AreTomoLive: automated reconstruction of comprehensively corrected and denoised cryo-electron tomograms in real time...

High-throughput data processing is necessary to realize the full potential of cryo-electron tomography and subtomogram averaging. The field's fragmented software landscape remains a considerable hurdle to this end. Here we present AreTomoLive, an automated preprocessing pipeline composed of two GPU-accelerated packages. The first, AreTomo3, streamlines tomographic alignment and reconstruction, with new features to fully account for sample geometry and locally correct the contrast transfer function. The second package, DenoisET, leverages AreTomo3's comprehensively corrected tomograms to retain more intermediate-resolution features during contrast enhancement. Collectively, this pipeline prioritizes automation to support data preprocessing concurrent with data collection at scale.