[3dem] CryoSPARC v4.5 now available

[Ali Punjani]

Dear 3DEM,

We are pleased to announce that CryoSPARC v4.5 has been released today with
a number of updates. The full list is detailed in the changelog:
https://urldefense.com/v3/__https://cryosparc.com/updates__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQFlYi5_f$ 

A few highlights:

   - A new Micrograph Denoiser
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/exposure-curation/job-micrograph-denoiser-beta__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQNaRluZU$ >
that
   significantly enhances contrast in micrograph images, works across a range
   of defocus and contrast levels, and can be trained in just a few minutes on
   new data.
   - Reference Based Auto Select 2D
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/job-reference-based-auto-select-2d-beta__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQK22jU6O$ >
    and Auto Select 3D
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/variability/job-reference-based-auto-select-3d-beta__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQPwWnO9x$ >
jobs,
   making it possible to achieve one-click automation of repeat structure
   determination in combination with Workflows
   <https://urldefense.com/v3/__https://guide.cryosparc.com/application-guide-v4.0*/workflows__;Kw!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQAzJklWa$ >. 2D or
   3D classes are compared to a reference structure and auto-selected based on
   thresholds or clustering.
   - The ability to upload files directly
   <https://urldefense.com/v3/__https://guide.cryosparc.com/application-guide-v4.0*/upload-local-files__;Kw!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQPw9eHKZ$ >
from
   your local computer into the CryoSPARC UI to streamline workflows that
   involve local visualization or generation of 3D maps or masks. Files are
   saved inside your project directories and can be imported and used in jobs.
   - The Orientation Diagnostics job produces a new “Relative Signal”
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-orientation-diagnostics*relative-signal__;Iw!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQGLvLqEn$ >
measure
   that can help directly identify underrepresented views that affect map
   quality and the cFAR diagnostic. New plots show the problematic regions of
   the viewing sphere and example projections.
   - A new Rebalance Orientations
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/job-rebalance-orientations__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQHXUh9jd$ >
job
   that removes particles from overpopulated viewing direction regions, which
   can improve downstream refinements when particles have a highly non-uniform
   orientation distribution.
   - Align 3D Maps
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-align-3d-maps__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQIGiMBGs$ >
uses
   a new precise volume alignment method and can update particle alignments
   and check hand flips, making it easy to align 3D classes and subvolumes.
   Plus, jobs that produce many 3D volumes now output them in groups for
   easy downstream connection
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-split-volumes-group__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQNzUgTUX$ >
   .
   - Support for Falcon C (2K) EER images, new convergence criteria in 3D
   Classification, updates to Reference Based Motion Correction, and more.

Alongside the release, we are continually updating our educational
materials and guides. Some recent items:

   - Local Refinement
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/local-refinement__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQNmRFOw0$ >,
   including an updated data processing Case Study
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-yeast-u4-u6.u5-tri-snrnp__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQN4Su_kq$ >
    and Mask Creation Tutorial
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/mask-selection-and-generation-in-ucsf-chimera__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQBvsY_MH$ >
   - A new tutorial on 3D Flex Mesh Preparation
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-flex-mesh-preparation__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQP-rW2bm$ >
   - Updated page on Ab-Initio Reconstruction
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-reconstruction/job-ab-initio-reconstruction__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQPGYEYZN$ >

Please see full update instructions here.
<https://urldefense.com/v3/__https://guide.cryosparc.com/setup-configuration-and-management/software-updates__;!!Mih3wA!DaO4W0aMpbz95BVrtKtVBBB2n4dS6x1pjSyA9B_wZIed4MLjxwQgp5nw1SVkXLdF2rZlfL-mahwh8XrZQH9-IQ65$ >
Thank you!

The CryoSPARC Team
Structura Biotechnology Inc.
cryosparc.com
structura.bio
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240507/9da75a25/attachment.html>