https://home.cryonav.org/index.php?action=history&feed=atom&title=CryoNAV_Tilt_Image_Exclusion 2026-06-24T19:11:55Z Revision history for this page on the wiki MediaWiki 1.43.1 https://home.cryonav.org/index.php?title=CryoNAV_Tilt_Image_Exclusion&diff=106&oldid=prev 2026-05-20T20:57:40Z

<p>Bot edit via cryonavedit.py: add reference pages and screenshots</p> <p><b>New page</b></p><div>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 &#039;&#039;per-step frame exclusion&#039;&#039;: bad views are flagged (never physically removed) and propagated through the pipeline so that alignment, CTF estimation, and reconstruction skip them consistently.<br /> <br /> == Core principle: monotonic superset exclusion ==<br /> <br /> Each processing step stores its own &#039;&#039;&#039;excluded_views&#039;&#039;&#039; parameter. Every downstream step&#039;s exclusion set &#039;&#039;&#039;must be a superset&#039;&#039;&#039; of the upstream step&#039;s -- views can be added but &#039;&#039;&#039;never un-excluded&#039;&#039;&#039;. The full stack is preserved on disk; exclusion is implemented via IMOD flags only.<br /> <br /> To un-exclude a view, the user must re-run from the step where it was first dropped, invalidating all downstream products.<br /> <br /> == Per-step exclusion points ==<br /> <br /> CryoNAV maps each pipeline step to its native IMOD flag:<br /> <br /> * &#039;&#039;&#039;coarse_alignment&#039;&#039;&#039; (&#039;&#039;tiltxcorr&#039;&#039;) -- flag &lt;code&gt;-SkipViews&lt;/code&gt;. First exclusion point; typically used for obvious ice contamination or drifted views spotted in the pre-aligned stack.<br /> * &#039;&#039;&#039;patch_tracking&#039;&#039;&#039; (&#039;&#039;tiltxcorr xcorr_pt&#039;&#039;) -- flag &lt;code&gt;-SkipViews&lt;/code&gt;. Add views where patch tracks fail.<br /> * &#039;&#039;&#039;bead_tracking&#039;&#039;&#039; (&#039;&#039;beadtrack&#039;&#039;) -- flag &lt;code&gt;-SkipViews&lt;/code&gt;. Add views where fiducial beads are lost.<br /> * &#039;&#039;&#039;seed_finding&#039;&#039;&#039; (&#039;&#039;autofidseed&#039;&#039;) -- &#039;&#039;&#039;no flag available&#039;&#039;&#039;. Exclusion is handled downstream by &#039;&#039;beadtrack&#039;&#039;.<br /> * &#039;&#039;&#039;fine_alignment&#039;&#039;&#039; (&#039;&#039;tiltalign&#039;&#039;) -- flag &lt;code&gt;-ExcludeList&lt;/code&gt;. Drop views with large residuals.<br /> * &#039;&#039;&#039;ctf_estimation&#039;&#039;&#039; (&#039;&#039;ctfplotter&#039;&#039;) -- flag &lt;code&gt;-ViewsToSkip&lt;/code&gt;. Drop views with unreliable defocus fits. Optional linear step.<br /> * &#039;&#039;&#039;ctf_correction&#039;&#039;&#039; (&#039;&#039;ctfphaseflip&#039;&#039;) -- no exclusion (processes views independently).<br /> * &#039;&#039;&#039;tomogram reconstruction&#039;&#039;&#039; (&#039;&#039;tilt&#039;&#039;) -- flag &lt;code&gt;-EXCLUDELIST2&lt;/code&gt;. Final opportunity, e.g. to drop extreme tilts.<br /> * &#039;&#039;&#039;denoising half-reconstructions&#039;&#039;&#039; -- flag &lt;code&gt;-EXCLUDELIST2&lt;/code&gt;. Inherits independently per endpoint.<br /> <br /> == CTF as an optional linear step ==<br /> <br /> CTF estimation sits between fine alignment and the endpoints &#039;&#039;&#039;per-endpoint&#039;&#039;&#039;. The upstream constraint for each endpoint is resolved as:<br /> <br /> * &#039;&#039;&#039;Tomogram&#039;&#039;&#039; -- if CTF is in its path, inherits from &#039;&#039;ctf_estimation&#039;&#039;; otherwise from &#039;&#039;fine_alignment&#039;&#039;.<br /> * &#039;&#039;&#039;Denoising&#039;&#039;&#039; -- same rule, evaluated independently.<br /> <br /> 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.<br /> <br /> == Why exclusion matters downstream ==<br /> <br /> * &#039;&#039;&#039;Alignment quality&#039;&#039;&#039; -- leaving in drifted or contaminated views inflates residuals and biases the tilt-axis solution.<br /> * &#039;&#039;&#039;CTF reliability&#039;&#039;&#039; -- views with poor Thon-ring fits, if not skipped, contaminate the per-view defocus model.<br /> * &#039;&#039;&#039;Reconstruction artifacts&#039;&#039;&#039; -- including bad views adds streak/ray artifacts in the back-projected volume.<br /> * &#039;&#039;&#039;Reproducibility&#039;&#039;&#039; -- because exclusion is flag-based and stored per step, every reconstruction can be regenerated exactly from the recorded &#039;&#039;excluded_views&#039;&#039; plus the original stack.<br /> <br /> == UI convention ==<br /> <br /> In the frame browser, each view is shown as: &#039;&#039;&#039;green&#039;&#039;&#039; (included), &#039;&#039;&#039;grey/locked&#039;&#039;&#039; (excluded upstream, inherited), or &#039;&#039;&#039;red&#039;&#039;&#039; (excluded at the current step). Submission is rejected if the user&#039;s set is not a superset of the upstream set.<br /> <br /> == See also ==<br /> <br /> * [[CryoNAV Overview Tomogram Processing|Tomogram Processing Overview]]<br /> * [[CryoNAV Key Concepts|Key Concepts]]<br /> * [[CryoNAV Quick Start Guide|Quick Start Guide]]<br /> <br /> [[Category:Reference]]</div>

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