Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow.

Abstract

Electron cryo-tomography (cryo-ET) is an imaging technique that produces relatively high-resolution three-dimensional images. With the advancement in microscopic and computational technologies, data collection and processing on both the hardware and software facets have become ever faster and more automated. Nowadays, tens of tilt series (up to several terabytes in total) can be collected per day, in turn shifting the experimental bottleneck to data processing. Here we present Ot2Rec, a novel workflow for performing tomographic image processing, providing access to several state-of-the-art tools within a single “wrapper” user interface. The functionality of Ot2Rec covers most tasks within a common image processing pipeline, from the motion-correction of raw multi-frame micrographs to the estimation of the true defoci from which the contrast transfer function (CTF) of images is calculated, and from the alignment of tilted image stacks to the full reconstruction of the final 3D tomogram. Moreover, Ot2Rec can carry out several novel post-processing operations such as simulation of stack point-spread functions and CTF corrections by means of deconvolution. Ot2Rec also provides automated reporting of processing parameters and quality metrics for optimisation and performance evaluation of processing workflows. Ot2Rec has been developed with the central philosophy of metadata unification. We have unified the metadata structure across the suite, so that the components within the suite can be used in a user/developer defined order (for instance, MotionCor2 -> CTFFind4 -> IMOD) with data flowing seamlessly between any pair of components and with consideration of required prerequisites. Lastly, Ot2Rec is an open-source program suite (Apache License V2). The raw code and documentation can be found at https://github.com/rosalindfranklininstitute/Ot2Rec.