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Dear cool people,</div>
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I am pleased to announce the release of <a href="https://urldefense.com/v3/__https://github.com/alexjnoble/VirtualIce__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKfVSkbqmA$" id="LPlnk" title="https://github.com/alexjnoble/VirtualIce">
VirtualIce v2</a> for generating half-synthetic cryoEM micrographs by realistically projecting particles onto annotated vitrified buffer images. Real micrograph backgrounds and realistic particle behavior provide realistic context, along with ground truth coordinates
& orientations.</div>
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I envision that VirtualIce may be useful for:</div>
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<div class="elementToProof">Visualizing potential new proteins and their behavior, allowing researchers to predict/identify how different views may appear and to diagnose issues such as preferred orientation or aggregation.</div>
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<div class="elementToProof">Developing new algorithms - particularly machine learning algorithms - for micrograph & particle analysis such as particle picking and heterogeneity analysis.</div>
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<div class="elementToProof">Accelerating the development of cryoEM pipelines, such as collection and live processing, by providing fully annotated high-magnification micrographs.</div>
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Version 2 features include:</div>
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<div class="elementToProof">Projecting any number of different structures onto micrographs (useful for heterogeneity/flexibility analysis and particle picking development).</div>
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<div class="elementToProof">Simulating realistic particle behavior, including preferred orientation, distribution, overlapping, aggregation, and ice thickness.</div>
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<div class="elementToProof">Supporting PDB/EMDB/local files, micrographs (.mrc), and micrograph annotations of obscuring objects (.json). Outputs micrographs (.mrc, .png, .jpeg) with coordinate files (.star, .coord, .mod) with orientations (.star) and cropped
particles (.mrc).</div>
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<div class="elementToProof">Filtering out particles based on overlap with other particles or obscured objects, or proximity to micrograph edges.</div>
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<div class="elementToProof">Simulating Poisson & Gaussian noise, CTF, and beam damage.</div>
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<div>Multi-CPU and multi-GPU processing.</div>
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Please see <a href="https://urldefense.com/v3/__https://github.com/alexjnoble/VirtualIce__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKfVSkbqmA$" id="LPlnk" title="https://github.com/alexjnoble/VirtualIce">
GitHub</a> for installation instructions, <a href="https://urldefense.com/v3/__https://github.com/alexjnoble/VirtualIce?tab=readme-ov-file*examples__;Iw!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKd0Uhmk-w$" id="LPlnk436500" title="https://github.com/alexjnoble/VirtualIce?tab=readme-ov-file#examples">
examples</a>, & a <a href="https://urldefense.com/v3/__https://github.com/alexjnoble/VirtualIce?tab=readme-ov-file*user-guide__;Iw!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKdX5BckFA$" id="LPlnk" title="https://github.com/alexjnoble/VirtualIce?tab=readme-ov-file#user-guide">
user guide</a>, and the <a href="https://urldefense.com/v3/__https://doi.org/10.1101/2024.09.28.615520__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKdsFTjykA$" id="LPlnk708864" title="https://doi.org/10.1101/2024.09.28.615520">
associated manuscript</a> for a full description of the software. VirtualIce requires the vitrified buffer micrographs from
<a href="https://urldefense.com/v3/__https://www.ebi.ac.uk/empiar/EMPIAR-12287/__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKelCxvMJA$" id="LPlnk254913" title="https://www.ebi.ac.uk/empiar/EMPIAR-12287/">
EMPIAR-12287</a> (ice_images folder) to be downloaded.</div>
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Best wishes,</div>
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Alex Noble</div>
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<a href="https://urldefense.com/v3/__https://www.linkedin.com/in/alex-noble-75209915/__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKcgW-COmQ$" id="LPlnk955298" title="https://www.linkedin.com/in/alex-noble-75209915/">[LinkedIn]</a> |
<a href="https://urldefense.com/v3/__https://x.com/alexjamesnoble__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKd4ssJicg$" id="LPlnk513862" title="https://x.com/alexjamesnoble">
[X]</a></div>
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