CryoNAV Tilt Image Exclusion
In cryo-electron tomography, individual tilt images may be unusable due to ice contamination, beam-induced drift, tracking failures, or unreliable CTF fits. CryoNAV supports per-step frame exclusion: bad views are flagged (never physically removed) and propagated through the pipeline so that alignment, CTF estimation, and reconstruction skip them consistently.
Core principle: monotonic superset exclusion
Each processing step stores its own excluded_views parameter. Every downstream step's exclusion set must be a superset of the upstream step's -- views can be added but never un-excluded. The full stack is preserved on disk; exclusion is implemented via IMOD flags only.
To un-exclude a view, the user must re-run from the step where it was first dropped, invalidating all downstream products.
Per-step exclusion points
CryoNAV maps each pipeline step to its native IMOD flag:
- coarse_alignment (tiltxcorr) -- flag
-SkipViews. First exclusion point; typically used for obvious ice contamination or drifted views spotted in the pre-aligned stack. - patch_tracking (tiltxcorr xcorr_pt) -- flag
-SkipViews. Add views where patch tracks fail. - bead_tracking (beadtrack) -- flag
-SkipViews. Add views where fiducial beads are lost. - seed_finding (autofidseed) -- no flag available. Exclusion is handled downstream by beadtrack.
- fine_alignment (tiltalign) -- flag
-ExcludeList. Drop views with large residuals. - ctf_estimation (ctfplotter) -- flag
-ViewsToSkip. Drop views with unreliable defocus fits. Optional linear step. - ctf_correction (ctfphaseflip) -- no exclusion (processes views independently).
- tomogram reconstruction (tilt) -- flag
-EXCLUDELIST2. Final opportunity, e.g. to drop extreme tilts. - denoising half-reconstructions -- flag
-EXCLUDELIST2. Inherits independently per endpoint.
CTF as an optional linear step
CTF estimation sits between fine alignment and the endpoints per-endpoint. The upstream constraint for each endpoint is resolved as:
- Tomogram -- if CTF is in its path, inherits from ctf_estimation; otherwise from fine_alignment.
- Denoising -- same rule, evaluated independently.
Most common configuration: tomogram uses CTF (inherits CTF exclusions), denoising skips CTF (inherits only from fine alignment). A view dropped purely for a bad CTF fit need not be excluded from a denoised half that bypasses CTF.
Why exclusion matters downstream
- Alignment quality -- leaving in drifted or contaminated views inflates residuals and biases the tilt-axis solution.
- CTF reliability -- views with poor Thon-ring fits, if not skipped, contaminate the per-view defocus model.
- Reconstruction artifacts -- including bad views adds streak/ray artifacts in the back-projected volume.
- Reproducibility -- because exclusion is flag-based and stored per step, every reconstruction can be regenerated exactly from the recorded excluded_views plus the original stack.
UI convention
In the frame browser, each view is shown as: green (included), grey/locked (excluded upstream, inherited), or red (excluded at the current step). Submission is rejected if the user's set is not a superset of the upstream set.