[3dem] CryoSPARC v4.7 now available

[Ali Punjani]

Dear 3DEM,

We are happy to announce the release of CryoSPARC v4.7
<https://urldefense.com/v3/__https://cryosparc.com/updates__;!!Mih3wA!C1eQpTgJdziAHPch6N6m3mV2a-q-7wwEe0HyOWS9upVuBamaUdmWyrsFIQ1X1ZrPUVUeA4q8PlXYa_0VChokwqvi$ > today!

A few highlights:

   - Micrograph Junk Detector (BETA)
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/exposure-curation/job-micrograph-junk-detector-beta__;!!Mih3wA!C1eQpTgJdziAHPch6N6m3mV2a-q-7wwEe0HyOWS9upVuBamaUdmWyrsFIQ1X1ZrPUVUeA4q8PlXYa_0VCn3d2RI1$ >:
   New pre-trained neural network model analyzes micrographs and identifies
   three classes of contaminants, including carbon/gold, intrinsic ice issues
   (cracks, non-vitreous ice, etc.) and extrinsic ice issues (ethane, ice
   crystals, etc.). The outputs can be used to view junk annotations and
   filter micrographs based on junk statistics (e.g., presence and fraction of
   junk area of each type). Particle picks which are on or near the labelled
   junk contaminants can be discarded.
   - Subset Particles by Statistic
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/job-subset-particles-by-statistic__;!!Mih3wA!C1eQpTgJdziAHPch6N6m3mV2a-q-7wwEe0HyOWS9upVuBamaUdmWyrsFIQ1X1ZrPUVUeA4q8PlXYa_0VCn46UBvF$ >:
This
   new job simplifies the process of separating sub-populations within a
   particle stack, based on metrics such as per-particle scale, NCC and power
   scores, etc. Particles can be subset by modeling the selected statistic
   using a Gaussian mixture model, or with manually entered thresholds.
   Separating particles in this way can be an efficient means of eliminating
   junk or otherwise low-quality particles.
   - The full changelog is available on our website:
   https://urldefense.com/v3/__https://cryosparc.com/updates__;!!Mih3wA!C1eQpTgJdziAHPch6N6m3mV2a-q-7wwEe0HyOWS9upVuBamaUdmWyrsFIQ1X1ZrPUVUeA4q8PlXYa_0VChokwqvi$ 

We also want to point out some recent case studies and videos for new and
advanced users alike:

   - Case Study: End-to-end processing of a ligand-bound GPCR (EMPIAR-10853)
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-end-to-end-processing-of-a-ligand-bound-gpcr-empiar-10853__;!!Mih3wA!C1eQpTgJdziAHPch6N6m3mV2a-q-7wwEe0HyOWS9upVuBamaUdmWyrsFIQ1X1ZrPUVUeA4q8PlXYa_0VCk8q3ASg$ >:
We
   cover the processing pipeline for an active G-protein coupled receptor with
   a ligand, G-protein and antibody fragment bound. The case study includes
   Micrograph Denoising, Junk Detection, Subset Particles by Statistic, Local
   Refinement and focussed 3D Classification to improve ligand density. Our
   final sharpened maps, half maps and masks can be downloaded for comparison
   with your results.
   - Case Study: DkTx-bound TRPV1 (EMPIAR-10059):
   <https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-dktx-bound-trpv1-empiar-10059__;!!Mih3wA!C1eQpTgJdziAHPch6N6m3mV2a-q-7wwEe0HyOWS9upVuBamaUdmWyrsFIQ1X1ZrPUVUeA4q8PlXYa_0VCk1mFrUV$ >
We
   process this dataset with a focus on particle curation, developing an
   intuition for when a domain may be blurred due to flexibility, and how to
   handle this type of flexibility.
   - Videos: Cryo-EM Image Processing Fundamentals:
   <https://urldefense.com/v3/__https://cryosparc.us16.list-manage.com/track/click?u=670f9d2780a80acff83747934&id=a71471ed21&e=e7c8307680__;!!Mih3wA!C1eQpTgJdziAHPch6N6m3mV2a-q-7wwEe0HyOWS9upVuBamaUdmWyrsFIQ1X1ZrPUVUeA4q8PlXYa_0VCtCBC4iq$ >
A
   series of six videos from the 2024 S2C2 Image Processing Workshop which
   cover cryo-EM fundamentals, a standard workflow for processing single
   particle datasets, considerations for working with symmetric samples, and
   ways to deal with discrete and continuous heterogeneity.

Please see this page
<https://urldefense.com/v3/__https://guide.cryosparc.com/setup-configuration-and-management/software-updates__;!!Mih3wA!C1eQpTgJdziAHPch6N6m3mV2a-q-7wwEe0HyOWS9upVuBamaUdmWyrsFIQ1X1ZrPUVUeA4q8PlXYa_0VCvyQvTvt$ >
for instructions on updating to v4.7.
Thank you!

The CryoSPARC Team
Structura Biotechnology Inc.
cryosparc.com
structura.bio
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