Latest Release

cryoSPARC v3.1

January 28, 2021

cryoSPARC v3.1

We’re excited to announce another release of cryoSPARC packed with new features, performance optimizations and various stability enhancements:

New
Non-Uniform regularization and adaptive pose marginalization
New
Alignment priors for soft penalization of unlikely poses
New
Reconstruction using higher-order CTF aberrations
New
Enforced point-group symmetry
New
Helical refinement now supports Non-Uniform regularization
New
Symmetry expansion now supports helical symmetry
New
In helical refinement, shifts along the helical axis can be limited to the asymmetric unit, improving resolutions for many datasets
New
"z-clip" parameter added to helical refinement's dynamic masking, to generate a mask covering only the central region along the z-axis

Stability and Performance Updates

New
New Extract from Micrographs (CPU) job, supporting particle extraction on CPU in parallel using multiple cores.
Extract from Micrographs (CPU) job
New
Admin users can now modify the list of users to whom a project is shared
Admin users can now modify the list of users to whom a project is shared
Update
Major updates to SSD caching to avoid issues of Detected file change due to change in file size and improve performance
Update
Several robustness improvements for Patch-CTF Estimation. Previous behaviour can be enabled using "Classic mode" parameter.
Update
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.
Update
Import Movies and Patch Motion now skip bad files instead of failing. Skipped files are added as a separate output.
Import Movies and Patch Motion now skip bad files instead of failing. Skipped files are added as a separate output
Update
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.
Update
Rebalance 2D Classes now has a "Override maximum superclass size" parameter that can be set to override the maximum size of all superclasses
Update
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)
Update
Homogeneous Reconstruct now has the option to reconstruct with helical symmetry, and to reconstruct with an inverted hand
Update
Homogeneous Reconstruct now supports input alignments on any pixel size, regardless of the reconstruction pixel size
Update
cryoSPARC Job Scheduler will now ignore CPU requirements when queuing jobs to non-cluster lanes; only RAM and GPU will be considered
Update
Change the parameter "Remove leading UID in input micrograph path" in Import Particles to be optional
Fixed
Discussion forum topics have returned to the dashboard
Fixed
Some users were unable to create an account or reset their password in Chrome
Fixed
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
Fixed a bug that caused the cryoSPARC start process to not complete
Fixed
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
Fixed a bug that caused the Import Project function to fail with _pickle.UnpicklingError: could not find MARK
Fixed
Filament tracer now eliminates particles beyond the micrograph's edge
Fixed
Fixed a bug that prevented the Rebalance 2D Classes job from launching on clusters
Fixed
Fixed a bug in the Volume Tools job that gave erroneous output when the "Invert mask" and "Fill holes" options were both true
Fixed
Fixed a plotting issue in Heterogeneous Refinement causing orientation plots to fail with a ValueError
Fixed
Fixed issue that prevented pre-v3.0 Extract From Micrographs, 2D Classification, and Create Templates jobs from being cleared
Fixed
Fixed issue causing static masks to be improperly resized in Homogeneous Refinement New, Non-Uniform Refinement New, and Helical Refinement
Fixed
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
Fixed bug where running "Clear Intermediate Results" on a project caused the outputs of Curate Exposures jobs within the project to be inadvertently deleted.
Fixed
Add support for pre-release versions of Topaz
Fixed
Fixed issue where job queue modal would display incorrect default lane/target info when 'default' lane doesn't exist
Fixed
Fixed issue where systemd service used wrong python interpreter
Fixed
Fixed issue where deleted sessions still appear in cryoSPARC Live browse view
Fixed
Fixed issue in cryosparcm updateuser when using lastname flag
Fixed
Fixed IndexError in motioncor2 wrapper job
Fixed
Fixed issue where Topaz denoise would not work

CryoSPARC Live

Update
Clicking on the number of failed exposures in the navigation sidebar will open a dialog displaying the error details for each exposure
Dialog for failed exposuress
Fixed
Fixed a case where a deleted session would display in the browse page when selected
Fixed
Fixed a bug that caused manual picks on "Test" exposures to be excluded from session statistics and from being extracted
Fixed
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
Fixed a bug in the cryoSPARC Live Worker that caused it to fail repeatedly due to uncaught exceptions caused by IO errors
Fixed
Blob and template particle diameters are now correctly shown as Å values

cryoSPARC v3.0.1

December 15, 2020

Update
Disable existing conda environments before activating cryoSPARC's conda environment
Fixed
Specifying initial user credentials in install.sh fails with "improper usage" because of incorrect arguments
Fixed
Command cryosparcm updateuser fails because of incorrect arguments
Fixed
cURL symbol lookup error on CentOS8 when starting cryoSPARC after update to v3.0.0
Fixed
Importing Projects from v2.15.0 or earlier into v3.0.0 fails with UnicodeDecodeError
Fixed
Command cryosparcw newcuda uses old pyCUDA binary that doesn't exist
Fixed
Deleting an Extract From Micrographs job fails with KeyError
Fixed
Importing particle pose information in Import Particles fails with TypeError
Fixed
Command cryosparcm backup fails if cryoSPARC is turned off
Fixed
Inspect Picks job fails with ValueError if using micrographs imported with "Constant CTF" parameter
Fixed
Symmetry Search Utility job fails with TypeError in "rise" mode

cryoSPARC v3.0

December 9, 2020

We’re excited to announce another release of cryoSPARC packed with new features, performance optimizations and various stability enhancements:

CryoSPARC Live New

New
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

CryoSPARC Release Highlights

New
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.
    cryoSparc new non-uniform refinement
New
Upgraded to modern Python 3.7 runtime, including new updated dependencies and installation. Easy upgrades and downgrades between cryoSPARC v2 and v3.
New
Support for CUDA 11 + Ampere Architecture GPUs (3080, 3090, A100, etc.).
New
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.
New
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.
New
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
    cryoSparc helical reconstruction
  • NEW Filament Tracer job tailored to the picking of filaments
    cryoSparc helical reconstruction
  • 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
New
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.
Extract from micrographs
New
New Homogeneous Reconstruction Only job type that performs 3D reconstruction from previously aligned particle images.
New
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 job priority queuing
New
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.
cryoSparc live session data management
New
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.
cryoSparc data management tab
New
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
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.
cryoSparc remove duplicate particles job
New
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
New Systemd Unit File to restart cryoSPARC after server shutdown: A systemd unit file is now included to allow running cryoSPARC as a service.
Update
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.
Update
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.
Update
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.
Update
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.
Update
Improved cryosparcm patch pre-apply validation.
Update
Reduced SSD-cache coordination bandwidth, improving the robustness of caching on multi-node systems.
Update
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.
Update
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.
cryoSparc last accessed timestamp
Update
Queuing interactive jobs always default to the master node.
Update
Ability to specify a first and last name for new users in the Admin panel and through the command line interface.
Update
Default umask is now 002, to allow write permissions by 'group' for folders created by cryoSPARC.
Update
Renamed internal installation directories from cryosparc2_* to cryosparc_*
Fixed
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).
Fixed
Import result group fails if some path fields are blank.
Fixed
Inspect Picks "use_denoise" button failed to actually load denoised micrographs, even if they were connected.
Fixed
Local Refinement now respects the static masking and minimization-over-per-particle-scale parameters, which were previously not used correctly.
Fixed
Setting "Override number of iterations" to True without providing a number of iterations previously prevented Local Refinement from ever terminating.
Fixed
Non-Uniform Refinement: Local processing causes an error if masks are too close to the edge of the refinement box.
Fixed
Local Filtering had SSD:True hard-coded, causing it to fail when running on resources without SSDs.
Fixed
Usernames are now correctly displayed in the details panel for a job.

cryoSPARC v2.15

May 13, 2020

New cryoSPARC Guide Beta

New
First version of a new, comprehensive cryoSPARC guide! Available at guide.cryosparc.com Beta. This guide will consolidate all existing documentation and be populated with cryo-EM data processing tutorials, tips, descriptions of methods, case studies, etc.
Searching in the new cryoSparc guide

Release Highlights

New
Use the new cryosparcm patch command to install bug fixes and improvements without a full update
Calling the cryoSPARC patch utility from the command-line
New
It is now possible to set a project-level default value for whether or not to cache particle images to the local SSD before running jobs within a project. The parameter can be adjusted from the sidebar when a project is selected
Project-level defaults for caching particle images on local SSDs
New
New Particle Class Probability Filter job: Filter particles based on the probability of matching their assigned 2D or 3D classes
New Particle Class Probability Filter job
Update
In the Topaz Denoise job, the default values for the following parameters have been altered to better suit Topaz: The default value for the "shape of split micrographs" parameter has been changed to 1536. The default value for the "padding around each split micrograph" parameter has been changed to 256.
Update
The Topaz Cross-Validation job has been updated with various improvements: Added option to output models from subsidiary training jobs when running cross-validation. Added expected number of particles and training radius as cross-validation parameters. Improved GPU distribution for subsidiary training jobs.
Update
All Topaz jobs now store preprocessed micrographs to avoid unnecessary preprocessing in subsequent Topaz jobs.
Update
Added option for the Extensive Workflow to run additional job types, including Local Motion Correction, Multi-class ab-initio and 3D Variability. This can be used as a full system test for new installs and updates.
New optionss in the Extensive Workflow job
Update
Use dynamically-generated SSD cache paths by including environment variables in the CRYOSPARC_SSD_PATH definition for a worker's config.sh
Update
Import Movies and Import Micrographs jobs are now parallelizable across multiple threads while reading the headers of all exposures to import
Update
Initial and final mini-batch size parameters for Ab-initio Reconstruction can now be set to zero to automatically tune based on the estimated particle size
Update
The project and workspace switchers, which allow you to quickly search and navigate, have been revamped. When you're viewing a project or workspace, the switcher will highlight and scroll to it, allowing you to easily navigate relative to them. When viewing a job within a workspace, the workspace switcher will display a link icon next to every workspace that particular job is linked to.
Updated project and workspace switcher
Update
The job history tab within the resource manager page now shows only jobs that have not been deleted by default. Select the 'show deleted' toggle to show only jobs that have been deleted.
Showing deleted jobs in the job history tab within the resource manager page
Update
Jobs can now only be imported from inside the project directory. This fixes a bug that causes particles to not be cached if they were imported from outside the project.
Update
Executing a cryosparcm command is now only allowed by the owner of the script and on the master node. You can override this parameter by setting CRYOSPARC_FORCE_USER or CRYOSPARC_FORCE_HOSTNAME to true in your shell (or permanently inside cryosparc2_master/config.sh).
Fixed
Bug where multiple jobs launched simultaneously using the same particles could result in endless "cache waiting" messages
Bug fix resolving cache waiting messages
Fixed
Full-frame Motion Correction runs out of memory on 8GB cards with K3 data. There is now a switch to reduce memory usage by approximately half
Fixed
ValueError was raised in 2D classification or Patch CTF Estimation jobs when movies that were imported separately but contain files with the same names get overwritten
Fixed
All refinement jobs now use the first (rather than last) FSC threshold crossing for filtering during iterations
Fixed
Bug in Particle Set Tools intersection when set A is smaller than set B
Fixed
Bug in Heterogeneous Refinement which fails if intermediate plots are disabled
Fixed
Manual Picker fails while calculating the contrast intensity range for a micrograph with an irregular shape
Fixed
Topaz Denoised micrographs display fail to display correctly in the Manual Picker job (as either gray or black images)
Fixed
Micrographs captured at a low magnification fail during Patch CTF Estimation with an IndexError
Fixed
Select 2D fails when trying to select classes from a particle .mrc file that is too large to fit in memory. Also fixed a bug where an IndexError is raised if a class has less than 3 particles in it.
Fixed
Exposure Group Utility job fails with a KeyError when an input dataset has a missing CTF result field
Fixed
Inspect Picks job fails if you try to extract locations and the box size set is not an even number
Fixed
Downsample Particles now exports particles in the correct order if the input particles are out of order on disk
Fixed
MotionCor2 Wrapper: total dose is incorrectly specified as the frame dose argument for dose weighting
Fixed
MotionCor2 Wrapper: output pixel size is incorrect after specifying a Fourier crop factor, causing CTF Estimates to fail
Fixed
Project directory sizes don't update when a project is deleted
Fixed
Allow importing movies shot on high-aspect ratio detectors (2:1 aspect ratio or higher)
Fixed
Resolved version incompatibilities with Topaz version 0.2.4a

cryoSPARC v2.14

February 20, 2020

Release Highlights

New
The job builder includes a search bar to quickly find the job you're looking for
cryoSparc job builder search
New
"Cache Particles on SSD" Job that will cache particles on a node of your choice
Update
Many optimizations across cryoSPARC jobs - datasets containing a large number of items will see significant speedups
Update
Added option to use pre-trained initializations in Topaz Train
Update
Added option to use pre-trained model when running Topaz Extract
Update
All jobs that output FSC plots have been updated to allow for downloading the raw data for external plotting
Update
Curate Exposures job can be run without connecting micrographs, allowing for CTF-based curation using only movies
Fixed
Topaz Denoise fails when trained model is input
Fixed
Template Picker fails on K3 micrographs motion corrected using external software
Fixed
Turning on the "Generate new FSC Mask" parameter in the Sharpening Tools job caused an AssertionError
Fixed
"Particles Excluded" output group image in Select2D job was the same as the "Particles Included" output group image
Fixed
New Homogeneous Refinement job sometimes fails when resampling initial model because boxes were not even sized
Fixed
Performance regressions in the "Extract from Micrographs" job where the time to extract particles increased non-linearly with a larger number of exposures
Fixed
In 2.14.2: "Inspect Particle Picks" job fails with a KeyError when it encounters an exposure with no particle locations

cryoSPARC v2.13

January 28, 2020

v2.13 is packed with a number of updates including interactive 3D variability analysis, reduced memory requirements for refinement of large box sizes, seamless support for negative stain and phase plate data, and more!

New
The 3D Variability Display job output now includes an in-browser, in-line interactive 3D scatter plot to analyze clusters in the distribution of particle reaction coordinates! The user can select which three reaction coordinates to display, and individual clusters can be shown or hidden. Read the new full tutorial, including examples of results:
3D Variability Display 3D Scatter Plot
New
When inspecting particle picks from template or blob pickers, particle pick scores (NCC) and power scores are automatically calibrated with respect to the defocus of each micrograph. This ensures that setting an appropriate threshold on one micrograph will yield good picks on other micrographs with very different defocus.
New
Negative stain and phase-plate datasets are now more easy to process. A single toggle can be set during import and no other parameter changes are necessary in subsequent job types.
New
The blob picker can now use "ring" shaped blobs, which perform well in picking viruses and other spherical particles (eg. apoferritin).
New
Relion 3.1 format .star files can now be imported without errors, though optics group data is not currently parsed.
New
Manual picker interactive job now has adaptive robust contrast normalization to make seeing particles in imperfect images easier.
New
Manual Picker interactive job now includes a "Contrast Intensity Override" slider that allows users to manually select the contrast bounds when viewing a micrograph. The average, patch-based intensity is used by default for the Manual Picker and Exposure Curation jobs.
3D Variability Display 3D Scatter Plot
New
Validation (FSC) Job: Validation of a refinement result (i.e. half-maps) using the FSC is now available as a separate job type, with optional mask input.
Update
Fourier-space plots in Homogeneous Refinement display correctly.
Update
Multiple updates to Topaz-wrapped jobs 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
Update
Passthrough output files now include the project and job numbers for easier referencing (e.g., P1_J1_passthrough.cs)
Update
Manual Picker job now fails by default if the CTF inputs are not connected. An override switch has been added to allow manual picking without CTF estimates, which is not the recommended workflow.
Update
3D Variability Display can now flip the handedness of output volume series.
Fixed
CPU and GPU memory usage of Homogeneous Refinement is substantially reduced. In tests, it is now possible to refine a 1024 box size on a 11GB consumer-grade NVIDIA GPU (GTX 1080Ti), though this does require ~160GB of CPU RAM. A smaller 256 box size can run on a 4GB GPU and requires only 6GB of CPU RAM.
Fixed
The template picker now uses substantially less GPU memory for large micrographs (e.g., K3 super-resolution data).
Fixed
Local per-particle motion correction of K3 data now works correctly.
Fixed
Bug that would cause cufftInvalidPlan error during refinement.
Fixed
Bug where two Select 2D jobs are jobs connected to each other, the last Select 2D job shows incorrect class average thumbnails.
Fixed
Bug where the command_vis would repeatedly try to start but fails, using 100% CPU in the process.
Fixed
(Added in v2.13.2) Bug where mrc volumes were being saved as float64 files, which the mrc file format doesn't support, causing the Sharpening Tools job to fail
Fixed
(Added in v2.13.2) Bug where Heterogenous Refinement and Multi-Class Ab-Initio jobs would fail due to a ValueError

cryoSPARC v2.12

November 29, 2019

Major updates to 3D Variability: Solve more modes, smaller motions, automatic classification of discrete classes, and more!

New
New "cluster" mode in 3D Variability Display allows for automatic hierarchical 3D classification based on variability coordinates: directly visualize and see how many discrete classes are present in a dataset, separate them by clustering, and reconstruct each separately. Then recursively perform 3D Variability to look for sub-conformations or flexibility within each cluster, or refine each cluster separately.
3D Variability Analysis
New
New "intermediates" mode in 3D Variability Display allows for weighted reconstructions of intermediate positions along each variability dimension: create more detailed videos of variability that minimize the effect of density appearing and disappearing during large motions. Also output weighted particle subsets for intermediate positions, for refinement of particular flexible conformations.
New
Default options in 3D Variability improve sensitivity to small variations in the 3D density. Plus support for coloured or white noise models, high-pass filter during optimization, per-particle scale optimization.
Fixed
Fixed streaking issue so that (many) more variability modes can be solved simultaneously.

Major updates to 3D Refinement: On-the-fly CTF refinement, aberration correction, exposure groups, substantial speed improvements!

New
Per-particle defocus refinement implemented on GPU allows CTF refinement in minutes for 100,000's of particles. Implemented as a standalone job and also as an in-line on-the-fly option during Homogeneous Refinement.
High-Resolution Structure
New
Global CTF Refinement and Local CTF Refinement jobs: CTF aberration support, also GPU implemented, corrects for beam tilt, trefoil, spherical aberration, and tetrafoil. Estimation of the new parameters can be done in a standalone job or as an in-line on-the-fly option during Homogeneous Refinement, yielding ultra-high resolution reconstructions.
Local CTF Refinement job card
Global CTF Refinement job card
New
New Exposure Group Utilities job allows users to split or combine datasets into multiple exposure groups for higher-order aberration correction. Create exposure groups using regular expressions and separators, and test your exposure group creation strategy.
New
First-pass optimization of GPU and CPU code for Homogeneous Refinement: now up to 5x faster, especially for symmetric particles.

New UI-based User Management System

New
New admin page with ability to change roles of existing users and create new users through the UI
List of users and new user form
New
Users can request to reset their password through the interface

Topaz Integration Beta

New
New Topaz wrapper jobs for integrating Topaz's particle picking and micrograph denoising functionality
  • 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
Topaz T20S tutorial
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

Other Updates

New
New Symmetry Expansion job expands particle poses around point-group symmetries, to support local refinement of subunits, as well as 3D variability of symmetric particles.
New
New Job Scheduler and Queuing Interface: Override the cryoSPARC scheduler to queue directly to a specific GPU
Updated queue dialog in cryoSPARC v2.12 allowing users to queue a job to specific GPUs
New
Ability to perform non-interactive threshold selection for particle picking and extraction, and non interactive selection of 2D classes, making it possible to process simple data completely end-to-end without manual intervention
New
Ability to interactively select all classes above or below a threshold in Select 2D job (right-click a class)
Select 2D Classes: Interactive thresholds
New
Multiprocessing robustness updates in preprocessing jobs (Patch Motion, Full Frame Motion Correction, Patch CTF Estimation) ensure that if a job fails or is interrupted, completed results are recovered and processing can be resumed.
Update
Orientation-precision plots in refinement are now coloured with minimum value zero so that differences in ratios can be easily spotted
Update
Relative ice thickness is now available in Exposure Curation
Update
2D Classification allows for changing the maximum alignment resolution and reconstruction resolution separately if desired
Update
Sharpening job now applied a spherical window by default
Update
Added option to skip header check when importing movies, which allows for faster importing on larger datasets
Update
Importing Movies, Micrographs or Particles will auto-populate the "exposure group ID" field of the dataset based on the project (each project increments from 0)
Update
Set the environment variable CRYOSPARC_DISABLE_IMPORT_ON_MASTER to allow master-direct jobs (import jobs, curate exposures, select 2D) to be queued on any machine you specify, and not only the master node
Update
If a job is queued to a specific GPU, it will be noted in the Resource Manager
Update
Job Cards now show queue message if placed in queue
Update
Job type is more prominently shown in the sidebar
Fixed
Ab-initio job with symmetry enforced fails with invalid memory access error
Fixed
Certain parameter descriptions in the Job Builder don't show
Fixed
Better logging in Align 3D Job
Fixed
Error in non-uniform refinement when run with CPU option
Fixed
3DFSC job doesn't accept mask inputs
Fixed
New ignore_pose option in import particles to enable import of locations when pose information is missing
Fixed
Deadlock in new job types like 3D var on some newer GPUs
Fixed
Select 2D fails when all classes are selected (i.e., if there are no particles in the templates_excluded output result group)
Fixed
White circles in 2D Class job when circular mask diameter parameter is too close to particle box size
Fixed
Exposure Sets Tool Job doesn't recognize particle inputs
Fixed
The 'more' button in the Job History page doesn't load new rows
Fixed
Copy to clipboard functionality is more reliable on various browsers
Fixed
Back button in File Browser correctly expands path variables
Fixed
Imported jobs caused the tree layout to fail or throw an error
Fixed
Project directory sizes are calculated more accurately
Fixed
When updating a worker's SSD configuration, the SSD option remained disabled even though user supplied a path to the SSD