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Dear 3DEM community,</div>
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We are excited to announce version 2.0 of CryoCloud.</div>
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The latest version of CryoCloud includes the following features:</div>
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CryoCloud Picker: our new ML-based Picker, CryoCloud Picker, is now available as a pre-processing job. Tests on multiple datasets incl. small membrane & nucleoproteins show a reduced false positive rate, an increase of true positive particles of 40% (i.e. particles
contributing to sub-4 A maps), increased & more detailed 2D classes, and enablement of initial map generation of difficult targets which failed using other ML pickers.</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Workflows (beta): a workflow editor is now available that allows setting up protocols to facilitate repeated and parallel analysis of datasets from motion correction to 3D refinement.</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
cryoET (beta): cryoET projects are now supported. We added jobs for automated tilt series alignment, tomogram reconstruction, template matching and subtomogram classification & averaging. TS alignment and tomogram reconstruction jobs support high-throughputs
of more than 500 TS per day.</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Interactive Graphs: we added interactive graphs and filters to all pre-processing jobs for improved data quality assessment and easier removal of bad data.</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Live results for pre-processing jobs: Motion & CTF results can now be inspected live during job runs and are updated every 10 seconds.</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Ice thickness: relative Ice thickness is now displayed as interactive graph in the CTF results page.</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Relion 5: all refinement jobs were updated to relion5 and Blush (Kimanius et al. 2024) can now be easily turned on with a toggle.<br>
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Improved 2D classification results page: added metrics to 2D class average tiles and included class ranker score (Kimanius et al. 2021) to enable unsupervised 2D class selection.</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Improved billing page: added graphs and a calendar functionality that allows visualizing all used cloud resources for custom date ranges</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Float 16: aligned micrographs & particles are now saved by default in float 16 for storage space savings.<br>
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Flexibility analysis & correction tools: cryoDRGN (Zhong et al. 2021) & Dynamight (Schwab et al., 2024) can now be run downstream of refinement jobs</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Model Building and refinement: added ModelAngelo (Jamali et al. 2024) for automated model building into density maps, and Servalcat (Yamashita et al. 2021) for structure refinement</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Many improvements for page loading times, data uploads, job setup pages & queuing.</li><li style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Free Plan for Academia: we are excited to offer a new free plan to all academic users that provides continuous access (limited to 3 cloud compute hours per month & 500 GB storage). Please use your institute’s email during the signup to facilitate the verification.</li></ul>
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All of these new features are now live and easily accessible via our web-apps User interface, which provides no-code access to dozens of GPUs per user, scalable cloud storage & archiving, and our collaboration & team features.</div>
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If you are interested to test CryoCloud with our 30 day free trial or sign up for our new free plan for academia, you can signup here:
<a href="https://urldefense.com/v3/__https://app.cryocloud.io/sign-up__;!!Mih3wA!DiP8fZDY-5tLOVFQbFSTKoaf5nCHxsf9Ag1ja0Grz2iq_U_i4D1jSC0xVaJduI_jvAMpei7jJlKAMh60hYDObA$" id="OWA43480c84-9e45-2c2c-a642-acc1d3aec239" class="OWAAutoLink">
https://app.cryocloud.io/sign-up</a></div>
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We are very grateful to all of our users and the cryo-EM community for your support and feedback.</div>
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Please reach out to <a href="mailto:hi@cryocloud.io" id="OWAe380a695-6a6a-aea4-06eb-31d5f9c6f80c" class="OWAAutoLink">
hi@cryocloud.io</a> for questions or inquiries.</div>
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Happy processing,</div>
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Robert</div>
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<p style="line-height: 105%;"><img style="width: 55px; height: 55px; margin-top: 0px; margin-bottom: 0px;" width="55" height="55" data-outlook-trace="F:1|T:1" src="cid:84bb425b-534b-41db-a041-6656e7c88ac3"><span style="font-size: 9pt; line-height: 105%;"> </span></p>
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<p style="line-height: 105%;"><span style="color: rgb(0, 112, 192);"><b>Robert Englmeier, PhD</b></span></p>
<p style="line-height: 105%;"><span style="font-size: 9pt; line-height: 105%;">Co-Founder & CEO at
</span><span style="font-size: 9pt; color: rgb(0, 112, 192); line-height: 105%;"><a href="https://urldefense.com/v3/__https://www.cryocloud.io/__;!!Mih3wA!DiP8fZDY-5tLOVFQbFSTKoaf5nCHxsf9Ag1ja0Grz2iq_U_i4D1jSC0xVaJduI_jvAMpei7jJlKAMh7wWjc9KA$" target="_blank" style="color: rgb(0, 112, 192); margin-top: 0px; margin-bottom: 0px;">CryoCloud</a></span><span style="font-size: 12pt; line-height: 105%;">
</span><span style="font-size: 12pt; color: rgb(0, 0, 0); line-height: 105%;"><a href="https://urldefense.com/v3/__https://www.linkedin.com/company/cryocloud__;!!Mih3wA!DiP8fZDY-5tLOVFQbFSTKoaf5nCHxsf9Ag1ja0Grz2iq_U_i4D1jSC0xVaJduI_jvAMpei7jJlKAMh5q4NWSXA$" style="color: rgb(0, 0, 0); margin-top: 0px; margin-bottom: 0px;"><img style="width: 11px; height: 11px; margin-top: 0px; margin-bottom: 0px;" width="11" height="11" data-outlook-trace="F:1|T:1" src="cid:a13dce41-f908-4b3c-928e-1926dc9e5a30"></a></span><span style="font-size: 12pt; line-height: 105%;"> </span><span style="font-size: 12pt; color: rgb(0, 0, 0); line-height: 105%;"><a href="twitter.com/cryocloud_io" style="color: rgb(0, 0, 0); margin-top: 0px; margin-bottom: 0px;"><img style="width: 11px; height: 11px; margin-top: 0px; margin-bottom: 0px;" width="11" height="11" data-outlook-trace="F:1|T:1" src="cid:404502b6-409d-40f9-bfe3-d28e2cc8f4ac"></a></span><span style="font-size: 5pt; line-height: 105%;"> </span></p>
<p style="line-height: 105%;"><span style="font-size: 9pt; color: rgb(0, 112, 192); line-height: 105%;"><b>Email</b>
<a href="mailto:robert@cryocloud.io" style="color: rgb(0, 112, 192); margin-top: 0px; margin-bottom: 0px;">
robert@cryocloud.io</a> </span><span style="font-size: 5pt; color: rgb(0, 112, 192); line-height: 105%;"> </span></p>
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