Software & Data Processing
Where the principles meet practice: real Cryo-ET data passes through a whole processing pipeline before it can be reconstructed and analysed. This base follows that pipeline — movie frames and motion correction, gold-fiducial alignment, CTF and dose weighting, even/odd splitting — and then how to use IMOD and ChimeraX to process the data and see the reconstructed volume.
Articles in this base 7 articles
Data-processing overview: from raw frames to 3D structure
An end-to-end roadmap — from a pile of raw movie frames to a 3-D structure you can view and segment, with what each step uses and what it produces
Movie frames and motion correction
A modern detector records a movie, not a picture — align the frames, dose-weight them, and sum, before anything else can happen
Data processing: CTF and dose weighting
The preprocessing between alignment and reconstruction — estimate and correct the CTF, weight by dose, and deconvolve to lift low-frequency contrast
Gold-fiducial alignment
Before reconstruction every tilt image must land in one common 3D frame — using gold beads as fiducials, or markerless patch tracking
Even/odd splitting
Cut the data into two copies with independent noise but identical signal — score resolution with FSC, and power self-supervised denoising
Running training: self-supervised missing-wedge restoration
With public tools, hand a noisy, missing-wedge tomogram to a network that needs no ground truth — prepare, train, predict, step by step
ChimeraX and IMOD: seeing and segmenting the 3D
The two tools you can't avoid in practice — IMOD to align and reconstruct, then a step-by-step tutorial for visualizing your MRC volume in ChimeraX, saving a figure, and tracing the structures out of it.