What's new in v2.15

May 13, 2020

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

New cryoSPARC Guide Beta

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

Release Highlights

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


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