What's new in v2.12

November 29, 2019

We're excited to announce another release of cryoSPARC packed with much requested features:

Major updates to 3D Variability: Solve more modes, smaller motions, automatic classification of discrete classes, and more!

New
New "cluster" mode in 3D Variability Display allows for automatic hierarchical 3D classification based on variability coordinates: directly visualize and see how many discrete classes are present in a dataset, separate them by clustering, and reconstruct each separately. Then recursively perform 3D Variability to look for sub-conformations or flexibility within each cluster, or refine each cluster separately.3D Variability Analysis
New
New "intermediates" mode in 3D Variability Display allows for weighted reconstructions of intermediate positions along each variability dimension: create more detailed videos of variability that minimize the effect of density appearing and disappearing during large motions. Also output weighted particle subsets for intermediate positions, for refinement of particular flexible conformations.
New
Default options in 3D Variability improve sensitivity to small variations in the 3D density. Plus support for coloured or white noise models, high-pass filter during optimization, per-particle scale optimization.
Fixed
Fixed streaking issue so that (many) more variability modes can be solved simultaneously.

Major updates to 3D Refinement: On-the-fly CTF refinement, aberration correction, exposure groups, substantial speed improvements!

New
Per-particle defocus refinement implemented on GPU allows CTF refinement in minutes for 100,000's of particles. Implemented as a standalone job and also as an in-line on-the-fly option during Homogeneous Refinement.High-Resolution Structure
New
Global CTF Refinement and Local CTF Refinement jobs: CTF aberration support, also GPU implemented, corrects for beam tilt, trefoil, spherical aberration, and tetrafoil. Estimation of the new parameters can be done in a standalone job or as an in-line on-the-fly option during Homogeneous Refinement, yielding ultra-high resolution reconstructions.
Local CTF Refinement job cardGlobal CTF Refinement job card
New
New Exposure Group Utilities job allows users to split or combine datasets into multiple exposure groups for higher-order aberration correction. Create exposure groups using regular expressions and separators, and test your exposure group creation strategy.
New
First-pass optimization of GPU and CPU code for Homogeneous Refinement: now up to 5x faster, especially for symmetric particles.

New UI-based User Management System

New
New admin page with ability to change roles of existing users and create new users through the UIList of users and new user form
New
Users can request to reset their password through the interface

Topaz Integration Beta

New
New Topaz wrapper jobs for integrating Topaz's particle picking and micrograph denoising functionality
  • Topaz Train, Topaz Cross Validation, and Topaz Extract jobs perform particle picking while the Topaz Denoise job performs micrograph denoising
  • Users only need to install Topaz to incorporate it within the cryoSPARC pipeline
  • Denoised micrographs are compatible with Manual Picker, Inspect Particle Picks, and Topaz's particle picking pipeline, assisting users and machine learning models in observing micrographs
  • Tutorial Topaz integration in cryoSPARC
Topaz T20S tutorial
Bepler, T., Morin, A., Rapp, M. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat Methods 16, 1153–1160 (2019) doi:10.1038/s41592-019-0575-8

Other Updates

New
New Symmetry Expansion job expands particle poses around point-group symmetries, to support local refinement of subunits, as well as 3D variability of symmetric particles.
New
New Job Scheduler and Queuing Interface: Override the cryoSPARC scheduler to queue directly to a specific GPUUpdated queue dialog in cryoSPARC v2.12 allowing users to queue a job to specific GPUs
New
Ability to perform non-interactive threshold selection for particle picking and extraction, and non interactive selection of 2D classes, making it possible to process simple data completely end-to-end without manual intervention
New
Ability to interactively select all classes above or below a threshold in Select 2D job (right-click a class)Select 2D Classes: Interactive thresholds
New
Multiprocessing robustness updates in preprocessing jobs (Patch Motion, Full Frame Motion Correction, Patch CTF Estimation) ensure that if a job fails or is interrupted, completed results are recovered and processing can be resumed.
Update
Orientation-precision plots in refinement are now coloured with minimum value zero so that differences in ratios can be easily spotted
Update
Relative ice thickness is now available in Exposure Curation
Update
2D Classification allows for changing the maximum alignment resolution and reconstruction resolution separately if desired
Update
Sharpening job now applied a spherical window by default
Update
Added option to skip header check when importing movies, which allows for faster importing on larger datasets
Update
Importing Movies, Micrographs or Particles will auto-populate the "exposure group ID" field of the dataset based on the project (each project increments from 0)
Update
Set the environment variable CRYOSPARC_DISABLE_IMPORT_ON_MASTER to allow master-direct jobs (import jobs, curate exposures, select 2D) to be queued on any machine you specify, and not only the master node
Update
If a job is queued to a specific GPU, it will be noted in the Resource Manager
Update
Job Cards now show queue message if placed in queue
Update
Job type is more prominently shown in the sidebar
Fixed
Ab-initio job with symmetry enforced fails with invalid memory access error
Fixed
Certain parameter descriptions in the Job Builder don't show
Fixed
Better logging in Align 3D Job
Fixed
Error in non-uniform refinement when run with CPU option
Fixed
3DFSC job doesn't accept mask inputs
Fixed
New ignore_pose option in import particles to enable import of locations when pose information is missing
Fixed
Deadlock in new job types like 3D var on some newer GPUs
Fixed
Select 2D fails when all classes are selected (i.e., if there are no particles in the templates_excluded output result group)
Fixed
White circles in 2D Class job when circular mask diameter parameter is too close to particle box size
Fixed
Exposure Sets Tool Job doesn't recognize particle inputs
Fixed
The 'more' button in the Job History page doesn't load new rows
Fixed
Copy to clipboard functionality is more reliable on various browsers
Fixed
Back button in File Browser correctly expands path variables
Fixed
Imported jobs caused the tree layout to fail or throw an error
Fixed
Project directory sizes are calculated more accurately
Fixed
When updating a worker's SSD configuration, the SSD option remained disabled even though user supplied a path to the SSD


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