Patch Motionis a very fast, auto-tuning patch-based local motion correction method built on top of CryoSPARC's original
Local Motion Correctionmethod (a variant of alignparts).
Patch Motionperforms the functions of both
Full-frame Motion Correctionand
Local Motion Correctionin one job. Particle locations are not needed beforehand. The job outputs non-dose weighted and dose-weighted micrographs, ready for CTF Estimation using the new
Patch CTFfits a locally-variable CTF landscape to each micrograph and is based on new robust methods for reference-free background and CTF envelope estimation, and LBFGS optimization to maximize simulated 2D CTF fit. Particle locations are not needed. Together these enable
Patch CTFto work very well on tilt data, bent/deformed ice, exposures containing very small particles, phase plate data and a range of defocus values.
Import Moviesjob, ensuring you specify the
Gain reference pathif available,
Raw pixel size (A),
Accelerating voltage (kV),
Spherical aberration (mm)and
Total exposure dose (e/A^2). If movies have been previously imported, you can start this workflow directly.
Patch Motion Correctionjob and drag in the imported movies as Inputs. You can choose to limit processing to a certain number of movies by entering an integer value in
Only process this many movies. This parameter is useful if you want to understand motion from a subset of movies in a large dataset.
Queuedand running, rigid and patch motion trajectory plots can be viewed in the job streamlog for each exposure (example below). The job will output dose weighted and non-dose weighted micrographs as a single output group. (Check out this tutorial on Inputs and Outputs in CryoSPARC to learn more about working with individual outputs.)
Patch CTFjob. Once
Queuedand running, you can view progress and diagnostic plots in the streamlog:
Manual Picker, New
Template Picker. (NB. CryoSPARC's new Blob Picker is a fully automatic picker that uses circular and/or elliptical blobs in less than 1s/micrograph on a single GPU.)
Extract from Micrographs. This job will also extract local CTF values from the Patch CTF model that has been estimated. Note that
Local Motion Correctionno longer needs to be performed. If you already have a group of extracted particles in an existing project, and have only re-computed the Patch CTF for corresponding micrographs, you can proceed to re-extract only the CTF values per-particle using a
Patch CTF Extractionjob, ensuring you drag the CTF-estimated exposures and particle locations as inputs. This will leave previously extracted or local-motion-corrected particle data intact.