CryoSPARC v4.0.0

CryoSPARC v4.0 is a major upgrade. Please follow our Guide: Updating to CryoSPARC v4.0.

All-new CryoSPARC interface designed for performance and productivity. Watch a video walkthrough of all the new features and read the comprehensive new guide.

• Redesigned interactive jobs (Inspect Picks, Exposure Curation, etc.) with significantly improved functionality and scalability. Easily handle large datasets (25K+ exposures)

• Integrated in-app 3D volume viewer to inspect volume outputs from all job types

• System for browsing and filtering projects, workspaces, sessions and jobs

• Tagging system to easily organize and record details about projects and jobs

• Multi-job selection and a new job comparison view

• Table view for projects, workspaces, sessions and jobs with CSV download support

• Two new ways to build jobs in addition to the drag-and-drop Job Builder:
  • Quick actions: right click a job and run common next steps (e.g., Blob Picker → Inspect Picks)

• Job cart: select outputs directly from completed job cards to generate a filtered list of applicable jobs. Create and connect in a single click

• Download a PDF report of each job including key stats and the event log

• And much more! Be sure to watch the video and read the guide

CryoSPARC Live is now integrated as part of the CryoSPARC interface. Seamlessly transition from the primary interface into a Live session within the same browser tab: How to Access CryoSPARC Live.

Improved algorithm and diagnostics in 3D Classification (BETA).

• New tutorial covering multiple datasets and use cases

• FSC-based regularization to improve class quality and variety
• Two new convergence criteria (class switches, density change)
• Separate solvent and focus mask inputs
• Option for hard classification
• Better tuned and refactored default parameters
• Updated diagnostics, including:
  • class "flow"

• focus mask overlay

• difference-from-consensus

Wrapper for DeepEMhancer, a deep learning model for automatic masking-like and sharpening-like post-processing.

"Average Power Spectra" Job for averaging the power spectra of aligned, 2D-classified particles for helical symmetry exploration.

Example of averaged power spectra from 2D classes of the NLRP1-CARD filament (EMPIAR-10564)

Verify CryoSPARC installation integrity with cryosparcm test install and cryosparcm test workers. Read the Guide: Installation Testing with cryosparcm test.

"Maintenance Mode" setting which may be toggled on/off to prevent queued jobs from running while allowing running jobs to complete.

Administrator-configurable login message and instance banner to show notices to users.

Improved project data management system, simplifying common projects tasks such as transfer and archival.

• New comprehensive Data Management Guide for v4.0
• New project Attach and Detach actions to easily move projects between CryoSPARC instances

• New project Archive and Unarchive actions simplify moving projects to archival storage or changing a project location on disk

• For new projects, the generated project directory name is a hyphenated variant of the project title instead of PXX. A configurable prefix may be added to project directory names for easy identification
• Projects now use an instance-lock to prevent accidental corruption due to multiple CryoSPARC instances modifying the same project simultaneously
• Projects and Jobs no longer prefix output files with cryosparc_PXX_ on disk, since project numeric identifiers may change when detaching and re-attaching a project. The prefix is added when downloading files through the browser instead

Improved CryoSPARC database and API security with authenticated access control.

Error reporting tools to simplify troubleshooting.

• Download a job error report bundle from the Event Log tab of the Job Dialog

• Download a system error report bundle from the Instance Logs tab of the Admin Panel

• From the CLI, the cryosparcm errorreport function generates a system level error report bundle when the web-app is inaccessible

cryosparcm filterlog command filters logs by days, date, name, function, and level and adopts a more consistent logging format including timestamps at the beginning of logs lines.

cryosparcm cluster validate function validates cluster configurations during installation.

View improved database backup functionality with recent activity records. Available in Instance Information → Backups.

Job: Non-Uniform Refinement now supports optional Ewald Sphere Correction via an advanced parameter switch.

All jobs which process masks and volumes now accept masks sampled at different box and/or pixel sizes relative to the volume, which are internally resampled when appropriate.

Local Refinement and Particle Subtraction now issue a warning if binary masks are used.

Job: Extract from Micrographs now supports extracting and downsampling to two different box sizes via Fourier crop to provide smaller particles for early classification and reconstruction steps.

Job: Global CTF Refinement default parameters no longer fit fourth order aberrations (Spherical Aberration and Tetrafoil) unless specifically enabled.

Job: Local Motion Correction now includes an option to downsample particles via Fourier crop after correcting per-particle motion.

Job: Ab-initio Reconstruction now includes an unused particles output when not all particles were used for reconstruction in the single-class case.

Job: Gctf is now a "Legacy" job. Turn on "Show legacy jobs" in the job builder to unhide the job. Gctf also includes a CUDA libraries parameter to override CUDA version for compatibility with available Gctf binaries.

Job: 2D Classification may now run without CTF correction by turning off the Do CTF correction parameter, which may be useful for negative stain data.

Negative stain 2D class averages, with and without CTF correction, from the MTA-HDAC-MBD core complex (EMPIAR-10539)

Improvements to CryoSPARC Live interface:

• In the Live Overview tab, enter rejection thresholds with free-form numeric input
• Display particle picks in more distinguishable colours
• Volume viewer includes action buttons for resetting and zooming

Added Maximum number of local maxima to consider picking parameter to Blob Picker and Template Picker in CryoSPARC Live.

Improved cluster job status updates before a job is launched for better visibility.

Silent password input prompt in cryosparcm commands; will not be printed in the command output.

Added cryosparcm cli functions get_project_symlinks and get_job_symlinks to find moved symlinks in jobs. Read the guide for more details.

Reduced excessive verbiage in log files for certain job types that process particles.

Added CRYOSPARC_DB_CONNECTION_TIMEOUT_MS configurable environment variable for adjusting connection timeout during database startup.

Improved libcufft library initialization when only major version files (e.g., libcufft.so.10) are available.

Updated Extensive Workflow to issue warning rather than timeout error caused by long-running jobs.

Previous v3.3 web application (now running at BASE_PORT + 7) does not start up by default. To start it, run cryosparcm start app_legacy.

CryoSPARC Live (liveapp service) is integrated into the main web application interface running at BASE_PORT and is no longer available at BASE_PORT + 6.

Automatically update session data sizes when a session is paused or completed for improved data management.

Exposure Sets Tools no longer fails to intersect on path if mscope_params result slot is connected to both Exposures_A and Exposures_B input groups.

Heterogeneous Refinement jobs no longer fails when Force hard classification is turned on and some classes become empty.

Additional corrupt exposure error handling for Full-Frame Motion Correction, Patch Motion Correction and Patch CTF jobs.

Scheduler no longer fails for all queued jobs when a single queued job fails to run.

cryosparcm restore no longer fails when restoring against an empty database directory.

Show database connection error message in job log if one occurs during job startup.

cryosparcm restart no longer restarts all services if an incorrect service name is provided as an argument.

Long running background processes in one project no longer block actions across all projects in the system.

Fixed phase_shift attribute in CryoSPARC Live overview plot that was previously displayed as radians instead of degrees with an incorrect label.

FFTs on CPU no longer use a minimum of 8 threads that was causing contention on some systems.