View source for 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 <code>-SkipViews</code>. First exclusion point; typically used for obvious ice contamination or drifted views spotted in the pre-aligned stack.
* '''patch_tracking''' (''tiltxcorr xcorr_pt'') -- flag <code>-SkipViews</code>. Add views where patch tracks fail.
* '''bead_tracking''' (''beadtrack'') -- flag <code>-SkipViews</code>. Add views where fiducial beads are lost.
* '''seed_finding''' (''autofidseed'') -- '''no flag available'''. Exclusion is handled downstream by ''beadtrack''.
* '''fine_alignment''' (''tiltalign'') -- flag <code>-ExcludeList</code>. Drop views with large residuals.
* '''ctf_estimation''' (''ctfplotter'') -- flag <code>-ViewsToSkip</code>. Drop views with unreliable defocus fits. Optional linear step.
* '''ctf_correction''' (''ctfphaseflip'') -- no exclusion (processes views independently).
* '''tomogram reconstruction''' (''tilt'') -- flag <code>-EXCLUDELIST2</code>. Final opportunity, e.g. to drop extreme tilts.
* '''denoising half-reconstructions''' -- flag <code>-EXCLUDELIST2</code>. 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.

== See also ==

* [[CryoNAV Overview Tomogram Processing|Tomogram Processing Overview]]
* [[CryoNAV Key Concepts|Key Concepts]]
* [[CryoNAV Quick Start Guide|Quick Start Guide]]

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