[3dem] VirtualIce v2 Release

[Alex Noble]

Dear cool people,

I am pleased to announce the release of VirtualIce v2<https://urldefense.com/v3/__https://github.com/alexjnoble/VirtualIce__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKfVSkbqmA$ > 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.

I envision that VirtualIce may be useful for:

  *
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.
  *
Developing new algorithms - particularly machine learning algorithms - for micrograph & particle analysis such as particle picking and heterogeneity analysis.
  *
Accelerating the development of cryoEM pipelines, such as collection and live processing, by providing fully annotated high-magnification micrographs.

Version 2 features include:

  *
Projecting any number of different structures onto micrographs (useful for heterogeneity/flexibility analysis and particle picking development).
  *
Simulating realistic particle behavior, including preferred orientation, distribution, overlapping, aggregation, and ice thickness.
  *
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).
  *
Filtering out particles based on overlap with other particles or obscured objects, or proximity to micrograph edges.
  *
Simulating Poisson & Gaussian noise, CTF, and beam damage.
  *
Multi-CPU and multi-GPU processing.

Please see GitHub<https://urldefense.com/v3/__https://github.com/alexjnoble/VirtualIce__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKfVSkbqmA$ > for installation instructions, examples<https://urldefense.com/v3/__https://github.com/alexjnoble/VirtualIce?tab=readme-ov-file*examples__;Iw!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKd0Uhmk-w$ >, & a user guide<https://urldefense.com/v3/__https://github.com/alexjnoble/VirtualIce?tab=readme-ov-file*user-guide__;Iw!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKdX5BckFA$ >, and the associated manuscript<https://urldefense.com/v3/__https://doi.org/10.1101/2024.09.28.615520__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKdsFTjykA$ > for a full description of the software. VirtualIce requires the vitrified buffer micrographs from EMPIAR-12287<https://urldefense.com/v3/__https://www.ebi.ac.uk/empiar/EMPIAR-12287/__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKelCxvMJA$ > (ice_images folder) to be downloaded.


Best wishes,
Alex Noble
[LinkedIn]<https://urldefense.com/v3/__https://www.linkedin.com/in/alex-noble-75209915/__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKcgW-COmQ$ > | [X]<https://urldefense.com/v3/__https://x.com/alexjamesnoble__;!!Mih3wA!FueZTh9EhyZdtIyfW5ENv2fp53xCjIvYjAVGYbUf2GFv5yEKIxOXkc105vmCHntso6fTfsvzzKd4ssJicg$ >
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20241011/e56f3771/attachment.html>