cryo-scanning transmission electron tomography, offer special challenges to conventional reconstruction workflows. The visibility of features, including gold nanoparticles introduced fiducial markers, varies strongly through the tilt series. As a result, tedious manual refinement may be required order produce successful alignment. Information from highly tilted views must often excluded detriment axial resolution reconstruction. We introduce here an approach series alignment based on identification particle clusters that transform coherently rotation, essentially those lie at similar depth. Clusters are identified by comparison with single untilted reference, rather than adjacent tilts. software, called ClusterAlign, proves robust poor signal noise ratio and varying individual fiducials is carrying ends where other methods tend fail. ClusterAlign used generate list tracked fiducials, align series, or perform complete 3D Tools evaluate error projection matching included. Execution involves no intervention, adherence standard file formats facilitates interface particularly IMOD/etomo, tomo3d, tomoalign.