Please see the full v5.1 changelog, update instructions, and compatibility notes here: cryosparc.com/updates/v5.1

The updated Volume Viewer no longer requires WebGPU, and will fall back to a new WebGL mode for browser environments where WebGPU is disabled. In WebGL compatibility mode, all new features are available with the exception of video export.

The legacy Volume Viewer (v5.0 and prior) can be optionally enabled if needed, for example to be able to view local resolution colour maps.

CryoSPARC Live now correctly detects new raw movies that are written by the microscope while a session is running.

CryoSPARC Live Overview no longer displays ice thickness measures above other attribute plots.

Manually Curate Exposures now correctly applies all thresholds that are set non-interactively via parameters.

SSD caching now falls back to a slower copy method when fast copying encounters errors on certain filesystems, especially Lustre.

In Micrograph Junk Detector, the “Junk mask dilation (+)/erosion (-) (A)” parameter now correctly applies erosion to the junk mask when a negative distance is specified.

When editing a Workflow, parameters that are optionally hidden are now correctly displayed.

Please see the full v5.1 changelog, update instructions, and compatibility notes here: cryosparc.com/updates/v5.1

Updated Volume Viewer now falls back to a legacy viewer if WebGPU is not enabled by the browser. The updated view can be enabled with workarounds.

CryoSPARC starts correctly on RHEL/Rocky/AlmaLinux 8.

CryoSPARC startup no longer fails with Error: Failed to import documents into Typesense when Tags are missing in some projects.

Patch CTF with junk masking turned on no longer fails on data that has been Fourier-cropped to a ratio of 3/4.

Queuing a job directly to a GPU now behaves the same as in v5.0, i.e., it launches the job immediately rather than waiting for the GPU to be idle.

The updated Volume Viewer features faster volume loading, real-time interactive thresholding using a new histogram control, new surface and maximum rendering modes, rendering modes with diffuse lighting and shadows, and more display controls. The Volume Viewer can now show masks over the volume, and you can customize volume and mask colours. In addition, it features a measurement tool, autoplay animation controls and image/video export.

The updated Volume Viewer utilizes WebGPU, a browser feature that is available in current versions of most major browsers such as Chrome, Edge, Firefox and Safari. Some browsers disable WebGPU when accessing an application at a remote URL over an unsecured connection. If the updated Volume Viewer does not load, please update to v5.1.2 or see workarounds.

Micrograph junk regions such as carbon, gold, ice crystals and defects labelled by Micrograph Junk Detector can now be masked out in downstream jobs (Patch CTF Estimation, Micrograph Denoiser, Blob Picker, Template Picker, Extract from Micrographs and Reference Based Motion Correction) so that junk regions no longer distort CTF estimation, denoising, picking or extraction. Junk masking ensures that usable micrographs are not discarded due to distorted preprocessing. It can improve downstream result quality including resolution and orientation distributions, and it enables streamlined processing of HexAuFoil® and other types of gold grids. Steps for enabling junk masking are described in the tutorial.

Spotlight Search provides a new way to find projects, workspaces, Live Sessions and jobs from a single search interface, with instant, typo-tolerant full text search across all titles and descriptions, and contextual result previews that let users inspect matches before navigating. Spotlight adapts to context: searching from within a project or workspace prioritizes results in the current scope, including when launched from CryoSPARC Live. Search can also find relevant tags, making it easier to discover related work across jobs and projects. Command + k opens the Spotlight from anywhere.

CryoSPARC workers can now run on ARM64 CPU (aarch64) Linux systems with NVIDIA GPUs, as well as on x86-64 CPU systems. The CryoSPARC master continues to run on x86-64 only, but can be connected to worker nodes of either architecture.

3D Variability Analysis can now downsample particles on the fly, using the downsampled box size during processing for particles and volumes. This can yield up to a 2x speedup in the total job runtime.

Reference Based Motion Correction is now further optimized for faster CPU and GPU operations that yield a total speedup of up 2x in job runtime.

The Event Log has been rebuilt to virtualize the entire log, so even very long logs open and scroll quickly. With the whole log navigable at once, you can search its text, jump instantly between matches, and jump straight to the events behind warnings, errors, and charts in the job dashboard. Checkpoints no longer split the log, and tailing (automatic scrolling to new events) is now the default: scroll back to any earlier event, then jump to the end to resume. Clicking an image in the log opens it in the dashboard lightbox. The log can be docked at the bottom or right side of the dashboard. The separate Event Log tab has been removed.

Images throughout the CryoSPARC interface are converted to WebP and cached in the browser, so they load much faster on later visits. The User Settings dialog provides visibility and control over what is stored. This change results in significant speed improvements when browsing commonly accessed projects, workspaces and sessions.

Workflows, Blueprints and Job Groups can now be created, edited and applied from the command line and Python scripts using the CryoSPARC API. Read more in the guide about how Workflows can be launched and controlled programatically.

When applying a Workflow, you can now select an existing tag to apply to all jobs created by the Workflow.

The Apply Workflow dialog keeps your changes if you close it, for example to check resources or adjust a job, and shows which Workflows have unsaved parameter changes.

Rebuilding is simpler: select jobs, choose Rebuild Workflow in the quick actions menu, then pick from the workflows those jobs belong to.

Creating a Workflow no longer runs out of memory in rare cases with complex job connections.

CryoSPARC admins can now restrict which filesystem locations CryoSPARC users can browse inside the UI. The File Access Configuration tab in the Admin Panel allows admins to configure per-instance and per-user directory allow lists, as well as default locations for importing data and for saving project directories. New users inherit instance-level settings by default.

The File Browser now naturally sorts filenames, so e.g., mic_2 will appear before mic_10.

CryoSPARC now monitors free space in the database directory. It warns you when space is low and switches to Maintenance Mode before space runs out. Configurable via CRYOSPARC_DB_MIN_SPACE_GB.

A new configuration variable (CRYOSPARC_DISABLE_THP_WARNING) turns off the Transparent Huge Pages (THP) warning for admins who use THP always on purpose.

cryosparcm start now stops with a clear message when cryosparcm upgrade needs to be run first, for example after moving the cryosparc_master or using an older database.

cryosparcw connect and cryosparcm worker connect accept a new --hostname flag, so a worker's display name can differ from its network hostname. cryosparcm job queue also now accepts a --target flag to directly specify a node on which to launch the job.

Admins can now reorder scheduler lanes using the command line and API (api.resources.reorder_lanes). See API documentation for details.

SSD cache now frees space before creating new files, preventing "no space" errors while caching.

Commands for updating project, session and job symlinks are now improved and simplified (see guide).

The Admin Panel now shows when each user's password was last reset.

Job error reports now include instance logs from the time the job was queued until it finished, not just the latest logs.

The GPU instance test now runs on every GPU, not just the first GPU on the node where it is launched.

Extensive Validation now runs on the master node by default, avoiding issues where worker or cluster nodes are unable to communicate with interactive jobs running on the master node. A warning message now appears if no compute resource is selected when launching Extensive Validation.

Benchmark job and Extensive Validation download test data into the project directory by default and reuse it instead of re-downloading.

Benchmark job no longer fails when benchmark data is outside the project directory or right after an automatic data download.

Downloaded CSV files now open correctly in Excel, including non-ASCII characters.

The window (circular mask) diameter for Streaming 2D Classification can now be set in the top-level Live Session configuration.

Exposure Group IDs created in CryoSPARC Live are now unique within the whole project, so they never clash with IDs from regular jobs. Each Live exposure group shows its ID as a badge you can click to copy.

Added icon to exposure thumbnails to indicate if the exposure is part of an ignored Exposure Group.

The Session sidebar has a button to refresh a session's size.

Export Particles and Export Exposures now run on the master node instead of the Session's auxiliary lane.

Streaming 2D Classification now correctly restarts after you change the number of classes or the box size.

Sessions size is recalculated whenever a session is paused.

The Session Priority parameter is now hidden from users who can't set job priority.

Fixed a bug where cloning a Live Session and attempting to “Extract from All” would lead to failure because templates were not loaded in the Live Template Picker.

Fixed a bug where a failing Live Session could block other Live Sessions actions.

Importing Session results no longer fails when every exposure was rejected.

Import Movies now automatically finds defective pixels (i.e., outliers) in gain reference files and creates a corrected copy of the gain reference that is used for downstream processing. The outlier pixels are marked as defects and are replaced with random noise in Patch Motion Correction to remove their effect. Import Movies plots the updated gain reference showing where defects were detected.

Ice thickness estimation in Patch CTF Estimation has been updated. The new method measures image signal power in three ice bands, providing more robust per-micrograph values. Micrographs can be curated using these new measures in Manually Curate Exposures.

Patch Motion Correction now exposes a parameter to manually override the extent (in Å) of patches used during motion correction.

CTFFIND (Wrapper) now runs CTFFIND5 and works on both x86-64 and ARM64 systems. The CTFFIND4 (Wrapper) job is now obsolete.

Gctf (Wrapper) (Legacy) is not available on ARM64 workers because there is no ARM build of Gctf.

Reference Based Motion Correction now reports box sizes within the Event Log and as info tags.

Import Movies shows an accurate scale bar, including for EER data.

Reference Based Motion Correction now warns if the F-crop box size is set to larger than the extracted box, and it writes the correct pixel size to output MRC headers when F-cropping.

2D Classification now aligns class averages to each other more precisely during the final iteration, and shows the class averages in register with one another, in a separate plot.

2D Classification no longer automatically turns off Force Max over poses/shifts when there are 20 or fewer classes. This change ensures that results remain qualitatively similar regardless of the number of classes.

In Select 2D Classes and CryoSPARC Live 2D class selection, resolution-based selection now includes the threshold value, and the right-click options are relabeled clearly (for example, "Select classes with resolution better than or equal to X Å").

Reconstruct 2D Classes now outputs particles along with 2D class templates.

Topaz Extract (Wrapper) now preprocesses any micrographs that are missing from the specified preprocessed directory, instead of failing.

Homogeneous Ab-Initio Refinement (BETA) is now more robust. The two independent half-maps are averaged together below the Gold-standard split resolution, similar to standard refinement. Later iterations use stochastic pose sampling for additional regularization that improves results and reduces the possibility of overfitting. FSC and cFSC curve plots are produced during iterations.

Homogeneous Reconstruction Only now has a parameter to enable Non-uniform Regularization. Non-uniform regularized half-maps are output and can be used as input to downstream Local Refinement.

In Non-Uniform Refinement, anisotropic magnification parameters can now be correctly optimized.

Homogeneous Refinement and Non-Uniform Refinement now estimate the automatic sharpening B-factor using the resolution mask instead of the refinement mask, providing more consistent results. This change also allows automatic sharpening to function correctly when refinement masking is turned off.

In Local Refinement, the Initialize from Input Half-Maps parameter is now on by default, meaning that Local Refinement uses input half-maps (if available) to independently initialize its two half-set refinements, thereby fully preserving gold-standard independence of half-sets from the upstream global refinement.

Local Refinement now plots both per-iteration and cumulative pose/shift change histograms.

Local CTF Refinement can now output per-particle defocus landscape curves as a CSV file.

Exposure Group Utilities now has an option to automatically determine the number of beam-shift clusters if it is not manually specified.

The cFAR score is now shown in the info tags of every refinement job.

Heterogeneous Reconstruction Only no longer fails when a class is empty and outputs an empty (zero) volume for that class.

Local Refinement no longer fails when Re-estimate Greyscale parameter is turned on.

3D Variability Analysis now sorts variability components by variance and prints the amount of variance explained by each variability component (i.e., the eigenvalue) in the event log. 3D Variability Display shows an updated scatter plot and histograms to help visualize the latent embedding.

3D Classification, Heterogeneous Refinement and multi-class Ab-Initio Reconstruction jobs now show a Class Distribution History area plot across iterations. Heterogeneous Refinement and Ab-Initio Reconstruction also add class percentage bar plots.

3D Flexible Refinement (3DFlex) Train has improved defaults for centering strength and rigidity parameters, and improved parameter tooltips.

Heterogeneous Refinement now correctly resamples input volumes whose physical extent differs from the input particles.

3D Classification and 3D Variability Analysis now include per-particle scale values in their particle outputs.

3D Classification now supports up to 300 classes.

Reference Based Auto Select 3D (BETA) with "select based on resolution" no longer fails on CPU-only nodes.

Sharpening Tools now uses the auto-tight FSC mask for all sharpening, B-factor estimation, and filtering operations, for improved consistency.

Volume Tools now zero-pads non-cubic volumes to a cubic box and produces a warning, instead of failing.

Volume Alignment Tools now applies the same transform to every input volume and mask, and also now retains the full resolution of output maps even if the Maximum alignment resolution parameter is set.

Simulate Data can now read in CTF values from input particles separately from reading in pose alignments.

Orientation Diagnostics now uses the correct axis limits in the azimuth/elevation region plot.

Passthrough inputs can now be individually disconnected while building a job.

CryoSPARC now calculates the amount of SSD cache space that a job will need before launching the job, and this value is provided to cluster submission scripts as a new variable, ssd_bytes. Cluster submission scripts can use this variable to allocate space or select a node type based on this information.

Job-level custom cluster variables that were set when a job was queued are now retained when the job is cleared.

When clearing a job, a new option appears allowing for also clearing all downstream jobs that depend on outputs from the selected job. Restarting a job also displays a new warning if there are downstream jobs that depend on the job’s outputs.

Job cards for queued jobs now show which lane and node the job is waiting on, and job cards for launched jobs more clearly indicate if the job is waiting on an external cluster manager (for example, SLURM). The job Dashboard and Event Log also indicate why a job is queued (e.g., waiting for upstream jobs to finish).

The Queue Dialog has a new Force Start option that starts a job without waiting for its parents to be completed. This option allows a job to run and make use intermediate results from its parent jobs while the parents are still running.

The job Event Log now shows how many CPUs were allocated.

Default Job Priority can no longer be set below zero, and scrolling over the field no longer changes it.

Interactive jobs are no longer queued to the last used target, instead they are queued to the master node.

Lane resource summaries now show correct CPU, RAM and GPU totals for lanes with multiple targets.

The Queue Dialog no longer gets stuck in GPU mode when switching to a non-GPU job, and cancelling Run on Specific GPU no longer disables the Queue button.

Low-level inputs that were disconnected when a job was being built are no longer erroneously re-connected when the job is cloned.

Fixed an issue in Chrome where momentum scrolling in the Job Builder could unexpectedly change a number parameter.

The Save results in 16-bit floating point parameter is now enabled by default in motion correction and extraction jobs. With this parameter enabled, micrograph and particle stack files are 50% smaller on disk, without a change in downstream processing results.

If a CryoSPARC project is being attached and the attachment process fails part way (e.g., due to corrupt files or network errors), the project is left untouched on disk, marked as “Import Failed”, and project/job actions are disallowed. This ensures the project can be safely detached again. Projects in “Import Failed” status also provide an option to “Force Import”, allowing the intact parts of the project to be marked as usable for continued processing.

Clear Non-Final Jobs is disabled when no jobs in the project or workspace are marked final, to avoid users clearing everything by mistake.

CryoSPARC now checks for running jobs, Live Sessions and tasks before data management operations. For example, you can no longer detach a project while one of its Live sessions is running.

Admin users can now choose a specific project owner when attaching a project.

If automatic project backup (autodump) fails, for example because the project directory has been unmounted or is inaccessible, CryoSPARC retries every hour and shows a warning notification.

Imported jobs now appear right away in workspace and project previews.

Moving a project to a different file system now runs in the background, and project actions are locked until the move finishes.

Jobs that previously failed to delete due to missing information about their child jobs can now be correctly deleted.

Jobs are no longer left stuck in a deleting state when a job deletion fails partway through.

Restarting a CryoSPARC instance with a very large number of open notifications no longer causes an error at startup.

Cleanup Data tool no longer incorrectly deletes final preprocessing jobs when both "Include final ancestor jobs" and "Clear non-final jobs” are selected.

Fixed a potential race condition in CryoSPARC Live session compaction that could cause deletion of files outside the session directory.

Current Jobs Dialog: You can now filter to show only your jobs.

Comparison View can sort jobs by a parameter, so you can see how results change as that parameter changes.

Selecting several projects, workspaces or sessions now shows a details panel with key stats and totals, such as the combined size of the selection.

Improvements to filtering: Projects can now be filtered by sharing status. Selecting jobs by tag or workflow now respects active filters, works when filtering by workflow, and is much faster in card view.

It is now possible to Select Ancestor Jobs and Select Descendant Jobs when multiple jobs are selected.

A new View Option allows turning off the pulse animation on running and interactive job cards.

You can now Copy and Paste Parameters from the job right-click menu.

New keyboard shortcuts: Shift+O returns all job cards to the normal (non-outputs) view. Shift-click a job UID in the sidebar to copy a link to the job. Shift-click the job type to copy its raw name.

Tree view: Deleted root jobs now disappear from the tree view right away. Linking or unlinking jobs now updates upstream job cards immediately, and the layout no longer recalculates when unrelated job details change. In addition, the tree view layout now handles circular connections without breaking.

If you are updating to v5.0.8 from a CryoSPARC v4 version, please see the full v5.0 changelog, update instructions, and compatibility notes here: cryosparc.com/updates/v5.0

Fixed a potential race condition edge case in CryoSPARC Live session compaction that could cause unintended deletion of additional files outside the session directory. Users of versions v5.0.0-v5.0.7 should not use the session compaction tool and should upgrade to v5.0.8.

Cleanup Data tool no longer clears final preprocessing jobs when both "Include final ancestor jobs" and "Clear non-final jobs" are selected.

Attaching a project containing jobs with unrecognized result data types no longer fails.

Very large Workflow JSON files no longer fail to import.

Updated dependency package version of brotli compression library to address CVE-2026-111497.

If you are updating to v5.0.7 from a CryoSPARC v4 version, please see the full v5.0 changelog, update instructions, and compatibility notes here: cryosparc.com/updates/v5.0

CryoSPARC Live session auto-pause now correctly triggers in cases when the session contains failed exposures, or has been previously paused and resumed manually.

Fixed an issue preventing CryoSPARC from running jobs correctly in the presence of GPUs with MIG mode enabled. Note: an individual job cannot make use of both MIG and non-MIG devices at the same time.

Orientation Diagnostics now outputs all computed metrics to the job summary stats for easier programmatic access via cryosparc-tools.

Projects that failed to save results to disk due to a temporary network or filesystem issue now automatically retry after a configurable interval (default: 1 hour) and display a warning to the user.

Fixed an issue where user python libraries loaded in the environment where CryoSPARC runs could interfere with some CryoSPARC processes.

Fixed an issue where new backups created using cryosparcm backup were completing successfully but not being displayed in the Backups tab of the manage dialog in the UI.

Resolved an issue where the job queue slide-over would freeze when switching from a GPU to non-GPU job while the GPU selection mode was active.

Resolved an issue where the job queue slide-over for interactive jobs would queue to a non-master node.

If you are updating to v5.0.6 from a CryoSPARC v4 version, please see the full v5.0 changelog, update instructions, and compatibility notes here: cryosparc.com/updates/v5.0

Resolved an issue where switching from the event log tab to the dashboard could cause incorrect chart images to show at earlier iterations for dashboard charts.

If you are updating to v5.0.5 from a CryoSPARC v4 version, please see the full v5.0 changelog, update instructions, and compatibility notes here: cryosparc.com/updates/v5.0

Local Refinement jobs no longer fail with a plotting error when intermediate iteration plots are being produced in certain cases.

CryoSPARC Live auto-pause now correctly pauses Live sessions in both standard and graceful modes, including for sessions where streaming 2D and 3D jobs are running.

Import Volumes job no longer fails when importing integer-type MRC volumes.

Resolved an issue where ‘undefined’ columns would display when downloading workspace and project CSVs.

CryoSPARC Live session configuration profiles are now included in automatic instance configuration exports, so that profiles are retained when restoring a CryoSPARC instance using cryosparcm recover

Set environment variable CRYOSPARC_CLI_SKIP_ACCESS_CHECK=true in both CryoSPARC master and worker config.sh files, in order to disable filesystem permission checks for cryosparcm and cryosparcw command-line arguments. This setting may be used with network file systems where listed UNIX access permissions do not match the true available permissions.

Improved detection and fallback for silent SSD cache file copy failures on some network file systems, including Lustre.

CryoSPARC command line and cryosparc-tools no longer produce errors when loading workspace or session objects.

When multiple particle set inputs are connected to a job, alignments3D_multi results will be removed rather than being passed through, in order to prevent failure in descendant jobs due to a mismatch in the number of classes present in the results.

Resolved an issue where connections between Workflow jobs would fail in some cases, due to the connection being made using the input slot name instead of the output result name.

Resolved an issue where the option to group jobs was presented when viewing all jobs within a project.

Resolved an issue where current resource usage would not load when interacting with the job context menu in the tree view.

Resolved an issue where the “Apply” action on the Live configuration tab would remain disabled after applying a configuration profile with missing required parameters.

Micrograph Denoiser jobs info tags no longer display number of training micrographs used if a pre-trained model is provided as input.

Legacy jobs now appear with formatted titles on the job cards and details view.

If you are updating to v5.0.4 from a CryoSPARC v4 version, please see the full v5.0 changelog, update instructions, and compatibility notes here: cryosparc.com/updates/v5.0

Resolved an issue in 3D variability analysis that could, for some datasets, cause streaking artefacts in 3D variability component volumes and skewed latent distributions.

Fixed an issue where, for some datasets, 2D Classification using the similarity plotting sorting would produce degraded result quality, due to large translations of class averages during the 3rd last iteration.

When deleting a detached project, a clearer description of the operation being performed is provided in the UI.

Fixed an issue where importing a job directory that had been symlinked (rather than copied) into the project directory would fail.

Fixed an issue where project directories that had been synced and restored from S3-like filesystems would fail to attach due to missing (empty) gridfs_data directories.

Fixed an issue where Ab-initio Reconstruction jobs within CryoSPARC Live would ignore the SSD usage parameter.

Fixed an issue where cloning a CryoSPARC Live session would result in the exposure groups being pre-emptively enabled.

Fixed an issue in CryoSPARC Live where it was not possible to select a source job for 2D templates from outside of the current project.

Improved handling of exported Live session exposures when no gain reference is provided.

If attaching a project fails, the project lock file (cs.lock, created during the attempt to attach) will no longer be deleted. If the project directory needs to be attached to a different instance later, the lock file can be manually deleted from the project directory.

Fixed an issue where installing worker updates could fail due to incorrectly changing the current working directory.

Shell control characters are no longer incorrectly escaped when submitting cluster commands.

Data cleanup tool no longer shows an error message when clearing intermediate results.

Fixed an issue where 2D Classification would fail when configured with 1 class and otherwise default parameters.

3D Flex Mesh Prep job no longer fails if only two segments are provided in the segmentation file and connection tree.

Fixed an issue in Topaz Cross Validation where the parameter being optimized incorrectly required an input value, and updated the job to instruct users to clear this field before running the job.

Topaz Cross Validation job no longer fails to launch when decimal values are provided for some parameters.

If you are updating to v5.0.3 from a CryoSPARC v4 version, please see the full v5.0 changelog, update instructions, and compatibility notes here: cryosparc.com/updates/v5.0

Jobs with integer parameter values larger than 8 bytes now pass validation. For users who updated to v5.0.0-v5.0.2: projects detached during upgrade due to OverflowError: MongoDB can only handle up to 8-byte ints can now be attached in v5.0.3.

Projects with empty project titles now pass validation. For users who updated to v5.0.0-v5.0.2: projects detached during upgrade due to String should have at least 1 character [type=string_too_short, input_value='', input_type=str] can now be attached in v5.0.3.

Fixed an issue where users could not edit the titles of jobs/workspaces/projects in projects that had been shared with them.

Correctly forward environment variables such as LD_LIBRARY_PATH to cluster submission commands, preventing failure.

Fixed an issue where SSD reserve would default to 0, instead of 10GB, for connected targets and clusters.

Fixed an issue where a launched job is marked as failed when using some terminal shells, if there is extra output in the shell configuration.

Fixed an issue where jobs that were cleared quickly after queuing were still launched.

For jobs created programatically or by CryoSPARC Live, the created_by_user_id field is now correctly set.

Homogeneous Ab-initio Refinement no longer fails with KeyError when run with helical data.

Fixed an issue where imported micrographs would display as too light or too dark in interactive jobs.

Extra "Random Seed Default" parameter no longer appears on newly-created Blueprints.

Fixed an issue where, under some conditions, a job fails with "unknown dataset field error" if two slots with the same type are connected.

Fixed an issue where .cs and .csg filenames for exported jobs or outputs would incorrectly differ.

Fixed an issue where a job would attempt to connect to the wrong master hostname if the master environment is active when the job launches.

cryosparcm service management commands no longer fail when running from a working directory that the current user does not have permission to access.

Extensive Validation no longer fails with an error indicating a checksum mismatch, when test data is downloaded automatically by CryoSPARC.

Exposure Sets Tool no longer fails on intersect action when only micrographs (not movies) are connected.

Fixed an issue where session restoration would crash due to missing a related notification.

Fixed an issue in 2D Classification causing it to crash when the output of intermediate plots was disabled.

Fixed an issue where Split Volumes Group did not correctly passthrough upstream particle metadata.

If you are updating to v5.0.2 from a CryoSPARC v4 version, please see the full v5.0 changelog, update instructions, and compatibility notes here: cryosparc.com/updates/v5.0

Fixed an issue where, in some environments, cluster job submission scripts would fail with ERROR: ld.so: object 'xxx/lib/libpython3.12.so' from LD_PRELOAD cannot be preloaded due to environment variables that were not correctly cleared.

Jobs no longer fail to launch on worker nodes that are running the tcsh shell.

Using the Export Exposures functionality in a Live session no longer fails when a gain reference was not specified in the Live exposure group configuration.

Live sessions no longer fail when no particles are picked on a micrograph and advanced parameter Enable Plotting in RTP Worker is enabled.

When configuring template picking in a Live session, 2D classes can now be loaded from any job type that outputs 2D classes.

Patch Motion Correction (and Live Worker) are now significantly faster when processing low-magnification movies.

3D Classification now correctly orders particle outputs when Reorder classes by size is turned on.

In Extensive Validation, Local Refinement now correctly uses the SSD cache based on the user specified parameter.

When editing thresholds in Manually Curate Exposures, micrographs with values equal to the default threshold are no longer excluded.

Resolved an issue where hovering/clicking on an exposure within the scatter plot in Inspect Picks and Manual Picker would not navigate to it.

Updating CryoSPARC no longer issues warnings about the use of an ephemeral port range if the port range was already set previously.

If you are updating to v5.0.1 from a CryoSPARC v4 version, please see the full v5.0 changelog, update instructions, and compatibility notes here: cryosparc.com/updates/v5.0

The http_proxy and https_proxy environment variables are no longer incorrectly ignored when contacting the CryoSPARC license server via a proxy.

3D Classification Jobs that had required parameters set to None now pass validation. For users who updated to v5.0.0: projects detached during upgrade due to TypeError: '<=' not supported between instances of 'float' and 'NoneType' can now be attached in v5.0.1.

Jobs that produce more than 500 outputs now pass validation during upgrade. For users who updated to v5.0.0: projects detached during upgrade due to Value should have at most 500 items after validation can now be attached in v5.0.1.

Jobs that included path parameters set to None now pass validation during upgrade. For users who updated to v5.0.0: projects detached during upgrade due to TypeError: argument should be a str or an os.PathLike object where fspath returns a str, not ‘NoneType can now be attached in v5.0.1.

The Job Dashboard displays all key job outputs, plots, and statistics at a glance, and is the new default view when opening a job card. Use iteration sliders to see how results and plots changed during processing.

Multi-select jobs and press spacebar: The Comparison View shows all selected jobs’ parameters, outputs, and plots side-by-side, making it easy to spot differences and make decisions about the effect of input or parameter changes. Use iteration sliders to visualize progress, and download outputs from multiple jobs in one click.

CryoSPARC v5.0 introduces a new automatic mask generation method that is robust across a wide range of resolutions and reduces the possibility of overfitting or overestimation of resolution, without users having to adjust masking parameters.

• Dynamically generated masks now use mask tightness and softness parameters that are based on the 3D refinement map's current resolution estimate, meaning that masks for lower-resolution structures automatically have softer padding.
• The new method is used for refinement masks (mask_refine) and resolution masks (mask_fsc), and makes it significantly less likely that user-set masking parameters produce masks that are too tight or too hard, especially for low or moderate resolution structures. Mask auto-tightening has also been made more conservative by default.
• Across all refinement jobs, both the refinement and the resolution masks are plotted each iteration, in a new plot that displays the extent of the mask edge falloff.

Refinement jobs now have a parameter “Use dynamic refinement mask” that can be turned off to allow the job to run without any refinement mask applied during iterations. In some cases, especially in Non-Uniform Refinement, using no mask can produce improved results.

All refinement jobs now output the refinement mask, resolution mask, and auto-tightened resolution mask as separate draggable outputs.

FSC curve plots are now standardized across CryoSPARC, with a consistent colour scheme that more clearly indicates which mask has been used to produce each curve, and whether correction via phase randomization has been applied.

If FSC resolution meets or exceeds the Nyquist frequency, refinement jobs now throw a warning to recommend re-extracting particles with a smaller pixel size.

The format of FSC txt files has been updated to include additional columns and column titles.

By default, refinements (Homogeneous, Non-uniform, and Helical) now perform per-particle scale optimization. The optimized values provide a measure of particle quality, which is used during 3D reconstruction to down-weight low quality particles. The per-particle scale values can also be useful for separating low-quality particles from a dataset.

All refinements, Local CTF Refinement, 3D Classification, and 3D Variability Analysis now create a Rejected Particles output group. The group is populated with particles that had zero or negative per-particle scale, indicating empty or inverted contrast that is ignored during 3D reconstruction.

The new Run Configuration options in CryoSPARC Live enable auto-start and auto-pause of Live Sessions to better match data collection workflows. Multiple sessions can be started at the same time, each pointing to a different raw data input directory (e.g., corresponding to multiple grids). Sessions can be started with Delay worker startup until ready so that Live Preprocessing worker jobs will not launch until new data is detected. Auto pause mode triggers when no new data has been detected for a configurable timeout and automatically pauses Sessions to free up GPU and license resources for the next session.

Auto Pause Mode automatically pauses the Live Session when there are no remaining exposures to process, with two available modes:

• Standard: Pause the session immediately after the idle timeout has expired. This will kill any running 2D/3D streaming jobs at the time auto pause is triggered.
• Graceful: Once the idle timeout has lapsed, also wait for 2D/3D streaming jobs to finish processing the available particles before pausing the session.
• An Auto Pause Timeout can also optionally be configured.

Ability to launch more than one Live Preprocessing worker job per GPU. Use Workers per GPU in the Configuration Tab to specify the number of Live Preprocessing worker jobs to launch per GPU worker. On some systems, running multiple workers jobs per GPU can improve preprocessing throughput.

Live Sessions can now be cloned in the UI. Cloning a session preserves configuration.

CryoSPARC Live Sessions will now inherit the project-level parameter for outputting in 16-bit floating point format.

Exposure filenames in Live now correctly pad UIDs with leading zeros.

The Live particle export job's output is now correctly named "Exported Particles".

Lane selections in CryoSPARC Live now display only those of which are available for the current user.

CryoSPARC Live's configuration profiles in v5 are not backwards compatible. New profiles can be created in v5 but will not be retained if downgrading to v4.

Upstream jobs in the tree view will now be collapsed into single grouped cards by default, making it easy to see where jobs from other workspaces are connected to jobs in the current workspace tree. Extremely large processing trees can be condensed to display only the jobs relevant in the current workspace.

Job Group cards now list their contents; hover over any job to view its specific details.

Groups in the tree or card view will no longer accept the addition of jobs that would cause a circular connection error when the group is collapsed.

Moving or unlinking jobs in the middle of a chain in the tree view will no longer cause data loading and/or layout issues in some cases.

Documentation icons have been added across the application that link out to relevant pages in the CryoSPARC Guide. These include documentation for core actions as well as CryoSPARC jobs, plots, and general onboarding.

Homogeneous Ab-Initio Refinement (BETA) uses the same algorithm as Ab-Initio Reconstruction (i.e., stochastic gradient descent) to refine a dataset to high resolution from scratch, while preserving gold standard independence of two half-sets and half-maps. Half-maps are aligned in 3D during optimization to keep them in register. The job type is inspired by recent results showing that Ab-Initio Reconstruction can produce improved map quality for small and challenging targets when run at high resolution (HR-HAIR: Kim et al. 2025).

Local Refinement now has an option to use input half-maps for initialization, allowing local refinement to retain the gold-standard separation of half-maps from an upstream Ab-Initio Refinement or other source.

Ab-Initio Reconstruction now supports spherical or cylindrical windowing of volumes during reconstruction, via the Volume window mode parameter. Window size can be controlled with Window inner diameter and Window outer diameter parameters. Spherical windows can help with reconstruction of smaller particles, and cylindrical windows with helical particles.

Ab-Initio Reconstruction now has a parameter Minimum alignment resolution that performs high-pass filtering on the volume (for the purpose of alignment only).

Fixed a bug in Ab-Initio Reconstruction that could cause NaN errors when class volumes were near empty.

2D Classification now aligns 2D classes to each other and plots classes in a sorted order determined by inter-class similarity, for easier visual comparison. This can be reverted to sorting by size, by modifying the "Plotting sort method" parameter.

Added a "Do orientation alignment" parameter to 2D Classification, turned on by default. If 3D alignments are available in input particles, this parameter can be turned off to allow for 2D Classification without alignment.

Added class index to sort options in Select 2D Classes.

3D Classification now includes the option (default: off) to use latent mixing coefficients during classification. When turned on, 3D Classification treats the current class sizes at a given iteration as a representative example of the underlying, true class sizes; formally, it applies a prior over class posteriors based on the current sizes of classes. This can result in more diverse class sizes, reducing the likelihood of 'uniform' class distributions.

In 3D Classification, the solvent mask is now automatically expanded to ensure it always fully contains the focus mask. Furthermore, if a solvent mask is not provided as input, there is a new option to Generate solvent mask from consensus (and a spherical mask is used if this option is turned off).

3D Classification now has a new real-space slice plot with improved contrast and a modified colourbar.

Local CTF Refinement now optimizes over per-particle scale and defocus in tandem. In testing, this can lead to better error landscapes and potentially improved defocus values.

Upgraded tagging experience: quickly create and manage tags.

• The "Edit Tags" menu for jobs now by default only shows tags created by the current user, with a toggle to view all tags in the instance.
• Added ability to tag multiple jobs at once using the multi-actions menu.
• Added new option to create a tag in the "Edit Tags" menu. Default tag will be created with the search term if applicable, or the "Create Tag" slideover will be opened to complete creation.
• Updated tag filter in jobs browse view to only show tags that have been applied to jobs in the view.
• Redesigned tag manage dialog panel for more information density and added ability to delete multiple tags at once.

Titles and descriptions in the details sidebar autosave when edited.

Upload Local Files now offers the option to automatically create and queue an Import 3D Volumes job for each volume when uploading .mrc or .map files if Auto-Import is checked off. The Volume Type dropdown (map_sharp, map_locres, etc.) will be automatically populated based on the file name.

Upload Local Files provides a message when attempting to upload an unsupported file type and lists the applicable file types that are allowed.

Copy/Paste Parameters: Use command+option+c to copy parameters from a selected job, and command+option+v to paste onto a selected job.

• Parameters can be pasted onto jobs of different types, useful between jobs with many of the same parameters such as 3D refinements.
• Parameters are copied to the clipboard as a valid CryoSPARC Blueprint, in JSON format for editing or sharing. These can also be copied from the job builder using the "Copy as Blueprint" button or command+option+c.
• Parameters can also be copied in plain text for pasting into lab notebooks, using the "Copy all parameters as text" option in the job builder.

Ability to search for parameters in the job builder.

When dragging an output group into a building job, there is now an option to replace the existing group connection if only one connection is allowed.

Added additional checks when building jobs to prevent incorrect number of input groups from being connected.

Prevent workflows from being applied if they are missing parent connections, preventing jobs from being connected with missing passthrough outputs.

Ability to queue GPU and CPU jobs to a hostname/target directly in the Queue slide-over, plus improvements to right-click queue menu:

• The Queue slide-over now shows a warning when the CPUs, GPUs or RAM of the selected lane/target are fully allocated.

• When right-clicking on a job, the quick access menu displays a coloured light icon and tooltip for each lane's current resource allocation, the compute requirements of the job, and a warning if one of the lane's compute resources is fully allocated. Lanes with insufficient resources for the job will appear under "Underprovisioned lanes".

The Instance Information tab, that displays all available worker and cluster lanes, has been redesigned.

• Search filters have been added, allowing the user to filter lanes by name, lane type, and compute resources.
• Each target card now contains a list of GPUs displaying their ID, name, and VRAM.
• A new table view has been added that displays instance information in a collapsible nested tabular format.
• Contents of target paths and cluster submission scripts can now be copied to the clipboard with a single click.
• JSON export of all targets can now be downloaded.

The Current Jobs dialog and Queue slide-over now display how many compute resources (CPUs, GPUs, RAM) are currently allocated in a lane, target, or job.

Job priority is now displayed on job cards.

Improved error messages when queuing to under-provisioned lanes or targets.

When launching a job directly on GPUs, the list of available GPUs now respect instance configuration, hiding GPUs that are marked as unavailable to CryoSPARC.

Added an 'info tags' option to the job CSV download, enabling access to the same statistics presented on job cards.

Option to download a CSV of just the selected jobs via the browse pages.

Improved job info tags and dashboard cards for Extract from Micrographs (including display of F-cropped box size and output pixel sizes), Subset Particles by Statistic and Helical Refinement.

Resolved an issue where the job report would fail to download for certain jobs that contained special characters in their event log output, title or description.

The shortcuts dialog has been reworked to show all available keyboard shortcuts inside of hierarchical sections in a single panel. To open the shortcuts dialog, click on the "keyboard" icon in the left navigation bar.

The keyboard shortcut for marking/unmarking a job as final has been modified from 'F' to 'Option + Shift + F'.

Selection menus for projects, workspaces, and sessions have been updated to show all items with no upper limit and no UI performance impact.

Added a toggle (default: off) to the Cleanup Data tool that controls whether final-ancestor preprocessing jobs (i.e., preprocessing jobs that are ancestors of jobs marked "final") should be cleared. Preprocessing jobs' outputs (micrographs, particle stacks) take a lot of disk space, but can be reproduced by re-running the jobs again as long as the raw data is available. Therefore, turning on this option can be useful to clear additional space without losing the ability to recreate final results. Read the Data Cleanup guide before proceeding.

A new command line endpoint delete_output_result_files allows deleting files produced by a job that are part of just a specific result, for example micrographs_non_dw for non-dose-weighted micrographs in Patch Motion Correction.

Added cryosparcm recover: a simplified way for CryoSPARC instances to fully recover from database loss or corruption without the need for database backups. See the Instance Recovery guide for more details.

When attaching a project, the project card and details sidebar now display the status of the attach process (i.e., in progress, successful, or failed). Projects that fail to attach will display an error banner.

When importing a job, the job card now displays the import status.

Clear and restart actions are now disabled for imported jobs.

Job search menu can now support viewing and searching any number of jobs in a view without a limit. Menu can be opened with new shortcut shift + j.

Upgraded multi-selection experience for jobs: identify, navigate to and view a summary of results within the sidebar. Sidebar cards include key information including info tags, runtime, custom parameters and resource usage, as well as actions to open the job dialog, target (go to) the relevant card in the browse view, and open the quick actions menu.

Clicking on a job header within the current jobs tab will open the job preview, similar to the browse views.

The current browse view (card, table, etc.) can now be toggled using the keyboard shortcut shift + { or }.

Resolved an issue when attempting to remove the 'Final or Ancestor of Final' filter within the browse system.

Resolved an issue were jobs of a certain status were not able to be unlinked.

Navigating the job card view using the arrow keys will no longer get stuck on groups.

Resolved an issue where the multi-select quick actions menu would not display when selecting dozens of jobs.

Reassign Particles to Micrographs now creates a separate output group for particles that did not match any of the input micrographs, rather than failing.

Import Particle Stack for helical particles now uses randomized filament_uid for each filament (rather than copying directly from rlnHelicalTubeID) to ensure the correct distribution of values.

Import 3D Volumes will no longer fail when importing EMDB volumes with IDs starting with zero.

Tooltip for the gain reference field in Import Movies accurately reflects the fact that TIFF gain references are supported.

Added a parameter to Patch Motion Correction and Reference Based Motion Correction jobs called "hot pixel threshold". This controls how many standard deviations away from the mean a pixel can be before it is considered a stuck or aberrant pixel, and ignored during motion correction.

Added a parameter to the Micrograph Junk Detector that sets a minimum area for junk labels below which particles won't be rejected.

Fixed a bug in the Micrograph Junk Detector which caused masks to be slightly offset for certain micrograph sizes.

Manually Curate Exposures will no longer fail if zero particles are connected.

In Manually Curate Exposures, the button to toggle display of annotation controls is now only shown when annotations are loaded.

Resolved an issue in Manually Curate Exposures, where the exposure grid view would not update after changing filters.

Deep Picker Train and Deep Picker Inference have been deprecated and are no longer present in CryoSPARC v5. Previously-run jobs are still visible in the interface.

Blob Picker now includes a warning if the Lowpass filter to apply to templates/micrographs parameter values are too high and incompatible with the specified "Minimum particle diameter" value.

Blob Picker now has two elliptical blob generation modes (stretch and squeeze) to account for different particle shapes, corresponding to thinner rods and flatter disks. It also has a parameter Blob size spacing (A) that controls the number of intermediate sized blobs that will be generated between min and max diameters, and prints the diameters of the circular, elliptical, and ring templates alongside the plots of the templates.

When turning on the "Pick on denoised micrographs" parameter in Template Picker or Filament Tracer, the "Use CTFs to filter the templates" parameter will be set to the correct value automatically.

Topaz Extract, Topaz Train and Cross Validation now have a progress bar during preprocessing. Topaz Train now logs the training status per epoch.

Topaz v0.3.0 is now supported.

Micrographs denoised using the Micrograph Denoiser are now compatible with Topaz v0.3.0.

Topaz jobs using Topaz v0.3.0+ now use a file with a list of micrograph filenames, to avoid "Argument list too long" errors.

Filament Tracer now prints the diameters (if template is not provided) of the filament. Filament tracer and template tracer no longer cause errors due to changes in blob picker parameter.

Several updates to Subset Particles by Statistic:

• The job now allows for subsetting by either Per-particle scale (used), which is the value used by the upstream job during back projection of particles, or Per-particle scale (optimal), which is the value computed but not necessarily used by the upstream job. The job defaults to per-particle scale (optimal) as the statistic.
• The job now allows for subsetting by the total amount of shift in either 2D or 3D alignments, and also by the azimuth or elevation from 3D alignments.
• The job has a new option to ensure that an equal number of particles are selected from each half-set split defined in the incoming particle stack. The job also allows splitting particle sets into the two gold-standard half-sets based on alignments3D/split.

Inspect Particle Picks no longer fails when there are too few particles, instead it will skip CTF bins that have zero particles and throw a warning instead.

Fixed issue in Downsample Particles where alignments3D and alignments2D were not being updated, causing the job to produce incorrect results when Recenter using aligned shifts was enabled.

BILD files are now output for viewing direction distributions in all refinements.

Refinement jobs now include cFAR scores in summary statistics, so that these values are available to scripts using cryosparc-tools.

Fixed issue in Helical Refinement where the Maximum out-of-plane tilt angle parameter value would reset to the default upon launching the job, regardless of its specified value.

In Orientation Diagnostics, a new expanded cFSC plot shows all cFSC curves, and raw cFSC data is now output to a csv file in the job directory to facilitate plot reproduction. In addition to cFAR, the job now reports 'tFAR', a variant of cFAR which uses toroidal Fourier segments rather than conical segments. In our testing, tFAR can better represent signal anisotropy under unimodal or bimodal viewing direction distributions. Both tFAR and cFAR scores are more prominently displayed in plots.

Updates to Sharpening Tools:

• The job now allows sharpening without applying an FSC filter. Instead, a Butterworth lowpass filter of custom resolution and order can be specified.
• The job now reads the FSC mask from the fsc_mask_auto slot in the input volume group. If desired, Sharpening Tools is also able to run without a mask.

Validation (FSC) no longer fails when using the CPU compute facility.

In Volume Tools, the default filter is changed to 8th order Butterworth.

Volume Alignment Tools now has a parameter to control whether the mask is multiplied onto the input volume.

Volume Alignment Tools now allows for only applying a mask as a valid action.

Volume Alignment Tools now correctly outputs masks with appropriate pixel size.

Align 3D Maps no longer applies a lowpass filter to outputted maps. A new parameter, Alignment resolution (A), is instead used to control the maximum frequency of information used for volume-to-volume alignment.

Improvements to the alignment algorithm used in Align 3D Maps. The objective function now accounts for overall greyscale differences between maps, which can improve resulting alignments in cases where input volumes came from different processing workflows.

Remove Duplicate Particles now logs the micrograph's pixel size that is used to compute inter-particle distances.

Exposure Group Utilities and other jobs that assign exposure group ids now correctly increment a project-level exposure group counter so that new exposure groups receive a unique id.

CryoSPARC v5's performance benchmarking system is not backwards compatible. New performance benchmarks can be recorded in v5 but will not be retained if downgrading to v4.

CryoSPARC v5 includes updated performance benchmark references on bare metal and AWS nodes.

cryosparcm worker connect and cryosparcm worker disconnect commands can be used to manage connected nodes from the master node. View the updated v5 cryosparcm reference here.

CryoSPARC will now check for conflicts with network ports at installation time.

CryoSPARC will now check for conflicts with active network ports at startup time.

Improved detection for when a scheduler target is the master node.

The default range of logs returned in cryosparcm log and cryosparcm errorreport has been increased from 7 days to 30 days.

Modified cluster launch scripts to append to the job log file instead of overwriting.

Prevent "Could not parse signed file" error during instance startup after changing license IDs.

Fix permissions error when creating job directories on NFS drives.

Worker updates are now copied directly instead of over SSH when updating standalone instances.

Notifications for actions and changes within a project are shown to admin users when viewing that project, regardless of who created it and the sharing permissions.

Native browser autocomplete dialogs are disabled when interacting with an autocomplete filter within the interface.

Sort order will now be respected for new jobs created in a workspace sorted by Job ID.

Resolved an issue where flags were not retained when rebuilding a workflow.

Sidebar action panel doesn't scroll on small height windows

Filter hidden parameters out of job card footer widget.

Fixed a bug which could allow a specific kind of movie, micrograph or particle file corruption (truncated frames) to go unreported.

Downstream programs that read MRC files from CryoSPARC and expect them to be in CCP4 format will no longer encounter errors due to checksums embedded in CryoSPARC MRC output files.

3D Variability Display interactive cluster plot legend now matches cluster numbers from job output.

Resolved an issue where the exposure count for Reference Based Motion Correction would always display as 0.