What's new in v2.8May 30, 2019
Here's an overview of the latest updates to cryoSPARC:
Migrating a cryoSPARC Instance
Our latest tutorial covers how to move your cryoSPARC instance from one location to another - either between folders, different network storage locations, or even different host machines entirely:
- Tutorial Migrating Your cryoSPARC Instance
Local Patch-Based Motion Correction Beta
A very fast auto-tuning patch-based local motion correction method, built on top of the original cryoSPARC Local Motion correction method (which is a variant of alignparts). On modern GPU/CPU/disk hardware, less than 10 seconds per movie (single GPU) for global full-frame + local anisotropic motion estimation and correction. High-quality interpolation. No need for particle pick locations. Outputs both non-dose-weighted and dose-weighted micrographs, ready for CTF estimation and extraction. Multi-GPU mode enabled for blazing fast preprocessing speed. Native support for parallelized TIFF and MRC.BZ2 decompression.
Local Patch-Based CTF Estimation Beta
A new fast auto-tuning patch-based local CTF estimation method. Deals easily with tilt data, bent ice, very small particles, wide range of defocus, phase plate data. Fits a locally-variable CTF landscape to each micrograph. No prior knowledge about tilt/etc needed. Based on a few new robust methods for reference-free background and CTF envelope estimation, and LBFGS optimization to maximize simulated 2D CTF fit. Outputs per-particle local CTF estimates, in ~3 seconds per micrograph (single GPU). Multi-GPU mode enabled for blazing fast preprocessing speed.
Create 2D templates for template-picking from any 3D volume. Useful for iterating particle picking after obtaining an ab-initio 3D structure or refinement, especially when rare views are difficult to pick without good templates.
Fully automatic fast blob-based particle picker. Can use both circular and elliptical blobs, to easily pick particles of various shapes and elongation. Less than 1 second per micrograph (single GPU).
Support for movies produced by K3 Camera (including fixes for quirks of Leginon/Gatan Latitude)
- Enhancement Memory usage for motion correction and picking is now minimized for super-res K3 movies
- Fixed Particles extracted from K3 Movies produced NaN values
- Fixed MRC mode 0 is now interpreted as uint8 rather than int8, to match Latitude for K3 movies
heartbeat time is now configurable (the amount of time that cryoSPARC core waits before labeling a job as
failed if there is no response from the parent process running the job). Addresses problem where long-running jobs stop communicating with the master process intermittently due to network issues.
- Edit the file
export CRYOSPARC_HEARTBEAT_SECONDS="360"to the end
- Restart cryoSPARC:
completedallowing it's latest outputs to be used for further processing) - use the new "Mark Job as Complete" button in the Job Details panel
.starfiles now also imports
rlnRandomSubsetto preserve the gold-standard split and
rlnOriginX/Yto preserve alignments of particles
We recommend updating to v2.8 today to ensure you can take advantage of all new features and fixes. Learn how to update your instance here.