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Pre-processing
Stage
1
of 8
Included on all plans
Patch-based CTF Estimation
Defocus and astigmatism fitted on every micrograph, with a patch-based model that resolves local defocus variations across the micrograph.
Patch-based
Runs on micrograph patches and provides a continous local defocus model.
GPU accelerated
Opitmized for speed & running on GPUs
What it does
A microscope does not transfer specimen contrast linearly. Defocus and aberrations modulate the signal so that some spatial frequencies come through inverted and others are lost. That modulation is the contrast transfer function, and until it is measured a micrograph cannot be corrected or combined with any other.
CryoCloud fits the transfer function for every micrograph: defocus, astigmatism, and a fit quality score that doubles as the earliest honest verdict on the image.
How it works
The fit is made against the power spectrum. Scattering from the ice produces concentric Thon rings whose spacing follows the defocus and whose ellipticity follows the astigmatism. A model is fitted to those rings, and the resolution out to which they still match gives the fit quality.
Other packages that determine one defocus value per micrpgraph assume the specimen is flat and level, which it never is. CryoCloud's patch-based option, models the defocus gradient across each micrograph and produces a defocus landscape from which per-particle defocus values are applied at extraction.
Both run on GPU, on every micrograph, as soon as motion correction has produced one.
Schematic, not measured data. Left, the Thon rings a power spectrum shows. Right, the fitted contrast transfer function drawn over one half of the same spectrum, ring for ring.
Where it sits
CTF estimation is the second job after CryoCloud MotionCorr, and all downstream jobs rely on an accurate defocus estimate. Picking, classification and refinement all use the contrast transfer function from the CTF estimation job.
The fit quality is also an early signal about the data quality. A poor fit points at thick ice, drift, or a defocus outside the intended range, which should ideally be corrected while session is still running.
At a glance
Stage
Pre-processing
Runs
Automatically | Manual
Hardware
GPU
Inputs
Motion-corrected micrographs
Outputs
Defocus, astigmatism and fit quality
With C3TF, a defocus landscape per micrograph, and per-particle defocus applied at extraction.
Replaces
CTFFind4
Availability
Included
CTF estimation runs on every micrograph you upload.
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Next in the workflow
Motion correction
CryoCloud MotionCorr
Patch-based motion correction with dose weighting, on every movie as it lands.
Particle picking
CryoCloud Picker
Generalised ML particle picker with higher accuracy, no per-dataset training.
Post-processing
CryoCloud Polishing
Per-particle motion refinement for the last stretch of resolution.