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Revision 155 as of 2019-12-16 07:02:38
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Revision 169 as of 2022-01-18 02:28:32
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Editor: SteveLudtke
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Deletions are marked like this. Additions are marked like this.
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= EMAN2 TUTORIALS = = EMAN2 Introductory Tutorials =
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== Beginners (introductory tutorials) ==

''Please note that we are continuously developing and updating the tutorials. Items that are greyed out
are planned but the tutorials have not yet been completed
. Most tutorials include the necessary data. If you have a request for a particular tutorial
''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
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=== Video tutorials and discussions === == Video tutorials and discussions ==
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=== Written Tutorials === == Written Tutorials ==
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==== Short tutorials and info sheets ==== === 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:
 * [[http://blake.bcm.edu/dl/eman2_tutorials_all.zip]]

Alternatively, these individual downloads cover the following standard workshop tutorial sequence:
  * [[attachment:EMAN2_GUITutorial.pdf|Quick Introduction to the EMAN2 GUI]] (30 min)
  * [[attachment:EMAN2_FlexibilityTutorial.pdf|2-D variability analysis tutorial]] (30 min)
  * [[attachment:EMAN2_SingleParticleTutorial.pdf|Single particle analysis tutorial]] (3-4 hr plus some waiting)
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial (small)]] (3-4 hr plus some waiting)

=== Short tutorials and info sheets ===
 * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW)
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==== Single particle analysis (SPA) - 2D particles ====
 * [[attachment:EMAN2-31Tutorial.pdf|Latest EMAN2.31 single particle tutorial PDF]]
=== Single particle analysis (SPA) - 2D particles ===
 * [[attachment:EMAN2_GUITutorial.pdf|Quick Introduction to the EMAN2 GUI]] (Start here if you have never used EMAN2!)
  * [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]]
 * [[attachment:EMAN2_SingleParticleTutorial.pdf|Single particle analysis tutorial]]
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 * [[attachment:EMAN2-31FlexibilityTutorial.pdf|2-D variability tutorial]]  * [[attachment:EMAN2_boxer_tutorial_2021_04.pdf|Particle picking tutorial (basic tutorial only)]]
 * [[EMAN2/Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance)
 * [[attachment:EMAN2_FlexibilityTutorial.pdf|2-D variability analysis tutorial]]
  * 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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 * Sample images to explore the GUI
  * [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]]
 * [[EMAN2/Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance)
 * [[EMAN2/e2gmm | 3-D variability analysis using GMM (Gaussian Mixture Model) and deep learning]] (requires CUDA, still under active development)
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==== Tomography - tilt series through subtomogram averaging ==== === Tomography - tilt series through subtomogram averaging ===
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  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutoria (small)]]   * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial (small)]]
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 * More advanced topics for subtomogram averaging
  * [[EMAN2/e2tomo_more|Advanced Subtomo]]
 * Preview tutorial for the new version of integrated subtomogram averaging (under development)
  * [[EMAN2/e2tomo_new|New Subtomogram Averaging]]
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==== Exchanging Data Between EMAN2 and Other Software ==== === Exchanging Data Between EMAN2 and Other Software ===
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=== Archive of Workshop Material (Lectures, specific tutorials, etc. === == Archive of Workshop Material (Lectures, specific tutorials, etc. ==

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

Written 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 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

Exchanging Data Between EMAN2 and Other Software

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

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