New 3D Classification Beta job can be used to quickly classify particles into many 3D classes, without re-alignment of particle poses and shifts. Sort out heterogeneity from million+ particle datasets with 100+ classes. Read a tutorial here.

New ruler and scale bar allow for interactively determining the size of a particle in cryoSPARC Live.

New Blob Picker Tuner determines optimal blob picker parameters from a minimal set of user-selected manual picks. Tunes blob size, shape, and picker score thresholds automatically. Read a tutorial here.

A technique for Ewald Sphere Correction implemented in homogeneous refinement and reconstruction jobs allows for higher resolution reconstructions of larger proteins. Read a tutorial here. The new technique corrects for the Ewald Sphere during pose alignment and during back-projection, and also correctly estimates/refines higher-order CTF aberrations (HOA) while accounting for the Ewald Sphere.

Anisotropic magnification can now be estimated during CTF refinement, and is corrected for in Refinement, Reconstruction, 3D Classification, and 3D Variability jobs.

Substantial speed and memory improvements to FSC calculations in all job types, speeding up FSC calculation by over 10x, and providing an overall speedup of up to 20% for homogeneous refinements. A benchmark refinement of 100,000 Ribosome particles at 360 pixel box size (EMPIAR-10028) takes only 5.2 minutes on a single NVIDIA V100 GPU.

Substantially improved TIFF read performance for some filesystems. Learn more.

cryosparcm log provides an improved log format and new filter flags.

Import 3D Volumes now supports importing multiple volumes, including importing entries directly from EMDB.

FSC Plots are now accompanied by an EMDB-friendly XML file.

Cache log now outputs average speed (MB/s) and estimated time to completion Patch 220824

Added option for sorting jobs by date and title. Projects and workspaces can be sorted by title as well

New Extract from Micrographs (CPU) job, supporting particle extraction on CPU in parallel using multiple cores.

Admin users can now modify the list of users to whom a project is shared

Import Movies and Patch Motion now skip bad files instead of failing. Skipped files are added as a separate output.

Clicking on the number of failed exposures in the navigation sidebar will open a dialog displaying the error details for each exposure

Disable existing conda environments before activating cryoSPARC’s conda environment

Specifying initial user credentials in install.sh fails with “improper usage” because of incorrect arguments

Command cryosparcm updateuser fails because of incorrect arguments

cURL symbol lookup error on CentOS8 when starting cryoSPARC after update to v3.0.0

Importing Projects from v2.15.0 or earlier into v3.0.0 fails with UnicodeDecodeError

Command cryosparcw newcuda uses old pyCUDA binary that doesn’t exist

Deleting an Extract From Micrographs job fails with KeyError

Importing particle pose information in Import Particles fails with TypeError

Command cryosparcm backup fails if cryoSPARC is turned off

Inspect Picks job fails with ValueError if using micrographs imported with “Constant CTF” parameter

Symmetry Search Utility job fails with TypeError in “rise” mode

New and improved cryoSPARC Live app, redesigned and reworked for robust and seamless real-time end-to-end cryo-EM data processing. CryoSPARC Live is built for data collection facilities, cryo-EM cores, industry labs, microscope operators and individual users who want to perform real-time cryo-EM data quality assessment and decision-making based on streaming 2D and 3D results that update in time with new data. CryoSPARC Live is also now the best and fastest way for users to perform their first-cut processing and curation on already available data.

• Expedited and optimized preprocessing, enabling up to 600+ movies per hour per GPU (motion correction, CTF estimation, particle picking and extraction)
• The ability to seamlessly reprocess data at any time, to curate exposures, test/refine picking strategies and the choice of particles for refinement, on the fly
• Streaming 2D classification, in-line Ab-initio Reconstruction, and Streaming high-resolution 3D Refinement, which update automatically as new particles become available
• Seamless integration with cryoSPARC, allowing for direct advanced processing from the results generated in cryoSPARC Live without any data shuffling

After extensive beta testing globally, cryoSPARC Live is now available free of charge for general academic use. To learn more and to access Live, please see: guide.cryosparc.com

• Watch Now: CryoSPARC Live Walkthrough

Improved Non-Uniform Refinement algorithm NEW and job type Beta. Higher resolution results and reduced sensitivity to parameter changes. For more details, see the new paper published in Nature Methods

Plus:

• Support for local and global CTF refinement during non-uniform refinement
• Fast, new GPU implementation of non-uniform regularization developed with support from NVIDIA

• Additionally, support for automatic adaptive marginalization over alignment variables (enabled by default) yielding further improvements for small molecules.

  

Upgraded to modern Python 3.7 runtime, including new updated dependencies and installation. Easy upgrades and downgrades between cryoSPARC v2 and v3.

Support for CUDA 11 + Ampere Architecture GPUs (3080, 3090, A100, etc.).

• Please ensure you’re running the latest NVIDIA Driver compatible with your GPU and CUDA Toolkit version. You can download the latest driver for your GPUs here. Visit Troubleshooting for common GPU errors.

Full support for Thermo Fisher Scientific EER data in cryoSPARC and cryoSPARC Live. EER data is decompressed on the fly and can be upsampled and split into the desired number of fractions during processing.

Improved defect file and defect pixel support in motion correction jobs in cryoSPARC and cryoSPARC Live. Defect pixels can be specified in a .txt defect file or as zeros in the gain reference.

Helical Reconstruction BETA: New suite of tools for end-to-end helical processing and refinement, including:

• New high-resolution Helical Refinement job that also supports non-uniform regularization, and enforcement and local optimization of helical symmetry

  

• NEW Filament Tracer job tailored to the picking of filaments

  
• Updates to Inspect Particle Picks to allow pruning of filament picks by curvature
• New Symmetry search utility for exploring the symmetry space in a helical volume

Extract From Micrographs will now re-center particles by default if they have already been extracted and aligned through 2D classification, 3D reconstruction, or refinement.

New Homogeneous Reconstruction Only job type that performs 3D reconstruction from previously aligned particle images.

Ability to set priority values for jobs and users in cryoSPARC and cryoSPARC Live, allowing jobs to run in priority order instead of the order they were queued. Learn more about this feature with our Guide to Priority Job Queuing

CryoSPARC Live Session Data Management: View, delete and archive data created by cryoSPARC Live on a granular level. Save space taken up by data generated in old sessions and projects, while still being able to browse and view results.

A new Data Management tab is available in the Resource Manager in cryoSPARC, displaying details of all projects and workspaces available to the logged in user. At-a-glance information includes: project creation and ownership info, project directory location, last accessed/viewed, project size and other details.

Reduced GPU memory footprint in Patch Motion Correction. The overall GPU memory footprint of patch motion correction has been reduced. This enables most K3-sized image data to be processed on 11GB GPUs. Additionally, a “low-memory mode” switch is now available, which reduces it even further (at expense of speed).

New Remove Duplicate Particles job checks for particles that are extracted too close together on a micrograph and keeps only one, to allow combining picks from multiple pickers without affecting FSC estimates.

Beta Patch Motion Correction in cryoSPARC and cryoSPARC Live now optionally support movie data that has been saved with a variable dose rate among frames (e.g., from Leginon)

New Systemd Unit File to restart cryoSPARC after server shutdown: A systemd unit file is now included to allow running cryoSPARC as a service.

Improvements to Patch CTF estimation for better CTF fit in cases where background or envelope estimation is difficult. Improved robustness in relative ice thickness measure.

Downsample Particles and Extract from Micrographs will now correctly scale particle alignment shifts, fixing issues where downsample was used immediately prior to local refinement or 3D variability.

Orientation distribution and posterior precision plots were added to Heterogeneous Refinement, and can be disabled by turning off the “Show viewing orientation distribution plots” parameter.

Import Micrographs now has an option to output constant CTF values, so that subsequent steps will ignore the CTF entirely. Useful for negative stain and exotic data collection.

Improved cryosparcm patch pre-apply validation.

Reduced SSD-cache coordination bandwidth, improving the robustness of caching on multi-node systems.

Smarter cluster job ID parsing following cluster submission. Ability to use shell redirects in cluster submission commands, enabling native support for the LSF cluster management system.

Each project, workspace and job now records a ‘last accessed’ timestamp, updating whenever a user views the project, workspace or job through the web application interface. This allows for administrators to quickly identify and remove/archive data that is no longer used.

Queuing interactive jobs always default to the master node.

Ability to specify a first and last name for new users in the Admin panel and through the command line interface.

Default umask is now 002, to allow write permissions by ‘group’ for folders created by cryoSPARC.

Renamed internal installation directories from cryosparc2_ to cryosparc_

Import Particles job fixes: Importing particle locations using micrographs created in v2.15+ failed because of a variable length UID prepended to the path of each micrograph; Using the “ignore raw data” parameter causes the job to fail with a missing pixel size error; Support for offsets specified in angstroms (_rlnOriginXAngst, _rlnOriginYAngst).

Import result group fails if some path fields are blank.

Inspect Picks “use_denoise” button failed to actually load denoised micrographs, even if they were connected.

Local Refinement now respects the static masking and minimization-over-per-particle-scale parameters, which were previously not used correctly.

Setting “Override number of iterations” to True without providing a number of iterations previously prevented Local Refinement from ever terminating.

Non-Uniform Refinement: Local processing causes an error if masks are too close to the edge of the refinement box.

Local Filtering had SSD:True hard-coded, causing it to fail when running on resources without SSDs.

Usernames are now correctly displayed in the details panel for a job.