What's new in v2.13

January 28, 2020

We're excited to announce another release of cryoSPARC packed with much requested features:

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

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


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