Prevent interface from becoming unresponsive when viewing the homepage in cases where the web application cannot load external resources.

Fixed issue where changelog grid styling was causing items to overlap on Safari.

Prevented an issue where available CryoSPARC updates would not display on the homepage and navigation bar.

When viewing jobs within a workspace there is an option to load all jobs at once rather than incrementally load as you scroll down the page.

New project-level option to set the default path to a Topaz executable. If set, all new Topaz jobs will automatically be populated with the specified project-level path.

Ability to use the spotlight to search for applicable jobs based on what project or workspace has been selected.

In Job: Exposure Group Utilities, when specifying a regular expression to split exposures or particles into exposure groups, all unmatched items will now be grouped together into a single, separate exposure group.

Added --offline and --skip_workers options to cryosparcm errorreport

• --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)

The first applicable lane is now pre-selected when queueing a job from the sidebar.

systemd setup is now simplified, and correctly enables CryoSPARC environment during systemd process startup. Read the guide here.

Resolved inconsistency between displayed values for accepted and rejected exposures (and threshold included and excluded) in the Curate Exposures job with specific threshold ranges set now match job outputs in all cases.

Inspect Picks in v4+ now rejects outlier particles based on absolute value of power score rather than percentile (matching the behaviour of v3.3).

Local Motion correction no longer fails when some movies have zero particles or when some movies are corrupt.

Multiple targets within a single lane will now correctly display in the instance section of the manage dialog.

Volume viewer will now properly resize to the available space when adjusting sidebars and resizing the window.

Clicking checkboxes on the job table view will now correctly additively select them.

Event log downloads will no longer break in cases where ASCII characters are not included in the pdf font set.

Users can now log in with emails where the domain does not include a .

The page will no longer automatically refresh when downloading files from the output actions menus in Firefox.

When viewing a volume in Firefox, the selecting the up/down arrows within the threshold control number input field will retain focus in the same way other browsers do.

Prevent Live session view from crashing if the session was started after being marked as completed.

When making picks on the micrograph in the Manual Picker job, the picks column will correctly update in the corresponding table row.

When attaching a project, workspaces no longer have an incorrect "Created By" field, but show the user that attached the project.

Project title is now a required field when creating projects from the command line.

Clear Intermediate Results no longer deletes non-final results from some refinement jobs when those results were used downstream.

Improved error messages and error checking in Topaz Train, Extract and Cross Validation jobs.

Topaz Denoise job now correctly allocates CPU resources when run without GPUs.

Installation test (cryosparcm test install) no longer fails if only clusters are connected to the instance.

Starting a Live session that was previously marked as "completed" no longer incorrectly pauses the session twice.

Queue dialog now correctly applies titles and descriptions that were set.

Queue dialog now has a tooltip to clarify the toggle to show or hide lanes with applicable targets based on job resource requirements.

Manually Curate Exposures job no longer fails for infinite or NaN CTF parameters, outputs a warning instead.

Ab-initio jobs no longer break display of job cards when there are many classes.

Inspect Picks job no longer fails during CTF calibration if exposures do not contain enough particle pick locations.

3D Classification no longer fails when Output Diagnostic Plots at every Interation is set to False.

When using cryosparcm cluster connect, the final connected cluster configuration is printed as the output of the command (returning to v3.3 behaviour).

The range values for threshold sliders and input controls in the Curate Exposures job will now round display values to expected precision in all cases.

The reload browser shortcut will no longer manually reject selected exposure in the Curate Exposures job.

Table index cells in the Curate Exposures job now correctly update their colour when setting thresholds or manually rejecting/un-rejecting.

Filenames and other non-number values will now display correctly in the hover preview popovers in all interactive jobs.

Input fields in the Curate Exposures job can now be incremented using the arrow keys without changing the selected exposure in the micrographs table.

Over 10x speedup in job completion processes (check and passthrough outputs) for jobs with many output groups (e.g., 3D Classification with 20+ classes). Also speeds up "Mark as Completed" action for jobs.

Added more detailed logging message when manually taking over projects in an instance using cryosparcm cli "take_over_projects()"

CryoSPARC environment no longer uses LD_PRELOAD to load libtiff, resolving issues where dependencies of libtiff (libLerc and libstdc++) would not be found on some OSes (e.g., CentOS 7).

Job: DeepEMhancer (Wrapper) now accepts a mask input for DeepEMhancer's binary mask normalization mode.

Job: Manually Curate Exposures now outputs a warning if not all input particles exist in the input micrographs.

Tensorflow test is now disabled by default during cryosparcm test workers. To enable, specify --test-tensorflow. Read the full installation test guide here.

The instance tab within the admin panel now loads primary system logs by default.

cryosparcm errorreport will now add the entire app, app_api, and app_legacy log files to the generated archive.

Updated the Windows shortcut for multi-selecting to use the ctrl key instead of the meta key.

Updated command_core request License-ID header check "Authentication failed" message with actionable suggestions.

Removed the cryosparcw executable path validation check by the master node when running cryosparcm cluster connect.

Fixed issue where running jobs could be marked as completed.

Prevent SSH and other command failures when system library versions don't match embedded CryoSPARC libraries.

Project data management table now shows projects shared with the user.

The tree view no longer resets its zoom level when creating or modifying jobs.

Resolved an issue in the job builder where scrolling was locked when hovering over an input box.

Items with many tags now display correctly in the sidebar details panel and on the cards.

The browse view no longer auto-scrolls to a newly created job.

Resolved issue where job cards were not properly displaying images and info tags.

Allow clearing long-running notifications from Notifications panel.

Fixed cryosparcm fixdbport error.

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.