Orientation Diagnostics job no longer requires tokens to run.

Jobs no longer fail and web interface no longer crashes until a full restart in some cases due to command server issue.

Users running v4.7.1-cuda12 can apply the equivalent patch v4.7.1-cuda12+250814

Ab-initio Reconstruction no longer fails with a NaN error when one or more densities become completely empty.

Subset Particles by Statistic job no longer fails when manual thresholds are specified in the job builder.

Select Volume job now produces passthrough outputs consistently based on input connections.

Support for NVIDIA Blackwell GPUs such as the RTX 5000 series is available in a special CUDA 12.8 build version of this release, v4.7.1-cuda12.

• The special build version has updated minimum system requirements:
  • NVIDIA Driver 570.26+ is required. Note that NVIDIA Blackwell devices are only compatible with the open driver.
  • The operating system must support GLIBC 2.28 or greater. Therefore, the oldest compatible operating systems are Rocky/RHEL 8 and Ubuntu 20.04. However, Ubuntu 22.04 or newer is recommended.
• To update to the special build, use cryosparcm update ‐‐version=v4.7.1-cuda12 . See more details here.
• The standard build, v4.7.1, does not have any dependency changes or system requirement changes compared to v4.7.0 and can be installed with standard update steps using cryosparcm update.

Select Volume utility job: Automatically select the highest resolution volume out of a number of input volumes, and output the best volume with its corresponding particle stack. This job can be useful for automated selection between multiple refinements with different parameters, for example CTF refinement parameters, masking parameters, etc.

Added a toggle to hide per-micrograph junk stats in Exposure Curation when viewing annotated micrographs

Added a timezone identifier to the job PDF output

Added imposed symmetry informational tags to Helical Refine job card

Certain job actions (clear, kill, restart) for Live Worker jobs that were disabled in v4.7.0 have been re-enabled through the jobs interface

Files downloaded from the event log will no longer have the file type appended twice.

Workflows can no longer be applied when the “Queue on Apply” option is selected, but the lane is left blank.

Filtering projects by both detached and archived now correctly displays projects to which the user has access.

Resolved an issue in Exposure Curation where the ruler tool would not activate when also viewing junk detector annotations

Fixed issue where Micrograph Junk Detector would fails with IndexError on some datasets.

Fixed issue where Micrograph Junk Detector would produce partially misaligned junk masks on some datasets.

Fixed issue where Patch Motion Correction would produce NaNs in the background estimate for some micrographs.

Fixed issue where some .tiff files that were missing the TIFFTAG_SAMPLEFORMAT tag would fail to be read.

Fixed issue where some .tiff files that had uint32 datatype would fail to be read.

Curate exposures no longer fails when the particles input is connected but contains zero particles.

Fixed builder logic issue where not all necessary parameters would show up in the Subset Particles by Statistic builder when selecting subset by Class Probability.

Resolved an issue in subset particles difference mode where the input particle stacks would not be both intersected and reordered if they needed to be.

Fixed issue where the Template Picker job would incorrectly re-center templates in some cases.

Fixes issue in the 3D Classification job where output tile figures would be incorrectly assigned to output groups in some cases.

Micrograph Junk Detector Beta automatically labels contaminants and junk objects to aid in micrograph curation and particle picking.

• Micrograph Junk Detector uses a neural network model that has been pre-trained on manually labelled micrographs across a variety of datasets, to predict three categories of junk: carbon/gold edges, intrinsic ice issues (e.g., cracks, non-vitreous ice, graphene wrinkles) and extrinsic ice issues (e.g., ethane contaminants, ice crystals).
• The job rapidly labels new micrographs (over 100 per minute on a single GPU) and produces junk annotations that are then used to filter particle picks in junk areas.
• Outputs of the Micrograph Junk Detector can be used in Manually Curate Exposures to view junk annotations, and to filter micrographs based on junk statistics (e.g., presence and fraction of junk area of each type).

Subset Particles by Statistic job: create subsets of an input particle set, based on individual particle statistics such as per-particle scale factors, classification probabilities, particle picking scores, pose changes, etc. The job can fit a Gaussian mixture model to separate clusters in the data, or allows thresholds to be manually set.

Reference Based Auto Select 2D Beta computes new metrics (Sobel and correlation scores) that can more accurately match 2D classes with projections of a 3D reference volume, allowing for more reliable automatic 2D class selection.

Reference Based Auto Select 3D Beta has a new mode for selecting 3D classes based on resolution metrics alone, without a reference volume.

Exposure attribute scatter plots in Manually Curate Exposures and Live overview tab are now powered by WebGL, supporting responsive zoom and select interactions even when viewing a large number (e.g., over 50,000) of exposures.

Particle Sets Tool job now allows computing intersections of particle sets when only ctf or location data is present.

Topaz Train job no longer uses denoised micrographs by default.

ResLog job's plot now has the y-axis in units of 1/Ų and y-axis titles are updated accordingly.

Global CTF Refinement job no longer produces incorrect results on certain combinations of hardware.

MRC files written in float16 format will now automatically revert to float32 if the range of float16 is exceeded. Additionally, if a nan or inf value would be written out, even in float32, an error is raised.

Fixed a bug in Reference Based Motion Correction whereby certain upstream F-crop ratios, including 3/4 in patch motion correction, could trigger an AssertionError. While some combinations of F-crop ratio and extraction box size may still be incompatible, the error message will now explain the cause more clearly.

Fixed an issue in Patch CTF Estimation which could cause a whole job crash if axis limits for the diagnostic plots of any micrograph were nan or inf.

Added option to output class volumes during O-EM iterations in 3D Classification.

CryoSPARC installation script no longer incorrectly skips updating .bashrc file in some cases.

Added more clear error messages in Reference Based Motion Correction that explain failures due to connecting incompatible empirical dose weights.

Fixed a bug in Rebalance 2D Classes where the job would fail if the "Do superclassification" parameter was set to false.

Fixed a bug in Downsample Particles where both the desired pixel size and box size needed to be specified in the builder.

Fixed an issue in 2D Classification where nan values would be produced when the minimum alignment resolution was set too high.

Fixed a bug where Ab-Initio Reconstruction would fail depending on the maximum resolution and initial resolution set.

Resolved character encoding errors in job report PDFs by switching from a WinAnsi-encoded base font to an embedded Unicode font (Roboto Mono), ensuring full support for extended characters.

Resolved an issue where applicable Workflows would not filter based on job selection.

Workflows now correctly reroute input connections from parent jobs when replacing the original job with a compatible one.

Added support for updating movie symlinks in sessions with cryosparcm rtpcli "session_replace_symlinks(\<project_uid>, \<session_uid>, \<prefix_cut>, \<prefix_new>)" , similar to job_import_replace_symlinks

It is no longer possible to install CryoSPARC in a path that is too long or deeply-nested, in order to prevent "No module named 'conda'" error.

New "Min plot interval" advanced parameter for 3D Flex Training job to limit plotting frequency and prevent potential web application overload. Defaults to 1 second.

Reduce likelihood of web application crash when viewing a job that removes entries from its event log, such as 3D Flex Training.

Prevent rare input load error for some empty datasets.

Resolved an issue where filesystem related errors would cause the application service to crash when downloading images, files or outputs from the web application.

More reliable project directory access and permission check to prevent errors on network file systems that do not correctly report their permissions flags.

Volume viewer and other visualization features no longer stop working until a restart occurs.

Fixed a problem in CryoSPARC command servers whereby an excessive number of file handles could be held open for a long time.

CryoSPARC worker processes now request that the OS not allocate transparent hugepages during memory allocations. This change improves performance and stability significantly, especially on nodes with multiple GPUs and multiple simultaneous jobs. Jobs will also emit a warning if the OS is set to always use transparent hugepages.

Job: Check for Corrupt Particles now checks for NaN values by default, and fails (rather than completing with warnings) if any corrupt files are detected. The job can then be marked as completed or re-run with the “Fail if corruption is detected” parameter turned off in order to use the output in which corrupt files have been filtered out. The job can also check MRC header checksums.

CryoSPARC now performs an explicit NaN values check when writing MRC files, and also writes a checksum to the MRC header for subsequent corruption detection.

2D classification jobs now request an appropriate number of CPUs when running on more than one GPU.

The SSD cache system is now more robust on cluster filesystems, and “File not found” errors during caching should no longer occur. The system also produces additional logs and diagnostics.

When the random seed parameter is manually overridden, 2D/3D classification and refinement jobs now correctly use the provided value and produce similar results when repeated, up to GPU floating-point determinism and precision.

Fixed a variety of rare edge cases that could cause issues in the high performance I/O system that was introduced in v4.6.

The default limit of open file descriptors is increased to avoid issues on some OSes.

Falcon C EER files no longer fail to import.

Resolved an issue were the application server could crash if a file was incorrectly deleted.

Resolved an issue where the volume viewer display of local resolution colour maps was flipped along the Z axis.

Resolved an issue where the volume viewer could display a stale volume result after clearing and re-running a job in some scenarios.

Resolved an issue where jobs with blueprints would always display in the job builder regardless of which filter tag was applied.

Resolved an issue in the cards view where job cards could appear blank when expanding a group in a workspace with a significant number of large groups clustered closely together.

Fixed an issue where loading 3DFlex mesh segmentation files in MRC format would fail due to an off-by-one error.

Support for CentOS Linux 7 operating system is deprecated. CryoSPARC v4.6 will continue to function on CentOS 7, but future versions will no longer support this operating system. CentOS Linux 7 reached end of life on June 30, 2024.

Up to 2.1x speedup across refinement and classification jobs due to a redesign of CryoSPARC's I/O system that provides significant optimizations to particle read times. In v4.6.0, a homogeneous refinement of 2.3M particles with box size 300 can now be completed in just 27 minutes.

Rebuilt tree, card, and table views for jobs, with significant performance optimizations to support large workspaces and projects. Up to 10x faster initial load time for the tree view, and subsequent updates when connecting and creating jobs are nearly instantaneous. In the card and table views, all jobs are now instantly accessible with detailed information loading progressively as you scroll.

Job Groups: collapse multiple jobs into a single card to maintain legibility and easy navigation within a workspace. Job Groups work across the tree, card and table views, and jobs can be easily added and removed from groups using multi-selection and the right-click menu. Learn more

Improved navigation: the job search menu and targeting system allow you to quickly find and automatically navigate to any particular job, or quickly jump to the latest created, completed, or running job.

Inspect Particle Picks now has a parameter called "Auto cluster", which clusters particles based on their NCC and power scores, and can automatically select a cluster that will ideally contain true particle picks based on those scores. This allows Inspect Particle Picks to be run without user intervention. Auto cluster is designed to be used with denoised micrographs from the Micrograph Denoiser job.

The local file upload tool now supports .seg segmentation files.

Labels designate type of output when downloading results from the job preview dialog output groups panel (e.g., map, mask, etc.).

Added the ability to mark or unmark a job as final from the job sidebar actions panel. Read more about data cleanup in this guide.

Added ability to sort projects, workspaces, and sessions by their titles.

Added filter bar toggles to the projects view to quickly show and hide archived and/or detached projects.

Archived and detached project filters are now additive, and can be toggled together to show both archived and detached projects, instead of just archived or detached projects.

Introduced a quick action to create Homogeneous Reconstruction Only from an Import Particle Stack job.

Unused particles will be connected when building a Homogeneous Refinement, Non-uniform Refinement or Heterogeneous Refinement from a quick action on Ab-initio.

Introduced a quick action to build a Blob Picker Tuner job from Inspect Particle Picks.

Added completed, failed or killed timing to the tooltip that displays when viewing the elapsed time of a job on the card.

Downloading a CSV of projects, workspaces, sessions and jobs will include relevant project or workspace ID and a timestamp representing when the list was generated.

Cluster configuration variables are now listed in ascending alphabetical order.

Various improvements to job informational tags: Support for Homogeneous and Heterogeneous Reconstruct Only jobs, Streaming Homogeneous Refinement, and symmetry relaxation parameters.

The Live Session data management tab is now deprecated and as such, a notice displays within the tab. It is recommended to perform Live Session compaction or restoration as a more robust way to compress, archive and restore sessions.

Resolved an issue where exposure pixel size shown in the Live session sidebar would not account for EER upsampling.

Reduced memory usage and lower likelihood of out-of-memory errors during data clean-up operations, job input loading and job output result saving.

Deep Picker Train and Deep Picker Inference jobs are now restricted in workflows, and are only allowed if they do not include any child jobs inside of the workflow.

Clicking the job's workspace in the details panel will no longer reset the current view to cards view.

Fixed an issue where the custom parameters tooltip in the job card's footer would continue to be hidden even after queuing a job.

Fixed issue where some workspaces were not being sorted into the correct order when sorting by job count.

Fixed issue where job CSV downloads were using the job's created at timestamp to populate the "Status Updated" field.

Resolved a case where filesystem errors could cause the web application server to crash when downloading job results.

Resolved an issue where refinements with downstream Local Resolution Estimation jobs did not have an option to load a colour map within the volume viewer tab.

Resolved an issue in the job report PDF where parameters set to false were reported as 'Not Set'. Instead, boolean parameters are now listed as 'True' or 'False'.

Denoised micrographs will now be correctly scaled to the canvas and line up with pick locations when downloaded from the exposure viewer.

Resolved an issue where jobs queued from the sidebar would sometimes show a perpetual loading indicator until deselected.

The volume viewer now has improved reliability, with reduced likelihood of issues when multiple large volumes are loaded.

Streaming refinement in CryoSPARC Live now re-scales a provided input volume and mask to match the extent and pixel size of the extracted particles.

Reference Based Motion Correction no longer fails with an error indicating that there are micrographs with fewer than 2 particles, when particle re-centering is turned on.

Import Result Group job no longer fails when importing a result containing a Topaz model.

Fixed a bug that caused the 3D Flex Generator job to run out of GPU memory for large datasets.

Ab-initio Reconstruction no longer fails when upstream particles have alignments3D metadata attached, and the number of particles parameter is set.

Fixed a bug that would cause the 3D Classification job to fail when class re-ordering was on, and the number of classes exceeded 12.

Orientation Diagnostics no longer fails when using imported half-maps.

Removed unnecessary SSD requirement in the Regroup 3D job.

Removed unused parameter “Recenter templates” from the Blob Picker job.

This version replaces CryoSPARC v4.5.2, released on June 3, 2024.

Check for Corrupt Micrographs job tests for and separates micrograph files that cannot be successfully read from disk.

Refinement jobs default parameters have been changed so that the jobs use the half-set split from the input particles by default. This ensures that repeated application of Reference Based Motion Correction and refinement does not cause mixing of the half-sets. The Particle Sets Tool job also now has an option to balance unequal half-set splits.

Orientation Diagnostics no longer fails on CPU-only worker nodes, and requests the correct number of CPUs when launching on a cluster.

Relative signal plots in Orientation Diagnostics jobs are now less crowded.

The Topaz Extract job now allows input in units of estimated particle diameter for the radius of extracted region parameter.

Import Result Group no longer fails to import exposures when some paths are missing.

Regroup 3D no longer outputs incorrect particles when classes are manually excluded.

Fixed an issue where for some large CryoSPARC Live sessions, scrolling through the exposure feed to earlier exposures could sometimes cause the application server to crash with a memory leak.

Excess UserWarnings are no longer printed in job log output.

The default value for CRYOSPARC_JOB_LAUNCH_TIMEOUT is now extended to 60 seconds.

Micrograph Denoiser no longer fails on launch due to PicklingError

Scale bars on the Import Movies job card are now the correct size

Gracefully handle missing chunks when attempting to save a file to the uploads directory via the local upload tool

Micrograph Denoiser Beta job produces enhanced contrast in micrograph images to aid particle picking and visual inspection.

• Micrograph Denoiser uses a neural network model that can be trained on as few as 100 exposures from a new dataset in just a few minutes on a single GPU. The trained denoiser can then be used on new micrographs from the same or a different dataset. A pre-trained general denoiser model is also available to use without any training required.
• The denoiser model is designed to work across a wide range of defocus and contrast levels.
• Denoised micrographs can be used seamlessly in blob and template picking jobs, and can substantially improve picking results. Denoised micrographs also show by default in all interactive jobs, making visual inspection of micrographs easy.

View low-pass filtered vs. denoised

Automatic selection of 2D classes or 3D classes given a 3D reference is now possible using new Reference Based Auto Select 2D Beta and Reference Based Auto Select 3D Beta jobs.

• These jobs align and compare classes to the reference volume and select classes either based on score thresholds or clustering.
• The jobs can be set up once on a dataset, and can subsequently allow one-click automated processing on new similar datasets using Workflows.
• The jobs also make it easy to sort and select from hundreds of 2D classes or dozens 3D classes in datasets with substantial heterogeneity.

Upload files from your local computer to the CryoSPARC system directly in the browser. This new ability streamlines workflows involving local visualization and editing of files such as 3D maps or masks. Uploaded files are saved to the selected project directory and can be imported and used in jobs. Read more in the guide.

Orientation Diagnostics job now reports Relative Signal — a new diagnostic that can help directly identify underrepresented views that affect map quality and the cFAR score. Relative signal is computed by considering FSCs within toroidal sections of Fourier half-maps to relate 3D signal quality to viewing direction. Two new plots are produced that show where on the viewing sphere relative signal is attenuated, with sample projections and an embedded structure to simplify interpretation.

New Rebalance Orientations job removes particles from overpopulated viewing direction regions. Rebalancing viewing directions can improve downstream refinements when particles have a highly non-uniform orientation distribution.

Jobs that produce multiple 3D volumes (such as 3D classification, Heterogeneous Refinement, 3D Variability Display, etc.) now output a "Volumes group" output that contains multiple volumes, and can be connected to a downstream job with a single input connection. This enables seamless handling of arbitrary numbers of 3D volumes and automation using Workflows.

Align 3D Maps has been reimplemented with a new 3D alignment method to increase the robustness and precision of volume-to-volume alignment. In addition, it can now:

• update particle alignments while searching over handedness,
• transform all maps and masks associated with an input volume slot,
• and accept inputs of different box and pixel sizes.

The file browser now features an expandable sidebar to search and navigate into project directories. Bookmark commonly-accessed directories, making them available for access at a later time through the sidebar. Read more in the guide.

Improved 'Inputs and Parameters' tab for jobs now displays additional input group information in a summarized view while retaining an option to view low-level connection details. By default only custom parameters are shown, making it easier to identify which parameters were set for a particular job.

Additional info tags now display on the job card with useful stats and summary data, for more jobs including Import Volumes, Exposure Curation, Exposure Sets Tool, and Helical Refinement. New quick actions allow quick creation and connection of many more job types in typical workflows.

The details section of the job sidebar now displays a more comprehensive summary of parents, children, and cloned jobs when hovered, including job type, status, summary stats, and custom parameters.

Support has been added for Falcon C camera .eer movies (2k x 2k physical pixels).

Various updates to Workflows:

• New rebuilding system allows retaining annotations and settings when updating an existing Workflow.
• Workflows can now be applied from anywhere in the application by selecting or creating a project and workspace from within the Workflow apply dialog.
• Filter controls have been added to allow collapsing/expanding all jobs in sidebar, filtering by flagged jobs, and navigating to a selected job.
• Fork option has been replaced with a "Create New" option in the edit dialog for simplicity and clarity.

Various improvements to Reference Based Motion Correction Beta:

• Input particles are now re-centred based on their aligned shifts, at the start of the job. This feature can be switched off. The upsampling factor for .eer movies can now be overridden.
• The job has been improved to be significantly more stable. An option has been added to prevent crashing if the input movies contain different frame counts (the option is off by default). This option relies on the assumption that the most common frame count is "correct", and will discard movies that don't match that frame count. The job also no longer terminates if the distances between particles results in a singular covariance matrix, as a pseudo-inversion is now used. The chance of getting NaN values in the highest-frequency column of the FCC plot (due to low signal near the FSC cut-off frequency) has been greatly reduced. The job also no longer crashes if the upstream motion correction skipped the movie's first frame.
• The job now outputs movies or particles that were rejected, as separate output groups. Trajectory plots now correctly reflect the micrograph's aspect ratio. The mask_refine low-level input is now optional (a mask must be supplied, but if the separate static mask connection is used, mask_refine need not be present).
• It is now possible to prevent the GPU responsible for generating 2D reference projections from also computing trajectory estimates. Using this option reduces VRAM consumption but requires the use of at least 2 GPUs.

Refinement jobs now produce a cFSC summary plot at every iteration, enabling anisotropy tracking throughout optimization (this includes homogeneous, non-uniform, helical, and local refinement). A new fast GPU-based implementation of the core cFSC computation adds minimal overhead, requiring less than a second of additional compute time for typical box sizes.

Several improvements to 3D Classification:

• In line with 3D Variability Analysis, the 'Target Resolution' parameter has been renamed to 'Filter Resolution' and must be explicitly set for the job to run. Also, the secondary RMS-based convergence criterion is now turned on by default. This secondary criterion can significantly reduce run times without substantially affecting the final class volumes.
• The job now includes particle pre-processing and symmetry enforcement, and class re-ordering is now turned off by default to avoid potential confusion.
• The job tile figure is now revamped to show class ids, relative populations, and a more distinctive difference-from-consensus projection for each class.

In Downsample Particles, users can now specify the desired approximate pixel size after Fourier-cropping, instead of specifying the Fourier-crop box size directly, if desired.

The 3D Flex Generator Beta latent space plot is now coloured according to the normalized difference in 3D deformation relative to the origin. Larger values indicate regions of the latent space that encode more substantial flexing of the particle.

Regroup 3D now allows for pairwise alignment of volumes prior to regrouping, as well as alignment of volumes within a superclass after regrouping. It also now allows regrouping of all volumes into one single superclass.

The Manual Picker interactive job now writes manually picked particle locations to disk every 10 seconds, to minimize data loss in case the job crashes.

The new and more reliable SSD cache system introduced in v4.4 is now enabled by default. It also now features a configurable distributed locking strategy to use when multiple running jobs access the SSD cache simultaneously; the default strategy is best in most cases, but use the master strategy for caches on distributed file systems such as GPFS and BeeGFS where POSIX locks are disabled or unavailable. See guide for details.

Deleting a project now completely removes the project folder on disk instead of leaving an empty folder.

Archived projects can now be deleted. Deleting an archived project will clear any remaining database references to the project and should clear up more space on disk. A deleted archived project cannot be un-archived. For more details about archiving, see the Data Management Guide.

Projects that are archived, detached, or deleted can no longer be shared with other users.

Reduced default RAM requirements for some utility jobs.

Jobs will provide a warning before starting if the amount of RAM available is less than the amount of RAM requested by the job.

Jobs will no longer fail on completion if they cannot generate their passthrough outputs properly. They will instead raise a warning and continue to completion with potentially missing passthroughs.

Running Export Exposures from CryoSPARC Live sessions now provides additional information about curation thresholds that were set in the session.

When maintenance mode is active, a banner will display in the header when viewing CryoSPARC Live sessions communicating to users that additional jobs or sessions will not be queued.

Ability to specify an arbitrary number of pre-processing GPU workers for a CryoSPARC Live session.

The Curate Exposures interactive job can now load micrograph thumbnails that were generated in CryoSPARC Live.

Imports in Import 3D Volumes are now sorted alphabetically.

Volume Tools now reports the centre of mass of the input volume, if it is a mask.

Volume Alignment Tools now has the option to automatically re-centre the input volume and particles based on the centre of mass of the supplied mask, especially useful for local refinements.

Local Refinement's fulcrum coordinates and Volume Alignment Tools' 3D centre coordinates now can be specified with units of pixels (px) or Angstroms (A).

Volume Alignment Tools' 3D rotation angles can now be specified with units of radians (rad) or degrees (deg).

Class Probability Filter now supports the new alignments3D_multi particle field.

Rebalance 2D Classes now always produces a "Particles Selected" output, containing selected particles from all of the superclasses.

Added parameters Use spherical mask, Spherical mask diameter (A), and Spherical mask diameter outer (A) to allow users to customize the spherical mask used in Heterogenous Refinement. The default behaviour is still the same.

Orientation Diagnostics will now use the mask_fsc_auto mask present within the input volume connection, if no separate mask input has been connected.

3D Flex Generator now outputs a JXX_particle_flows.npy file that saves the trained mesh deformation (flow) of each particle.

New Freeze latents during training parameter in the 3D Flex Training job allows 3D Flex to better preserve the 3DVA motions when trained from 3DVA latents.

Inspect Particle Picks now shows the picking statistics histogram in the job's event log when the job completes, including a border showing the selected thresholds.

The exposure viewer in interactive jobs and CryoSPARC Live always pans when holding down the middle-mouse button, enabling navigation around the exposure while performing an action such as manual picking or measurement.

Refinements with global pose search now throw warnings if symmetry expanded particles are connected.

Reduced default workers and threads parameters for Topaz Preprocessing job.

Correctly set CPU resource requirements for Topaz jobs based on number of CPUs and number of workers specified in parameters.

Added a Downsampling mode parameter to Topaz jobs with options of "manual" or "auto". If set to manual, the user enters Downsampling factor as before. The default is now auto, where the user enters Estimated particle diameter (A) and the downsampling factor will be automatically calculated based on the type of model used.

Exposure Group Utilities in "cluster&split" mode now respects the "Starting Exposure Group ID" parameter.

New cluster_vars argument for Job.queue method for queueing to clusters.

Allow copy or symbolic link operations in project directories for files outside the project.

Replaced the "Output F-crop factor" parameter in Reference Based Motion Correction with the ability to directly specify the desired output box size.

Previously, refinement jobs recorded internal runtime summary statistics in the database at every iteration. Stats from intermediate iterations are unnecessary and are no longer generated, and existing intermediate stats in the database will be removed in a migration upon updating to v4.5. We expect this change to noticeably improve performance in the web app when viewing or interacting with jobs due to the removed data's size.

Repetitive warning messages from libtiff during normal reading of .eer movies have been suppressed, reducing the size of the job log.

Fixed a bug where ab-initio volumes could not be deselected after being selected in CryoSPARC Live sessions.

Fixed an issue where it was possible to detach projects that still had jobs queued in the scheduler.

Fixed a bug that could cause motion correction and CTF estimation jobs to freeze forever if a child process terminates abnormally.

Prevent applying previously-downloaded patches that don't apply to the current version of CryoSPARC.

Fixed issue where thumbnails for Import Movies might not zoom in properly

Fixed a bug introduced in v4.4 that would cause Patch Motion Correction jobs to fail if cleared and re-run, due to the missing input for empirical dose weights.

Patch Motion Correction now correctly updates the frame count in exposure metadata, in case it was recorded incorrectly by the import job (e.g. if "skip header check" was used). This will help Reference Based Motion Correction to pre-screen its input movies for those with mismatched frame counts, potentially averting a crash.

Allow using Job Cart with Reference Based Motion Correction.

Fixed issue which could cause Local Motion Correction to crash at the end of the job while computing summary statistics, on an otherwise successful run.

Fixed issue where particle diameter was not being calculated correctly in Manually Curate Exposures jobs with connected particle inputs.

Resolved a bug in Inspect Particle Picks where particle picks from denoised micrographs would report NCC scores outside of [0,1], causing them to be inaccessible to filter.

Fixed a bug in 2D Classification where if hard classification is enabled, particles would be assigned posterior scores of 0, causing particle counts to be incorrect in Select 2D and subsequent jobs.

Added override parameter for micrograph pixel size in 2D Classification to fix an issue where duplicate particle removal used the wrong micrograph pixel size on particle datasets from before version 4.5.

Fixed 2D Classification plots to be consistent with Select 2D Classes job.

Fixed an issue in Helical Refinement where input scales were previously reset to 0 if greyscale estimation is disabled.

Fixed plotting bug in 3D Classification which resulted in the focus mask being shifted from its true location by one pixel along each axis.

Global CTF Refinement now throws an explicit error when the maximum and minimum fit resolutions are incompatible.

If inconsistent aberration values within a single exposure group are found, refinements with global CTF refinement enabled now fail at the start of the job, rather than midway through.

Fixed bug that would prevent 3D Variability Display from skipping reconstruction in cluster mode.

Removed the download PDF option for cluster plots in 3D Variability; the PDFs take a long time to open due to the large number of points being plotted.

Fixed an issue in which .seg-format 3DFlex mesh segmentation files with certain topologies would fail.

Fixed an issue in which .mrc-format 3DFlex mesh segmentation files skipped the first segment.

Particle Sets Tool now correctly uses both a particle's file path and its index within the file to identify matches when intersecting by path.

Fixed an issue where Symmetry Expansion and Volume Alignment Tools would ignore any additional particle blob slots (including those produced by Flex Data Prep, such as blob_train).

In Simulate Data, fix to computation of the additive noise variance. The added noise no longer erroneously depends on the chosen CTF parameters.

SSD cache system no longer fails when some input particle files are symbolic links that resolve to the same file.

Prevent invalid multi-instance access when the environment of one instance is active while running cryosparcm commands for another.

Fixed a bug which caused the Gctf wrapper job to fail if LD_LIBRARY_PATH was unset.

Normalize project directory names when creating or attaching to avoid duplicate entries in the database.

Correct Benchmark job directory access when there is a trailing slash in the specified benchmark data directory.

Restrict accidental cloning of certain Live-managed jobs.

Fixed an issue where event log PDF downloads for certain jobs (eg. Manually Curate Exposures) would fail due to control characters being interpreted incorrectly.

Fixed an issue where the interactive scatter plot for 3D Variability Display would not update its layout when the window resized.

Job PDF report now states the version of CryoSPARC the job was run with, not the version of CryoSPARC running when downloading the report.

Resolved an issue where job output image previews did not display on the 'Outputs' tab when previewing a job.

cryosparcm commands configuredb and patch no longer show a segmentation fault after successful completion.

Log messages for project and job size updates no longer contain inconsistent counts.

Fixed issue introduced in v4.4.1 where benchmark job would not complete GPU Engine benchmarks.

Reference-based motion correction no longer fails if GPUs are configured in EXCLUSIVE_PROCESS mode.

The volume viewer now supports many more types of volume outputs: map, map_sharp, map_aligned, map_half_A, map_half_B, map_sym, map_sym_sharp, map_filtered, map_3DFSC

Attempting to unarchive a project will now fail if the directory specified does not contain a the same project UID that is being unarchived. The target project directory’s project.json file is checked to see if it matches the UID of the project selected in the UI.

Exposure Group Utilities now creates the exposure and particle output groups at build time rather than run time, enabling the job to be used in Workflows.

Align 3D’s volume output group now outputs a map output, identical to the map_aligned output, for enabling drag-and-drop connection to refinement job input groups.

The Benchmark job now includes a new class3D-small benchmark to test minimum supported hardware specs (32GB DRAM, 11GB VRAM). GPU benchmarks also now allow any specific benchmark to fail without halting the overall benchmark job.

Fixed an issue where the default blueprint ‘2D Classification (Small Particle)’ would fail due to a missing custom parameter.

Fixed an issue which caused the 3DVA Display job to sometimes duplicate upstream 3DVA component slots at build time.

Fixed an issue causing Remove Duplicate Particles and 2D Classification to occasionally fail with an AssertionError.

Fixed an issue where the ability to toggle display of denoised micrograph within Exposure Curation was not showing.

Fixed an issue which caused I/O error messages to be displayed without the specific reason for the failure.

Fixed an issue which could cause reference based motion correction to crash when a defect file was in use.

Fixed an issue where reference based motion correction could crash with a message about the variable ‘uid’ being referenced before assignment.

Increased memory limit per movie for reference based motion correction from 100 GB to the machine’s physical RAM.

Fixed an issue where thumbnails were not being updated when manually rejecting exposures in the exposure curation cards view with a filter set.

Project level parameter defaults are longer reset when creating a job from a blueprint (all parameters are still reset when applying a blueprint to an existing job).

Template picking in Live no longer fails when only one template is selected.

External dependencies that were removed in older versions of CryoSPARC are no longer installed.

Fixed an issue where all required directories were not being checked for existence when restoring from backup.

MONGO_EXTRA_FLAGS is no longer included in the default configuration file after installation.

Improved error message when driver version is incorrect

CryoSPARC Live session worker jobs no longer fail during particle picking on sessions created prior to v4.4

CryoSPARC Live sessions created prior to v4.4 no longer fail during pausing and exporting particles

Class Probability Filter job no longer fails when particle blobs are not available

Benchmark job correctly runs with more than one GPU

Benchmark job no longer fails if benchmark data is outside the project directory

Small Particle parameter definition in default blueprint is now correct

CryoSPARC now bundles CUDA Toolkit 11.8; a separate CUDA Toolkit installation no is longer required by the CryoSPARC worker application. BREAKING: CryoSPARC v4.4 requires NVIDIA driver version 520.61.05 or newer.

Introducing Workflows and Blueprints:

• Workflows: Workflows make it easy to replicate processing that you've done before. Select a chain of jobs to create a templated processing Workflow, and re-create it in any project or workspace with a single click. Annotate the Workflow with a description and tags, set up default or locked parameter choices, and easily share Workflows from one CryoSPARC instance to another.
  • Workflows are flexible. You can create a linear Workflow that for example, starts with an import job and proceeds all the way to a refinement, to make it easier to process a new dataset using an existing set of steps. Alternatively, you can select a portion of a processing workflow that you would like to re-use for exploratory processing (e.g., for sorting particles or separating heterogeneity).
  • Use Workflows to save time, to maintain consistency and repeatability, and to capture important target-specific or facility-specific processing details and patterns so that new users can get a head start.
  • Watch a tutorial video and read the in-depth Workflows guide to get started.

• Blueprints: Blueprints allow you to define custom parameters and annotations as a template for any job type. Apply the Blueprint to an existing job or create a new job from a Blueprint directly from the job builder, in any workspace or project.
  • Save time and avoid mistakes in entering parameter values by creating Blueprints for e.g., import jobs for specific microscope setups, classification and refinement jobs for specific protein types or sizes, settings for specific computational configurations, etc.
  • Create Blueprints to avoid searching across projects for the parameters of previous runs of a particular job type. Easily export, share, and import Blueprints from one CryoSPARC instance to another.
  • Read the in-depth Blueprints guide to get started.

Reference Based Motion Correction (BETA) in CryoSPARC improves final resolution and map quality by re-estimating per-particle motion trajectories using a reference volume, similar to Bayesian Polishing (Zivanov et al, 2019).

• Before running Reference Based Motion Correction, you must run Patch Motion on your input movies and take the extracted particles through a 3D refinement.
• The reference density and particle poses from 3D refinement are used to go back to the input movies and re-extract particles with optimized motion trajectories. Reference Based Motion Correction is multi-GPU accelerated and optimized, and includes a new method for hyperparameter optimization.
• The job also computes optimal empirical dose weights by comparing aligned particles against the reference density, and uses these to weight contribution from early and late frames of the input movies. This dose weighting is often responsible for a large part of the improvement from Reference Based Motion Correction. In CryoSPARC v4.4, Patch Motion correction can now accept empirical dose weights as input, e.g. from previous processing of a similar dataset, so that empirical dose weights can be applied right from the start of the processing pipeline.
• Reference Based Motion Correction can also perform motion estimation of particles from multiple heterogeneous classes simultaneously, and uses particles from all classes in each micrograph to constrain motion trajectories, potentially leading to improved results over processing each class separately.
• Watch a detailed tutorial video to learn how to use the job, and read the job documentation for theory and more details about the method.

Orientation Diagnostics, a job that rapidly computes a set of easily interpretable diagnostics to identify orientation bias and anisotropic signal content in 3D refinement results. Quickly identify potential data collection, sample preparation, or particle picking/curation issues with two complementary statistics: Conical FSC Area Ratio (cFAR), sensitive to anisotropy in signal content and alignments and Sampling Compensation Factor (SCF*), sensitive to anisotropy in alignments (Baldwin and Lyumkis, 2020).

• Several new diagnostic plots allow for in-depth analysis of directional variation in FSCs and particle scale factors. The generated diagnostics include the values and plots previously produced by the 3DFSC wrapper job, which is now a legacy job.
• Read a tutorial on how to use the job, and read the job documentation for theory and more details about the method.

Non-Uniform Refinement is up to 2x faster: the core computation for non-uniform cross-validation regularization is optimized on GPU to be 7x-10x faster. This translates to approximately 2x faster overall run time for Non-Uniform refinement jobs, and Helical and Local Refinement jobs with non-uniform regularization enabled.

3D Flex Reconstruction job now supports CTF aberrations during high-resolution reconstruction. Also, there is now an option to read particles from SSD cache or from project directories during reconstruction, rather than loading all particles into RAM. This option substantially decreases the CPU RAM requirements for reconstruction.

• In addition, 3D Flex dependencies are now bundled with CryoSPARC and no longer require a separate online installation step. 3D Flex now supports the latest NVIDIA GPU compute capabilities 8.9 and 9.0.

Symmetry Relaxation: There is now an option to relax the pose search over symmetry-related views in Homogeneous and Non-Uniform Refinement.

• A "break symmetry" option is available in Homogeneous Reconstruction that randomizes particle poses over the chosen symmetry group.

float16 Support: Particles and motion-corrected micrographs can now be output in 16-bit floating point format, via a new parameter in motion correction and extraction jobs. This can cut disk usage in half for large projects. The option to output float16 can also be set as a project-level default parameter.

AFIS Beam Shift Import: In Import Movies and Import Micrographs, beam shift values for data collected in EPU via the Aberration-Free Image Shift (AFIS) method can now be directly imported, and exposure groups created based on clusters of beam shift values.

• For existing exposure datasets in CryoSPARC, add beam shift information using the new Import Beam Shift job. In the Exposure Group Utilities job, cluster exposures into exposure groups based on imported beam shift values automatically.

Regroup 3D job quickly creates a set of 'superclasses' from a larger set of upstream 3D Classification or Heterogeneous Refinement classes. It uses a lightweight spectral clustering algorithm that can aid in identifying dominant conformational variations.

Heterogeneous Reconstruction Only job reconstructs multiple classes from upstream 3D Classification, Heterogeneous Refinement, or Regroup 3D outputs. It uses weighted back-projection via upstream class posteriors, with an option to apply hard classification. It includes similar reconstruction options as the Homogeneous Reconstruct Only job (including symmetry, box size, etc.).

Viewing direction distribution plots now include an option to export as a BILD file for visualization in UCSF Chimera(X).

Experimental SSD cache system with significantly improved reliability and support for network drives. To enable, add export CRYOSPARC_IMPROVED_SSD_CACHE=true to cryosparc_worker/config.sh. See the guide for more details.

Improved behaviour of the Data Cleanup Tool to streamline compaction of projects and workspaces:

• All options are unchecked by default.
• When running the Cleanup Data tool on a single workspace within a project, jobs that are linked to other workspaces will no longer be deleted by the tool; instead those jobs will be unlinked from the workspace being cleaned and will remain present in the other workspaces.
• CryoSPARC Live jobs, which are excluded from the cleanup process, are marked as "Skipped" and their size is now displayed.
• The total project directory size is now displayed in the cleanup tool along with the total size of data that the tool can clear, which may be different due to imported and manually copied files that may be present in the project directory.

2D Classification implementation that reduces memory usage and provides speedups with larger datasets. The original implementation is available as a legacy job type.

Reconstruct 2D Classes job that reconstructs 2D class averages from previously classified particles.

Ability to set custom parameters within the Live session view when configuring custom Streaming 2D Classification, Ab-inito and Streaming Refinement jobs.

Job cards now indicate warnings and errors, along with a text preview. If a job contains warnings or encountered an error, an icon will display in the cards and tree view. Hovering over the icon will display more information about the warning/error. A subset of the error will be visible directly on the job card view if applicable.

Ability to copy parameter code name via the 'Inputs and Parameters' tab when previewing a job. This name can be used in cryosparc-tools scripts.

If a job exists in more than one workspace, an icon and informational tooltip will be show on the cards view. In addition, jobs that display in the tree view but are not explicitly linked to the selected workspace are marked with an icon and informational tooltip for additional context.

Ability to star a Live session from within the session view through the primary dropdown menu.

Import Particles contains a new set of parameters to enable build-time output group generation and validation. This allows Import Particles to be used within Workflows for automated processing.

Simulate Data job that is now GPU accelerated. The previous implementation is available as a legacy job.

The Performance Benchmarks system now captures benchmarks from the core algorithms used in 2D Classification and 3D Classification jobs. In addition, reference GPU Benchmarks have been added for the RTX 4090, A100 PCIE-40GB, RTX 3090, and A4000 GPUs, as well as for AWS EC2 g5 instances with FSx for Lustre and local NVME SSDs.

The Validation (FSC) job now outputs an additional FSC figure with square plot markers along with a line, to more clearly see each resolution shell.

3D Variability Display now includes an option to create intermediate reconstructions with equal numbers of particles in each frame. The job now also allows up to 100 input components instead of 20.

2D Classification now has an option to set a minimum alignment resolution that provides the ability to high-pass filter references during classification and can be useful for smaller particles in some cases. The job also has an option to display a scale bar on the 2D class averages figure.

Heterogeneous Refinement now correctly accounts for the Backprojection resolution factor parameter; the job card image display is improved when there are classes of very low resolution; the Initial random assignment iterations parameter now applies only if non-distinct initial volumes are provided; and the job now outputs a volume series containing all the classes that were produced.

3D Classification now filters the consensus volume according to its FSC and outputs the result for downstream use.

Sharpening Tools job now estimates a B-factor using a Guinier plot if a sharpening B-factor is not provided, with options to include mask and FSC weights prior to estimation.

Downsample Particles now allows 'uncropping': when the desired box size is larger than the input particle box size, the particles are padded in real space and the padded region is filled with the mean value of the particle.

Downsample particles now has an option to re-center particles according to their shifts.

The Rebalance 2D Classes job now displays a plot of the pairwise affinity matrix between 2D classes, and also updates particle's 2D alignments to be in-register within each superclass. Also, the job now always outputs combined datasets for particles and templates, even if "Split outputs" was activated.

The legacy web application (deprecated since CryoSPARC v3.0 in December 2021) that could be spawned via cryosparcm start app_legacy and operated at BASE_PORT + 7 is no longer bundled with CryoSPARC.

The CryoSPARC database now has journaling turned on by default, increasing durability in the event of a failure.

When a job is in building status, any custom parameters set are visible on the job card in the tree view.

CryoSPARC Live sessions now use 10% less storage space per micrograph in the database by reducing the number of plots created during preprocessing. To turn on all plotting, enable the "Enable Plotting in RTP Worker" session parameter.

CryoSPARC Live Session UIDs now increment monotonically, independent from Workspace UID.

Micrograph images with pick locations overlayed can now be downloaded from the micrograph viewer in CryoSPARC Live.

The job details sidebar now shows the last time a job was exported and the path to which it was exported, to make it easy to find exported data.

The recent jobs sidebar can now be toggled to show either the user's jobs only or all instance jobs, as well as showing completed, failed, and killed jobs.

In Blob Picker and Filament Tracer, the templates are now available as outputs, along with the particles.

The Template Picker now has a parameter to disable automatic re-centering of the template image, which has been known to cause issues in some cases.

Exposure Sets Tools and Particle Sets Tools now generate their output groups before they are run, allowing these jobs to be part of pre-defined Workflows.

Volume Tools now can invert masks without applying a threshold.

Volume Tools now specifies that the units for the dilation radius and the padding width are in pixels, and the default soft mask padding is set to 12 pixels.

Volume Alignment Tools now has an option to reassign particles' UIDs, for assisting the refinement of particles with custom symmetry operators.

Homogeneous Reconstruction Only now includes the posterior precision as an output, as part of the the volume group.

DeepEMhancer job now includes an option to enable dynamic allocation of GPU memory, obviating the need to set an environment variable.

DeepEMhancer model path can now be specified as a project-level default parameter.

The Deep Picker job now runs with Tensorflow v2.8.

Many jobs now use a common progress bar in the event log.

When queueing a job via the sidebar, the last used lane will now automatically be selected, if applicable.

When importing a job, the path will now default to the project directory of the selected project.

Initial loading of the job tree view is improved.

Summary data shown on job cards is improved across CryoSPARC.

Additional quick actions are now available for swift creation of commonly run jobs.

Additional project-level filters can now be used to show archived or detached projects.

PatchCTF can now correctly handle high-magnification micrographs without throwing AssertionError: Get rid of patches that are too close to edges.

2D classification no longer displays classes upside-down relative to the image plotting convention used in the rest of CryoSPARC.

Resolved an issue where a list of all jobs are not available via the header quick switcher when viewing all jobs within a single project.

Resolved a bug where it is possible to create Session configuration profiles with the same name.

Resolved a bug where when deleting a workspace the interface does not redirect to the project level.

Resolved an issue where the number of GPUs a job is utilizing is formatted incorrectly on the job card.

When queueing a job via the sidebar, the cluster submission script variable configuration panel is now hidden if no custom variables are defined in the script.

Resolved an issue on Firefox where the exposure feed in a Live session view can not be controlled via the mouse scrollbar.

Resolved an issue on the job cards display where the border outlining parents, children and cloned jobs is too thin.

Fixed a issue where queued jobs can be accidentally deleted via the multi-action sidebar panel.

Resolved an issue where the 'Build' button in the job preview dialog does not function correctly in certain cases.

Resolved an issue in the jobs tree view where the final or final ancestor status of a job is not visible until selected.

Fixed an issue in 2D Classification where the greyscale background of class averages is incorrectly computed from the values in the corners of the average.

Fixed pymongo.errors.WriteError: Size must be between 0 and 16793600(16MB) when processing a live session with a large number (>10,000) of movies.

It is now possible to specify --cpus in cryosparcw connect without also having to specify --update.

Exposures processed by CryoSPARC Live now have their average intensity computed.

Fixed a bug where Particle Subtraction does not process all of the particles if the half sets are not of equal sizes.

Resolved a bug where 3D Variability's tile image displays components in the wrong order after job completion.

2D Classification no longer erroneously removes duplicates by default for particle datasets with filament present.

Fixed bug where Helical Refinement in building mode doesn't allow modifications to the "enable FSC noise-substitution" parameter

Fixed bug where flipping the hand of a volume (in volume tools, homogeneous reconstruction, Align 3D, and 3D Variability Display jobs) causes symmetric volumes to no longer be aligned to the conventional symmetry axes.

Fixed bug causing 2D Classification to calculate the wrong inter-particle distance when removing duplicates when downsampled particles are provided as input.

Fixed bug causing an UnboundLocalError in Patch CTF Extraction.

Disabled menu items no longer erroneously open sub menus when hovering.

Fixed issue where the spacebar shortcut for opening job dialogs stops working due to conflicting event handlers.

Fixed an issue where the scatter plot in Manually Curate Exposures does not updating the rejected status of micrographs correctly.

Deleting a job while the queue slideover is open no longer causes it to lose context and go blank.

Select 2D job now correctly reports error messages when it cannot connect to the backend.

Installer no longer writes duplicate PATH entries for cryosparc_master/bin directory into .bashrc.

CryoSPARC Live processing jobs no longer use more memory than needed when plotting.

Errors that happen when CryoSPARC Live is watching for new files are now isolated so that errors in one session do not affect other running sessions.

CryoSPARC Live can now run reconstruction processes (2D Classification, Refinement) on a lane with multiple one-GPU targets.

The reliability of cryosparcm update is now improved in the case where the master is connected to itself as a worker.

CTFFIND4 jobs no longer fail due to localization settings on some systems.

Leading and trailing spaces are now automatically removed when setting parameters.

Local Motion Correction no longer fails when no particles are extracted from one or more exposures.

3D Classification no longer fails during noise estimation if the largest class contains fewer than 100 particles. A warning is also now printed if any per-particle scale factors become NaN.

The new parameter Disable auto batchsize now allows disabling the automatic GPU processing batch size calculation in non-uniform and homogeneous refinement that can sometimes cause the jobs to run out of GPU RAM. Extraneous batch size parameters from local refinement are removed.

Fixed bug where background subtraction of density maps during ab-initio and heterogeneous refinement is incorrect.

Fixed erroneous component ordering in 3D Variability Analysis Display when using 10+ components.

Fixed confusing labelling of variability component plots produced at the end of 3D Variability Analysis jobs.

MRC format volume outputs from CryoSPARC now include mx/my/mz values in the header which fixes display issues in some visualization programs.

Resolved an issue in the job builder where numerical inputs display inaccurate tooltip information on hover.

Moving jobs between workspaces now correctly updates workspace statistics.

The workspace count statistic is now correctly incremented when a new workspace is created in a project.

Fixed an issue where the lock file within a project locked to another instance is overwritten rather than blocking the attachment of the project in another instance.

Homogeneous Reconstruct Only job now correctly allows for turning off the real-space window on particles.

Fixed an issue where in some cases, memory usage of the CryoSPARC master processes could grow without bound after restarting the instance.

Sizes of job directories on disk are no longer updated more often than necessary.

CryoSPARC Live sessions are now automatically paused when the instance is restarted.

Fixed an issue where a project could be detached while a CryoSPARC Live session was still running.

CryoSPARC Live no longer monitors worker jobs when not necessary.

Prevent “syntax error” following successful CryoSPARC update

Data Cleanup Tools

• 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.

Performance Benchmarking Utilities

• 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.

Particle caching in CryoSPARC jobs now support multiple threads (default 2), increasing copy speed on certain filesystems. To modify, specify CRYOSPARC_CACHE_NUM_THREADS in cryosparc_worker/config.sh. Read the guide for more information.

Interactive Job Improvements

• 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

Extensive Validation (previously called Extensive Workflow) job extended to support multiple datasets and also has a new "Benchmark" mode where timing results are reported and browsable using the new Performance Benchmarking system.

The cryosparcm compact command can reduce the amount of disk space used by the MongoDB database. This, along with other steps, may be useful for reducing used storage space in instances with large database sizes. See the Guide: Reduce Database Size for more details.

Interactive job improvements:

• 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

Non-uniform Refinement implementation speedups up to 15% on certain GPUs and box sizes.

Import Particles job is now 50-70% faster.

Improved speed of the caching system by reducing the number of file lookups, and improved logging of the cache system while a job is running.

CTFFIND4 is updated to v4.1.14.

Import and utility jobs that previously ran only on the master node can now optionally be launched on any worker node or cluster lane. The CRYOSPARC_DISABLE_IMPORT_ON_MASTER environment variable is no longer used.

Added star button to top navigation bar in browse system to allow starring a workspace from the jobs page.

Quick access panel will now remember selections on a user basis rather than a browser tab basis.

The load all jobs view option is now saved per-user rather than based on the browser.

Event log view options have been moved into a new view options menu to minimize interface clutter.

Sessions can now be marked as completed from the session browser view.

Archived and detached projects no longer show within the session browser.

An Additional spotlight action added to navigate to the job history page.

The 'view job' button in the sidebar can be ctrl/cmd clicked to open in a new tab

For job types that take random seed parameters, the random seed that was used is now saved in the input parameters of the job for easy reuse. The random seed will stay consistent if the job is cleared and re-run.

2D Classification, 3D Classification, and 3D Variability Analysis jobs will now produce intermediate results at each iteration, but will delete intermediate results from previous iterations as each new iteration completes. This behaviour can be turned off with a project-level or job-level parameter that will keep all intermediate results.

Jobs that fail to report heartbeat to the master node within the required timeout but continue running in the background will now be killed on their worker node, rather than being allowed to continue running after having been marked as failed due to missing heartbeat.

Worker installation job launch test (cryosparcm test workers) timeout increased to 2 minutes from 10 seconds.

The config.sh file with environment variables will now be included in the cryosparcm snaplogs bundle of logs.

CryoSPARC running version is now available in the Job PDF download.

MongoDB database journaling can be enabled by adding export CRYOSPARC_MONGO_EXTRA_FLAGS=" " to cryosparc_master/config.sh.

Topaz Extract job no longer extracts particles from denoised micrographs by default.

3DFlex Generate job no longer ignores the Number of Frames parameter.

Fixed unnecessary AssertionError in Flex Mesh Prep job when pixel size between input mask and volume match but have rounding error difference

Heterogenous Refinement job no longer fails with AttributeError when "Refinement box size (Voxels)" parameter passed None as a value.

Worker installation test (cryosparcm test workers) no longer fails when worker target does not have SSD configured.

CryoSPARC Live Session compute configuration parameters no longer fails to be changed if a worker lane that was previously selected is removed from the CryoSPARC instance.

Fixed select confirmation appearance in Edge browser on Windows.

Fixed bug where Job PDF would show incorrect parameter values in some cases.

Fixed issue where PDF event log download was crashing due to control characters being interpreted incorrectly during text cleaning.

Corrected sorting order of the job event log PDF.

Added optimistic job count update to stop the user interface loading state from glitching when deleting a workspace job when few exist.

Resolved error where Import Result Group fails to import Topaz jobs correctly, causing downstream jobs to fail.

Resolved error where Import 3D Volumes job fails with "Unable to connect to EMDB server" when trying to load volumes from EMBD.

Allow retrieving job and workspace documents from the CLI without errors.

Improved handling of missing job parent in tree view.

Live no longer stops finding new exposures until the next restart.

Correct free SSD cache storage calculation to prevent infinite cache hang when there is enough available SSD storage

Correct retrieval of legacy cluster configurations

Live no longer stops finding new exposures

SSD Cache system correctly retries up to 3 times on network timeout

A project-level parameter now controls whether or not jobs output intermediate results, with default on. Turning this off will save disk space, without having to manually clear intermediate results after the jobs complete.

In Particle Sets Tool and Exposure Sets Tool jobs, add note in event log indicating that result groups are taken from set A for the intersect dataset.

In Average Power Spectra job, print particle pixel size and power spectra sample spacing to the event log.

Manual Picker no longer fails when micrograph CTF input is not provided.

Resolved an issue where loading external data for the homepage modules would fail if a non-standard response was received.

Prevented a database error from occurring when no recent items existed for a user.

Fixed issue where copying to the clipboard would not work in some cases depending on how CryoSPARC was hosted over an internal network.

Priority field in the job queuing slide-over is now required and cannot be empty.

Resolved an issue where a previously selected entity was still selected after creating a new project.

Resolved an issue where clearing a job would not reset its queue priority.

Resolved an issue where completed jobs that were deleted displayed within project, workspace and session cards.

In 3D Classification, fixed KeyError with CTF fields when “Output results after every F-EM iteration” is enabled.

Fixed an issue where re-ordering classes and outputting intermediate results in 3D Classification conflicted and caused the job to fail. These options are now mutually exclusive.

In Global CTF Refinement, throw a warning if the spherical aberration refines to a nonpositive value.

In 3D Classification, add "Force re-do FSC split” parameter that forces re-splitting the particles into half-set splits from scratch. Disabling this allows for preserving the input splits, for particles from previous helical refinements, symmetry expansions, or local refinements.

Fixed a problem in 2D classification where many classes would be blank or very faint if multiple GPUs were used.

Fixed issues when running multiple jobs using the same SSD cache space.

Fixed 3DFSC crashing due to list index out of range error.

In 3D Classification, removed extraneous alignments3D entry in particles_all_classes dataset output which caused csparc2star.py to assign all particles to a single class.

CryoSPARC now fully supports CUDA 11.8, enabling support for NVIDIA Hopper and NVIDIA Ada Lovelace GPUs (NVIDIA H100, NVIDIA RTX 40 Series), including for 3DFlex.

The browse system has been updated with various incremental improvements including table header sorting, customizable view options, and upgraded CSV download functionality.

• 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.

Within the details sidebar of a job, you can click on a particular cloned, parent, or child job to view it in the current tab. Command/ctrl click it to open that job in a new tab.

Within the 'Metadata' tab in the job preview dialog, there is a button to download the JSON data of a job to your clipboard.

Added a quick action to perform CTF Estimation via CTTFIND4 from a Patch Motion Correction job.

Introduced a workaround for a bug in CUDA 11.8 which formerly caused jobs relying on CUDA Fourier transforms (cuFFT) to run slower than they should (sometimes dramatically so).

When importing movies and micrographs, the 'Skip header check' parameter is now enabled by default.

Performance and stability improvements to all interactive job tables and the browse table in Live sessions.

Improvements to the context menu for job cards within the current jobs dialog.

Optimized current jobs tab within manage dialog and added a running timer for each job.

Fixed bug in 3D Classification that caused csparc2star.py to produce erroneous star files if class reordering was turned on.

If a job is running on a cluster, the available memory usage statistic is no longer displayed within the event log.

If specified, the cropped box size is correctly displayed on the card of a Volume Tools job.

Resolved cases where the outputs view mode toggle was triggered while attempting to perform a browser or operating system keyboard shortcut.

Removed variables ram_gb, num_cpu, and num_gpu from appearing as custom variables in a cluster configuration.

• 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

Fixed reading of .mrc.bz2 gain reference files in CryoSPARC Live.

Fixed issue on some OSes where building pycuda would fail during installation.

Fixed error message during job heartbeat failure to correctly specify heartbeat timeout.

Fixed "wrong generation counter" error during some long-running jobs.

Performance optimizations to the volume viewer in Live Sessions and the job preview dialog.

Fixed 2D Classification to allow manual overrides to Force max over poses/shifts parameter if classes is set to 20 or fewer.

Removed the parameter "Overall normalizer (override)" in particle extraction. The parameter had no effect.

Resolved an issue where clearing intermediate results for projects triggered multiple notifications.

Resolved an issue where viewing a job without selecting the card would select and pin it to the sidebar.

Resolved an issue where the current jobs tab within the manage dialog would crash the application in some situations when interactive jobs were queued or active.

Resolved a bug where it was not possible to define a threshold for the 'Timestamp' attribute of exposures in a Live Session.

Resolved an issue that caused an 'Invalid path' error when building Topaz or DeepEMhancer jobs.

Added a new Restack Particles job for consolidating particle files. More information available in the guide.

New 3D Classification parameters

• 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

In addition to CPU memory used, available CPU memory can now be displayed in the job event log. It is also displayed in the job log PDF.

Added options to sort projects by their size.

Added a new project-level action to delete detached projects from the CryoSPARC database. More information is available in the updated data management guide.

Exposure preview context menus in CryoSPARC Live now feature a button to reject/unreject the exposure.

Additional timestamp information added to job output log.

The job preview dialog project and workspace breadcrumbs have been updated to native browser links to allow them to be opened in a new window or tab.

Buttons with a corresponding keyboard shortcut will now show that shortcut in their tooltips.

The tree view now supports using the shift key to toggle the outputs view on all job cards.

Multi-select context menu improvements

• 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

In 3D classification, ensure solvent mask is generated from consensus volume if (only) a focus mask is supplied.

Fix a memory leak in 3D Classification related to plotting. With the fix applied, peak memory usage should be significantly reduced, with jobs that have a large number (50+) of classes seeing the most benefit (up to a 75% reduction).

Fix incorrect batch size during class ESS tuning in 3D Classification that required excessive amounts of GPU memory.

Errors reading TIFF files during import movies could cause abnormal termination.

Event log would flash and jump in a perpetual loading state in some cases.

Job description would automatically close while being edited in some cases.

Clearing intermediate results on jobs with empty output result groups would cause an error.

Jobs exported from this version may now be correctly imported in older versions of CryoSPARC.

Added a guard against creating redundant outputs in Extract From Micrographs (CPU).

Improved database startup reliability following updates.

Prevent wrong generation dataset error for some jobs that process a large amount of micrographs or particles.

Prevent Extract From Micrographs (GPU) job from using too much GPU memory, causing exposures to fail with cufftAllocFailed or cufftInternalError.

Fixed a bug affecting some OSEs in the dependency installation for 3DFlex jobs (cryosparcw install-3dflex) that caused a gcc compilation error during the PyCUDA build.

Fixed a bug that caused 3DVA display to fail when using a subset of variability components.

Fixed a bug causing restarted jobs with GPU requirements to override the scheduler and jump to the front of the queue on the specified lane.

3D Flexible Refinement (3DFlex) (Beta) is a motion-based deep generative model for continuous heterogeneity. It can model non-rigid motion and flexibility of a protein molecule across its conformational landscape, and can use the motion model to combine signal from particle images in different conformations to improve refinement resolution in flexible regions.

• 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.

cryosparc-tools (Beta) is an open-source Python library that enables powerful scripting access to CryoSPARC.

• 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

Multi-select actions allow for cloning multiple jobs at once, cloning a chain of jobs between two selections, queuing, clearing or deleting multiple jobs at once, and more. Learn more about multi actions here.

Restart job action allows a job to be restarted from a killable or clearable state. This new action kills, clears, and queues the job to the same lane with the same parameters with which it was initially run.

Ability to configure custom variables for use in cluster submission scripts directly through the Cluster Configuration Tab in the Admin Panel. Custom variables can be configured at the instance level, target level and job level. See Guide: Configuring Custom Variables for Cluster Job Submission Scripts for more details.

Ability for admins to restrict users to view and run jobs on specific lanes using the Lane Restrictions Tab on the Admin Panel. See Guide: Lane Assignments and Restrictions for more details. By default, when a CryoSPARC user is created, they are assigned all existing lanes.

Multiple updates to Job: 3D Classification. Refer to the job guide and updated Tutorial: 3D Classification for details.

• 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

Job: Remove Duplicate Particles now allows for duplicate rejection based on 2D and 3D alignment error, in addition to NCC score.

Job: Symmetry Expansion now includes a parameter that enables splitting the output particle stack by the applied symmetry operator.

Job: Volume Alignment Tools now allows for application of arbitrary rotations to input volumes, particles, and masks.

Job: Select 2D Classes now exports an .mrc stack containing only selected classes, and an .mrc stack containing only rejected classes.

Job: 2D Classification now by default removes duplicate particles after classification based on a minimum separation distance between pick locations.

2D Classification jobs that perform binary class re-centering now show the binary masks used, generated from the specified threshold.

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

Job: Import Particle Stack now copies rlnAutopickFigureOfMerit into CryoSPARC's pick_stats/ncc_score upon import, if available.

Job: Global CTF Refinement now allows for initializing the spherical aberration to a custom value, prior to fitting.

Ability to prevent CryoSPARC from requesting external resources external HTTPS resources used to display information modules on the homepage by setting CRYOSPARC_DISABLE_EXTERNAL_REQUESTS environment variable to true. Details.

The CryoSPARC updater (cryosparcm update) has several enhancements, including:

• 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.

Ability for instances with the CRYOSPARC_DISABLE_IMPORT_ON_MASTER environment variable to queue jobs to the master node.

The signatures for the CLI functions delete_project and delete_workspace have changed. Please see the cryosparcm cli reference page on the CryoSPARC Guide for more information.

Project directories can now be renamed by using the edit button beside the "directory" field in the details section of the project sidebar.

Job: Reassign Particles to Micrographs will now copy the exposure group data from the micrographs to the particles if the particles.ctf slot and the exposure.ctf or exposure.mscope_params slots are connected.

Job: Import Movies info tag now displays the size of each exposure and number of frames.

When viewing jobs in a flattened view (e.g., all jobs in a project) the clone job action sub-menu now provides all workspaces as options to clone into.

Restrict some cryosparcm commands to owner UNIX account, including createuser, updateuser, resetpassword and patch.

Close open file handles during Import jobs.

User IDs are now visible in the output of cryosparcm listusers

job_type variable is now added to available cluster submission script variables provided by CryoSPARC. This value can be used for tracking which CryoSPARC job types are running on a cluster lane or for determining resource requirements for a cluster script.

qstat_cmd_tpl and qdel_cmd_tpl will have access to the same variables that are injected into send_cmd_tpl, including any user-configured custom variables.

Additional logging for master cache functions.

Interactive jobs now print out more informative errors in a scrollable, clearable log at the top of the interactive panel in the job dialog.

Resolved an issue where when viewing all parameters of a job within the comparison dialog incorrect custom parameter values were shown.

Jobs created via quick actions are no longer created in a different workspace or session than the one currently selected.

NCC score slider in CryoSPARC Live no longer loses all picks when set to 0.

Fixed ValueError in Manually Curate Exposures due to outliers during histogram creation.

Fixed bugs in Job: Gctf (Wrapper) that caused local CTF refinement to fail.

Fixed bug in Job: 3D Variability Analysis that prevented job from completing when number of components is set to 1.

The job dialog outputs tab now correctly displays the name of low-level results.

Fixed a bug that prevented correct download links for each output group of a job from being displayed within the sidebar details panel when a job is selected.

Fixed a bug that prevented multiple entities from being selected via the checkbox within the table view.

Scroll bars are no longer shown overtop of menus and dialogs in Safari.

Hostname no longer appears twice on instance management cards.

The sidebar action panel now collapses automatically after an option has been selected.

Fixed issue where a "Not Found" message would flash in the sidebar on load.

Fixed bug that resulted in incorrect cropping of some PNG figures in the event log.

Fixed bug in Job: Simulate Data that caused incorrect particles' CTF parameters when "apply CTF" was disabled.

Job: Simulate Data no longer requires the SSD cache

Residual plots in Job: Global CTF Refinement now properly account for phase ambiguities of 2π.

Fixed KeyError in Inspect Particle Picks caused by micrographs that contain no particle picks.

Fixed bug in Job: Homogeneous Reconstruction Only with helical symmetry enforced and custom box size.

Fixed bug in CryoSPARC Live that caused failed exposures to be double-counted as queued exposures.

Fixed issue where retrieving CryoSPARC Live sessions via the CLI would fail.

Fixed issue where slow database command response times would cause problems when configuring the database (e.g., updating CryoSPARC).

Extensive Workflow now runs on a worker with 32GB of RAM.

Installation and update are now cancelled if Python dependency installation fails.

Prevent job heartbeat failures following multiple disconnects and reconnects.

Fixed bug that raised a JSONDecodeError when calling cryosparcm eventlog on Job: 3D Variability Display.

Fixed bug that caused command_core, command_rtp and command_vis logs to not be properly rotated.

Event logs for motion correction and extraction jobs now count movies/micrographs starting from one instead of starting from zero (e.g. "completed 20/20" instead of "completed 19/20").

Fixed bug whereby ice thickness reported by Patch CTF (including in CryoSPARC Live) can be NaN.

Prevent file reading operations from failing on systems that incorrectly seek

Fixed bug that caused extracted particle count not to be displayed on the details panel when viewing a Live session

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.