CryoSPARC v4.7.0

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.