• A new suite of tools to simplify the process of tracking and reducing disk space usage in CryoSPARC. Supporting five ways to clear up projects or workspaces:
  • Mark certain jobs as final and automatically clear everything except for jobs needed to replicate those results
  • Compact CryoSPARC Live sessions, removing preprocessing data but storing particle locations and parameters needed to restore the session later
  • Restack particles to remove filtered out junk particles and then automatically clear deterministic preprocessing jobs that can be re-run later if needed
  • Clear intermediate results of iterative jobs across a project or workspace
  • Clear killed and failed jobs that take up disk space but can’t be further used
• Featuring a comprehensive Cleanup Data user interface, on-demand refreshing of project and job size statistics, data usage summaries in the project details sidebar, and new right-click menu options for selecting ancestors and descendants of jobs manually. See the Data Cleanup guide for more details.

• A new system for measuring and comparing key aspects of CryoSPARC performance across CPU, File system, and GPU operations. The benchmarking jobs break down critical elements of CryoSPARC high performance code paths and measure detailed timings to shed light on which parts of a system may be bottlenecking performance.
• A new performance benchmark user interface allowing for visual comparison of different benchmark runs as well as reference benchmarks published along with CryoSPARC. The interface can display detailed timings from benchmarking jobs or job runtimes from full runs of the Extensive Validation (previously called Extensive Workflow) test set.

• New plots, displays, and interactive tools across all interactive jobs, including a new exposure image grid view in the Exposure Curation job for ease of assessing and manually curating exposures, and the ability to set threshold parameters when starting the job to bypass interaction and automatically filter data.
• Several usability enhancements, including:
  • Extraction is now optional in the manual picker
  • Datasets without pick statistics can be used in Inspect Picks
  • Charts in Exposure Curation remember their expand/collapse state when reloaded
  • Exposure Curation now displays particle picks if available
  • Optimized micrograph image loading for faster response times

• Flipped Select 2D resolution threshold selection option for clarity
• Added total picks across all exposures as info badge in Manual Picker top bar
• Added filter to Select 2D job to allow showing of only selected or unselected classes (sorting options can be applied to filtered classes)
• Added info badge to Inspect Picks job to display the total number of particles within the applied thresholds
• Manual Picker and Inspect Picks jobs now display all available data fields in the micrograph table
• Added an exposure image preview when hovering exposure table rows in interactive jobs
• Individual tab has been renamed to diagnostics in Exposure Curation job for clarity of function
• Thresholds of 0 now filter micrographs correctly in Exposure Curation job
• Support added for right clicking to remove picks in Manual Picker job

• A view options menu can be accessed from the browse system control bar allowing card and table details to be shown or hidden to suit user preference.
• The view options menu table section items can be dragged and dropped within the list to re-order the table view columns.
• The CSV download feature now includes an additional dialog allowing the user to select what information to include or exclude and the ability to re-order the table columns.

• The above variables are internal variables set by CryoSPARC and cannot be used/modified as custom variables
• Updated guide with a list of internal cluster variables and instructions for modifying resources requested in a cluster submission script

• Added an option (default: on) to re-order classes by number of particles at the end of processing
• Added maximum F-EM iterations which will terminate classification even if convergence criteria are not met

• The job card action menu trigger button will now always display that job’s specific action menu even with multiple jobs selected
• Opening the action menu on a job card not included in a multi-selection will show that job’s specific action menu instead of the multi-select action menu
• The multi-select action menu can now be opened by right clicking the workspace background and not just jobs within the selection

• 3DFlex jointly learns a single canonical 3D density map of the particle, latent coordinates for each particle image, and a flow generator network. Given a latent position, the flow generator outputs a 3D deformation field mapping the canonical density to a particular conformation
• 3DFlex requires tuning of some parameters and optionally can take custom inputs defining geometry and topology of the target molecule
• Read an in-depth guide, including new example results using 3DFlex
• Watch a walkthrough video covering how to using the new algorithm in CryoSPARC
• Read the bioRxiv preprint from April 2021. An updated paper will be made available soon.

• Programmatically read and write exposure, particle and volume data
• Easily perform advanced operations on metadata (alignments, CTF, etc) and programmatically insert modified data back into CryoSPARC
• Access project, workspace and job data
• Build and run jobs to orchestrate custom cryo-EM workflows
• Extend CryoSPARC functionality with third-party software packages
• cryosparc-tools is on GitHub and available via pip and can be used outside of the CryoSPARC environment in your own programs and tools
• Read the full documentation including example usage

• Per-particle scale optimization is now built-in to the job
• New 'class flow matrix' diagram helps to visualize class changes across F-EM iterations
• New ‘Δ’ text column lists class size differences across F-EM iterations
• Updated aesthetics for class flow diagram to improve clarity of edges
• Unique volumes are no longer required for initialization

• Ability to only download the master and worker update packages without doing a full update. Read more here
• Ability to skip downloading the master and worker update packages, and update using the previously-downloaded packages. Read more here
• The CryoSPARC instance is only shut down after confirming the master and worker update packages are downloaded and valid, reducing downtime during an update
• The output log of the update process is now written to cryosparc_master/run/update.log, and can be read any time using cryosparcm log update.

• --offline skips retrieval of database statistics and worker instance information (intended for use when the CryoSPARC instance is not running)
• --skip_workers skips retrieval of worker instance information (intended for use when there are issues connecting to worker nodes)

• 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

• 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
    
    

    

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

• 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

• 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

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

• 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

Watch the CryoSPARC Live highlights video

• 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

• Watch Now: CryoSPARC Live Walkthrough

• 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.
  

  

• 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.

• 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

• Tutorial 3D Variability Analysis Tutorial: Part Two

• Tutorial Particle Picking Calibration

• Tutorial Negative Stain and Phase Plate Data Workflows in cryoSPARC

• Added multiprocessing to substantially improve preprocessing times in all Topaz jobs
• Added parameter to select number of CPUs in the Topaz Extract job
• Topaz jobs now automatically account for negative stain data
• Topaz-extracted particles no longer cause 2D classification jobs to occasionally fail due to inconsistent CTF outputs

• Tutorial 3D Variability Analysis: Part One

• Tutorial On-the-fly CTF refinement in homogeneous refinement

• Tutorial Local CTF Refinement
• Tutorial Global CTF Refinement

• Tutorial Exposure Groups

• Tutorial Create new users through the UI
• Tutorial Manage existing users through the UI

• Tutorial Resetting a password through the UI

• 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

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

• Tutorial Queueing Directly To A GPU