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.

Improved performance in large projects. Faster Tree View updates and instantaneous input drag-and-drop connections.

New Volume Alignment Tools utility, supporting re-centering and symmetry alignment of 3D volumes.

Specify path of directory containing preprocessed micrographs for Topaz Train and Extract Patch 211214

New 3D Classification advanced parameter “Output data after every full iter” to enable data outputs (volumes, particles, volume series) after every full iteration Patch 211214

cryosparcm cli “update_parents_and_children_for_project(project_uid)” function to fix broken tree view input/output connections in previously-imported projects Patch 220215

Exposure/Particle Sets Tool option to ignore leading UIDs when comparing paths for intersection mode Patch 220215

Support for reading .mrc files containing float16 data (datatype code 12) Patch 220215

Option to remove all duplicates in Remove Duplicate Particles job Patch 220315

Pre-processing jobs no longer fail immediately when a child process encounters a segmentation fault Patch 220518

Patch Motion jobs now use an improved IO library, providing substantial speedups on some cluster file systems Patch 220518

Blob Picker Tuner job now reports progress during optimization Patch 220518

Validation (FSC) job now takes in an optional Override Pixel Size (Å) parameter to allow adjusting the final pixel size and resolution estimate if incorrect pixel size was specified during processing Patch 220518

Align 3D job now takes in particle stack(s) and rotates/shifts the alignments of the particles to match the rotation and shift applied to the volumes during 3D alignment Patch 220518

Project deletion (and other long running actions) are now decoupled from instance-wide locks, allowing a cryoSPARC instance to continue to perform unrelated actions while a deletion is ongoing Patch 220518

Patch Motion Correction now supports Fourier crop ratios of 1/8 and 1/16 Patch 220824

3D Variability Display (Cluster Mode) now has a volume series output Patch 220824

Exposure processing priority in a cryoSPARC Live session can now be modified. For more information, see: the Guide page on Session-level functions Patch 220824

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

cryosparcw call <cmd> enables execution of a command in a transient cryoSPARC worker environment Patch 220824

cryosparcm eventlog <project_uid> <job_uid> prints all text from a job’s overview tab to stdout Patch 220824

3DVA Display job can now output particle sets corresponding to intermediate states.

Added option to select a subset of variability components in 3DVA Display job.

Volume Tools job now accepts a custom output filename. The default output name has also been updated to be more informative.

Display path of job working directory at the top of the event log.

Automatically delete SSD cache files that have not been used in more than 30 days during job caching steps.

Specify path to custom Certificate Authority bundle for external SSL requests.

CLI endpoint to safely update a project’s directory (update_project_directory(project_uid, new_project_dir)).

Ability to use common path field (vs. UID) to intersect or split in Exposure Sets Tool and Particle Sets Tool.

CryoSPARC Live Data Management now supports executing a script upon a datatype’s state change. Add export CRYOSPARC_LIVE_DATA_MANAGEMENT_SCRIPT_ENABLE=true and export CRYOSPARC_LIVE_DATA_MANAGEMENT_SCRIPT_PATH=/path/to/script.sh in cryosparc_master/config.sh to enable this feature.

Particle subtraction now respects refined higher-order aberrations.

Added FSC mask auto-tightening to the standalone Validation (FSC) job.

Extraction Box Size in Local Motion Correction now uses the input particle box size by default.

3D Classification volume outputs are now unmasked, fixing downstream refinements Patch 211214

New printout for each 3D Classification iteration to clearly specify O-EM/F-EM iterations left Patch 211214

3D Variability Display has more informative .mrc volume file names (simple/intermediates mode) Patch 220215

Improved error details when a cli method call fails Patch 220315

Improved logging in Extract From Micrographs (GPU), now shows number of particles rejected near edges of each micrograph Patch 220315

Improved EER read performance for some file systems Patch 220315

CryoSPARC Live Session Data Management: All datatype sizes are now updated when a session is “paused” or “completed”.

Helpful error messages when calling cryosparcm/cli functions with incorrect arguments.

Check for Corrupt Particles job now has an option to check for NaN values in the particle data files to test for data corruption on disk.

Extraction jobs now have an option to force re-extraction of CTF values for each particle from the input micrographs.

Outputs in the Sharpening Tools job are now separated into two output groups and can be directly connected to downstream Volume Tools jobs Patch 220518

Warnings in the Import Particles job’s Overview tab are now more visible when fields are missing in the imported metadata files Patch 220518

Warnings in the Check For Corrupt Particles job’s Overview tab are now more visible when corrupt files are found Patch 220518

The Local Refinement (NEW!) job now explicitly requires an input mask Patch 220518

Blob picker output images now show more contrast for negative stain data Patch 220518

Further improvements to error messages when problems are encountered while reading particles or micrographs Patch 220824

Volume series outputs in 3D Variability Display no longer require a zip system dependency Patch 220824

3D Variability Display (Cluster Mode) 1D histogram now includes a legend Patch 220824

Warning if all three dimensions of the input data for Import Templates match, which suggests that a cubic (3D) volume has been input instead of a stack of 2D templates Patch 220824

Summary of rejected particle counts and reasons for rejection in Extract From Micrographs jobs Patch 220824

Jobs now fail if they require more SSD cache space than the total available space or quota Patch 220824

If available, show MRC file name in job log when file cannot be read Patch 220824

Improved error formatting when running functions via cryosparcm cli Patch 220824

Fixed contrast issues in Inspect Picks, Manual Picker and Curate Exposures jobs when viewing a micrograph that wasn’t motion-corrected in cryoSPARC.

Fixed issue in Volume Tools that caused ringing artefacts when downsampling masks.

Added resolution parameter to low-pass filter templates in Blob and Template Picker jobs.

Fixed libtiff error when running the worker on a read-only file system.

Corrected volume flip in cryoSPARC Live 3D volume web viewer.

Fixed a bug that caused stale notifications to persist after restarting cryoSPARC.

Fixed a bug where it was not possible to queue a job into a new workspace.

Fixed a bug where topics from the cryoSPARC Discussion Forum would not display on the dashboard.

Updated the job queuing interface to clarify which nodes certain jobs are launched on. Interactive jobs are always launched on the master node. Import jobs are launched on the master node unless CRYOSPARC_DISABLE_IMPORT_ON_MASTER is set to true, in which case import jobs can run on any lane/node selected. All other job types launch on a lane/node the user selects.

Fixed bug where symmetry alignment during refinement often aligned volumes incorrectly if they were already aligned.

Fixed bug where volumes are improperly aligned to symmetry axes in helical refinement.

Fixed an error during startup that occurs when an instance has less than 1000 notifications v3.3.1

Fixed plotting error during (legacy) local refinement Patch 211202

Use correct license check SSL certificate configuration when running cryoSPARC in insecure mode Patch 211214

Fixed Blob Tuner Error when Blob picker finds no particles Patch 211214

Passthrough GS split in 3D Classification Patch 211214

Check for empty splits in Homogenous Reconstruction job Patch 211214

Prevent crash of Rigid Motion Correction, Local Motion Correction and Extract Particles jobs when encountering corrupt exposures. The jobs now continue after any error in a single exposure, and output all incomplete exposures as a separate output Patch 220118

Set class field for 3D Classification particle outputs (fixes bug with downstream particles and csparc2star.py) Patch 220118

In 3D Classification, viewing direction distribution plots work with empty classes Patch 220118

In Topaz Extract, use provided preprocessed directory when no pre-trained model is specified Patch 220118

Importing projects retain job tree view input/output connections Patch 220215

Symmetry Search Utility no longer fails with KeyError Patch 220215

Topaz Train imported jobs no longer reference preprocessed micrographs directory from old project Patch 220215

Remove unused “Number of GPUs to parallelize” parameter from Local Motion Correction (non-multi) Patch 220215

Include 1st and 99th percentile particles in Inspect Picks threshold range Patch 220315

Use high-order aberration information in ResLog job Patch 220315

Local Motion does not fail when some movies do not include particles Patch 220315

Filter correct component reaction coordinates in 3D Variability Display job Patch 220315

Prevent error in Local Motion Correction when zero-shift frame is set Patch 220315

Improve multithreaded performance for some operations Patch 220315

Local motion no longer fails when zero shift frame is not set by previous motion correction job.

AttributeError raised in Filament Tracer job when only one particle pick is found on a given filament.

GPU FSC calculation in Refinement jobs raises AssertionError when used with box sizes under 84.

Topaz job now correctly fails when topaz subprocess fails.

Micrograph contrast in Manual Picker job is sometimes set to a value that clips the image.

Support for 3DVA Display clustering with one component.

Return HTTP 404 response when GridFS image requests are not found.

Allow clearing Extract Particles jobs created before the previous patch Patch 220518

Prevent Motion Correction job failure due to low-level memory error from corrupt TIFF files Patch 220518

Corrected stdout/stderr redirect options in cryosparcm cluster example scripts Patch 220518

Manual picker and Inspect picks jobs no longer overly downsample rectangular (K3) images Patch 220518

Job status timestamps are now correctly cleared when a job is cleared Patch 220518

Patch CTF job no longer fails with data from spherical aberration-corrected microscopes Patch 220518

Local Resolution Estimation job now reads the mask from the “Static Mask” input group Patch 220824

.mrc.bz2 files with an MRC extended header now load correctly Patch 220824

workspaces.json now correctly updated when a cryoSPARC Live session is running Patch 220824

Prevent SSD cache system failure when file size is missing in cache files database collection Patch 220824

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

Check Particles job for verifying data integrity of particle stacks Patch 210511

Computational batch size parameter in Heterogeneous Refinement job Patch 210511

cryosparcm changeport command and related utilities for changing the base port Patch 210601

New utility cryosparcm licensestatus to verify if a license is valid Patch 210629

cryosparcm status now reports patch version Patch 210713

Set environment variable CRYOSPARC_SSD_CACHE_LIFETIME_DAYS in cryosparc_master/config.sh to auto-remove cache files older than the given number of days Patch 210803

New TIFF reading strategy for improved performance on network file systems such as GPFS and Lustre. To enable, add export CRYOSPARC_TIFF_IO_SHM=true to cryosparc_worker/config.sh Patch 210817

”Reassign Particles to Micrographs” job to reassign particles to their associated micrographs Patch 210831

Full Prefix/suffix cutting parameters for matching between input movies and micrographs in “Import Micrographs” job Patch 210831

Extend master/worker communication timeout with CRYOSPARC_CLIENT_TIMEOUT environment variable Patch 210831

Download EMDB-friendly XML files from FSC figures Patch 211012

Substantially improved performance in iterative particle-processing jobs (2D Classification, Refinement) when particles are stored on some types of filesystems (including FSx for Lustre), resolving cases where some users found that jobs run in v3.1 were slower than in v2.15

Deep Particle Picking jobs (Deep Picker Train, Deep Picker Inference) now require CUDA Toolkit 11+

The ‘Metadata’ tab within the job preview dialog is more performant and features expandable sections and colour highlighting based on data type

Import Particles no longer ignores the rlnImagePixelSize column while trying to import a particle .star file

CryoSPARC processes are now less likely to become orphaned due to more robust supervisor management configuration

Removed unused cuBLAS dependency that caused multiple GPU contexts on all GPUs in a system to be created even when using only a single GPU

GPU status info is now updated when a worker is connected for the first time, or when a worker connection is updated

New option to work around bug in CUDA on CentOS 7 that causes cuMemHostAlloc failed errors in multiple job types. To engage this, add export CRYOSPARC_NO_PAGELOCK=true to the cryosparc_worker/config.sh file.

Patch CTF Estimation no longer fails when encountering an error on a specific micrograph. Failed micrographs are outputted to a separate group if exceptions are encountered and processing continues.

Local Resolution job now prints local resolution statistics (minimum, median, maximum, 25th percentile, 75th percentile) in job event log Patch 210401

CryoSPARC Live Data Management now supports executing a script upon a datatype’s state change. Add export CRYOSPARC_LIVE_DATA_MANAGEMENT_SCRIPT_ENABLE=true and export CRYOSPARC_LIVE_DATA_MANAGEMENT_SCRIPT_PATH=/path/to/script.sh in cryosparc_master/config.sh to enable this feature Patch 210401

Issue in Patch Motion that causes dose weighting to be incorrectly applied in some cases. This was caused by the introduction of variable-dose support in v3.1.

Patch CTF Estimation fails with IndexError: index 0 is out of bounds for axis 0 with size 0

Patch CTF Estimation fails with ValueError: Axis limits cannot be NaN or Inf

Patch CTF Estimation sometimes reports underestimated CTF fit resolution in cryoSPARC Live, in cases where the correlation between the fit and the actual signal is very poor at low resolutions

Issue that can cause exposure groups set up at import to be lost during processing, specifically through wrapper jobs for GCTF or CTFFIND

Issue where Deep Picker Train job would fail reporting that there are no training particles on any micrographs

Topaz wrapper TypeError during negative stain processing: can’t multiple sequence by non-int of type numpy.float32

Issue causing IndexError in wrapper for Motioncor2

Issue in particle simulator job where all particles would be modulated by the same CTF regardless of specified input CTF parameters

Issue in cryosparcm cli delete_user command that prevented an admin user from being authenticated

Issue in Extract From Micrographs (CPU) job requiring a GPU dependency, causing it to fail on CPU-only workstations

Import Job/Import Result Group fails with Unable to find data referenced by cs files when importing a mscope_params result group due to empty fields Patch 210401

Local Motion correction with EER data Patch 210413

Jobs no longer wait on cache forever after the cache is unlocked in other jobs Patch 210413

Restore missing “Use Class Weights” parameter in Deep Picker Train job Patch 210413

Prevent LD_PRELOAD warning when launching cluster jobs Patch 210413

ValueError during 3DFSC job volume output stage Patch 210511

Empty workspaces after importing project Patch 210511

Prevent error when extracting particles generated by Topaz Patch 210601

Prevent error in Deep Inference job during plotting Patch 210601

Prevent error caused by MotionCor2 wrapper outputting incorrect shape Patch 210601

Improved error messages when reading invalid exposures or particle stacks Patch 210601

Prevent numeric initialization error in Ab-Initio Reconstruction jobs for some systems Patch 210615

Prevent numeric error in Inspect Picks job Patch 210615

Statistic showing the total number of particles being processed by Ab-Initio Reconstruction job in cryoSPARC Live sometimes isn’t updated Patch 210629

Prevent mrc_readmic (1) 447: Invalid argument errors that occur after extracting particles in a pipeline where micrographs were imported multiple times Patch 210629

Prevent I/O exceptions from terminating the cryoSPARC Live Worker while processing exposures Patch 210713

Allow shell operators during cluster job submission, enabling redirections required for LSF Clusters Patch 210713

Exception handling for Clear Intermediate Results Patch 210831

Corrected cryosparcm cluster example JSON output Patch 210831

Consistent exposure/particle matching in Deep Picker Patch 211012

Prevent startup error when system does not report CPU frequency Patch 211012

Prevent loss reporting error during Topaz jobs Patch 211012

Prevent create directory errors on some file systems Patch 211012

Non-Uniform regularization and adaptive pose marginalization

Alignment priors for soft penalization of unlikely poses

Reconstruction using higher-order CTF aberrations

Enforced point-group symmetry

Helical refinement now supports Non-Uniform regularization

Symmetry expansion now supports helical symmetry

In helical refinement, shifts along the helical axis can be limited to the asymmetric unit, improving resolutions for many datasets

”z-clip” parameter added to helical refinement’s dynamic masking, to generate a mask covering only the central region along the z-axis

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

Major updates to SSD caching to avoid issues of Detected file change due to change in file size and improve performance

Several robustness improvements for Patch-CTF Estimation. Previous behaviour can be enabled using “Classic mode” parameter.

You can now quickly queue interactive jobs via the job details in the sidebar. The queue dialog has also been updated to clarify what machine the interactive jobs will run on.

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

Import Particles no longer ignores the data_optics section while trying to import a particle .star file. Exposure groups and CTF parameters other than high-order aberrations are retained from data_optics table.

Rebalance 2D Classes now has a “Override maximum superclass size” parameter that can be set to override the maximum size of all superclasses

When launching a job, hidden files (files that start with a ’.’) will be ignored when checking if the job directory is empty if the CRYOSPARC_IGNORE_HIDDEN_FILES environment variable exists (add to cryosparc_master/config.sh)

Homogeneous Reconstruct now has the option to reconstruct with helical symmetry, and to reconstruct with an inverted hand

Homogeneous Reconstruct now supports input alignments on any pixel size, regardless of the reconstruction pixel size

cryoSPARC Job Scheduler will now ignore CPU requirements when queuing jobs to non-cluster lanes; only RAM and GPU will be considered

Change the parameter “Remove leading UID in input micrograph path” in Import Particles to be optional

Discussion forum topics have returned to the dashboard

Some users were unable to create an account or reset their password in Chrome

Fixed a bug in Import Particles that caused it will fail when trying to convert rlnOriginX/rlnOriginY to rlnOriginXAngst/rlnOriginYAngst while importing Relion 3.1 star files

Fixed a bug that caused the cryoSPARC start process to not complete

Fixed a bug that caused the string of characters appended to the micrograph file paths created by cryoSPARC to be a variable length (now 21 characters)

Fixed a bug that caused the Import Project function to fail with _pickle.UnpicklingError: could not find MARK

Filament tracer now eliminates particles beyond the micrograph’s edge

Fixed a bug that prevented the Rebalance 2D Classes job from launching on clusters

Fixed a bug in the Volume Tools job that gave erroneous output when the “Invert mask” and “Fill holes” options were both true

Fixed a plotting issue in Heterogeneous Refinement causing orientation plots to fail with a ValueError

Fixed issue that prevented pre-v3.0 Extract From Micrographs, 2D Classification, and Create Templates jobs from being cleared

Fixed issue causing static masks to be improperly resized in Homogeneous Refinement New, Non-Uniform Refinement New, and Helical Refinement

Fixed issue preventing Helical Refinement from running with static masks that were sampled on a different grid than the volume; fixed related bug with static masks being improperly rotated when the “Align input structure to helical (z) axis” parameter was activated

Fixed bug where running “Clear Intermediate Results” on a project caused the outputs of Curate Exposures jobs within the project to be inadvertently deleted.

Add support for pre-release versions of Topaz

Fixed issue where job queue modal would display incorrect default lane/target info when ‘default’ lane doesn’t exist

Fixed issue where systemd service used wrong python interpreter

Fixed issue where deleted sessions still appear in cryoSPARC Live browse view

Fixed issue in cryosparcm updateuser when using lastname flag

Fixed IndexError in motioncor2 wrapper job

Fixed issue where Topaz denoise would not work

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

Fixed a case where a deleted session would display in the browse page when selected

Fixed a bug that caused manual picks on “Test” exposures to be excluded from session statistics and from being extracted

Job cards in the “current jobs” and “target” modals will now open their respective job modals when clicked. Job cards will also display the job’s priority if one has been set

Fixed a bug in the cryoSPARC Live Worker that caused it to fail repeatedly due to uncaught exceptions caused by IO errors

Blob and template particle diameters are now correctly shown as Å values

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.