Differences between revisions 171 and 177 (spanning 6 versions)
⇤ ← Revision 171 as of 2022-08-30 03:40:53 →
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Editor: SteveLudtke
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← Revision 177 as of 2023-05-08 18:48:00 → ⇥
Size: 7747
Editor: MuyuanChen
Comment: two new tutorials
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 * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]] - These are a valuable supplement to the tutorials here, but are NOT a replacement
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== Written Tutorials == == Standard Tutorials ==
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 * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW)  * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022)
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  * WARNING - there seems to be a bug in EMAN2.31 so the realign and rerefine buttons do not work properly. Skip that step in the tutorial
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 * [[EMAN2/e2gmm|3-D variability analysis using GMM (Gaussian Mixture Model) and deep learning]] (requires CUDA, still under active development)
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  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial (small)]]   * [[EMAN2/e2TomoSmall|Tomography and Subtomogram Averaging Tutorial]]
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  * [[EMAN2/e2tomo_more|Advanced Subtomo]]
 * Preview tutorial for the new version of integrated subtomogram averaging (under development)
  * [[EMAN2/e2tomo_new|New Subtomogram Averaging]]		   * [[EMAN2/e2tomo_p22|Advanced SPT methods]] - Latest (2023) workflow for in situ SPT.
  * [[EMAN2/TomoSymmetry|Working with pseudosymmetric particles]] - Improving resolution and exploring variability in symmetric particles
  * [[EMAN2/e2tomo_more| Miscellaneous tools]] - Various SPT tools that may not be included in the main workflows.

=== Gaussian Mixture Model - Variability analysis both for SPA and SPT data ===
Strongly suggest reading [[https://www.nature.com/articles/s41592-021-01220-5|the paper]] (PMC8363932). While there have been some very significant improvements, it lays a foundation. This project has also bifurcated, as explained in the first tutorial below.
 * [[EMAN2/e2gmm|GMM GUI Tutorial - supports both SPA and SPT projects]] - suggest starting here for most users
 * [[EMAN2/e2gmm_refine|GMM-based orientation refinement]] - Improve resolution for flexible samples.
 * [[EMAN2/e2gmmOriginal|Original GMM tutorial accompanying the paper]]

EMAN2 Introductory Tutorials

Please note that we are continuously developing and updating the tutorials. Most tutorials include the necessary data. If you have a request for a particular tutorial please feel free to email sludtke@bcm.edu .

Video tutorials and discussions

  • EMAN2 Video Tutorials - These are a valuable supplement to the tutorials here, but are NOT a replacement

Standard Tutorials

Tutorial Data Downloads

The actual tutorials are in the sections below, this section contains the various test data sets.

Individual tutorial data downloads are available below, but for convenience, we have combined the data for the GUI introduction, single particle analysis tutorial, single particle 2-D dynamics tutorial and small tomography tutorial into a single download:

Alternatively, these individual data downloads cover the following standard workshop tutorial sequence:

Short tutorials and info sheets

Single particle analysis (SPA) - 2D particles

Tomography - tilt series through subtomogram averaging

Gaussian Mixture Model - Variability analysis both for SPA and SPT data

Strongly suggest reading the paper (PMC8363932). While there have been some very significant improvements, it lays a foundation. This project has also bifurcated, as explained in the first tutorial below.

Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions)

Archive of Workshop Material (Lectures, specific tutorials, etc.

EMAN2/Tutorials (last edited 2024-04-05 01:51:27 by MuyuanChen)