Differences between revisions 150 and 170 (spanning 20 versions)
⇤ ← Revision 150 as of 2019-12-11 15:57:30 →
Size: 6258
Editor: SteveLudtke
Comment:
← Revision 170 as of 2022-02-27 02:31:26 → ⇥
Size: 7326
Editor: SteveLudtke
Comment:
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
= EMAN2 TUTORIALS = = 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 .''
Line 3: Line 4:
== Beginners (introductory tutorials) == == Video tutorials and discussions ==
 * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]
Line 5: Line 7:
''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 feel free to email sludtke@bcm.edu.''		 == Written Tutorials ==
=== Tutorial Data Downloads ===
The actual tutorials are in the sections below, this section contains the various test data sets.
Line 9: Line 11:
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:
Line 10: Line 13:
=== Video tutorials and discussions ===
  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]		  * http://blake.bcm.edu/dl/eman2_tutorials_all.zip
Line 13: Line 15:
=== Written Tutorials === Alternatively, these individual data downloads cover the following standard workshop tutorial sequence:
Line 15: Line 17:
==== Short tutorials and info sheets ====  * [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]]
 * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
 * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * [[http://blake.bcm.edu/dl/tutorial_tomo_mini.zip|Tomography Mini-tutorial Data Download]]

=== Short tutorials and info sheets ===
 * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW)
Line 21: Line 29:
==== 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]]
Line 24: Line 34:
 * [[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
Line 25: Line 39:
 * [[EMAN2/Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance)
 * [[EMAN2/Eman1Transition|EMAN1 to EMAN2 Transition Guide]] - Also with useful quickstart guides for users of other software
 * [[OxfordWs2012|Tilt Validation tutorial]]
 * [[RctTutorial|Random Conical Tilt Tutorial]]		  * [[EMAN2/e2gmm|3-D variability analysis using GMM (Gaussian Mixture Model) and deep learning]] (requires CUDA, still under active development)
 * These haven't been updated in a while, please ask if you have problems
  * [[EMAN2/Eman1Transition|EMAN1 to EMAN2 Transition Guide]] - Also with useful quickstart guides for users of other software
  * [[OxfordWs2012|Tilt Validation tutorial]]
  * [[RctTutorial|Random Conical Tilt Tutorial]]
Line 30: Line 45:
==== Tomography - tilt series through subtomogram averaging ====

 * Complete workflow for tomography and subtomogram averaging (subnanometer resolution, 2+ days, full workstation)		 === Tomography - tilt series through subtomogram averaging ===
 * Complete workflow for tomography and subtomogram averaging (subnanometer resolution, 2+ days, full workstation) - The small tutorial below is more up to date as of Feb 22
Line 35: Line 49:
 * Small version of workflow for tomography and subtomogram averaging (~15 A, 1 day, possible on a laptop). Note that the large version of the tutorial above is updated regularly. If you have issues with this tutorial check the corresponding section in the full tutorial above.
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutoria (small)]]		  * Small version of workflow for tomography and subtomogram averaging (~15 A, 1 day, possible on a laptop).
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial (small)]]
Line 40: Line 54:
 * 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]]
Line 41: Line 59:
==== Exchanging Data Between EMAN2 and Other Software ==== === Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions) ===
Line 46: Line 64:
== Advanced Users and Programmers ==
 * [[EMAN2/Galleries/Testimages|Generate and display an EMAN2 test image]]
 * [[EMAN2/Tutorials/RotateTranslate|Rotate, translate, scale or mirror an image]]
 * [[EMAN2/Tutorials/AddAndMultiply|Add and multiply images, add and multiply by constants]]
 * [[EMAN2/Tutorials/ri2ap|Convert a real/imaginary image into an amplitude/phase image and vice versa]]
 * [[EMAN2/Tutorials/iter_pixels|Iterate through the pixels of an image]]
 * [[EMAN2/Tutorials/make_a_projection|Make a projection of a 3D model, project through the asymmetric unit]]

{{attachment:2d_image_3dplot_2.png}}

 * [[EMAN2LogLevel|Change log level in EMAN2]]

=== Archive of Workshop Material (Lectures, specific tutorials, etc. ===		 == Archive of Workshop Material (Lectures, specific tutorials, etc. ==
Line 85: Line 91:
 * Single particle reconstruction tutorial from 2008 Workshop ( - [[attachment:workflow_tutorial_2010_08_25.pdf|Full tutorial on single particle reconstruction using the workflow]] (uses [[http://blake.grid.bcm.edu/dl/data/workshop5.iso|Workshop demo data DVD]])
Line 89: Line 94:
 * Single particle reconstruction tutorial from 2008 Workshop ( - [[attachment:workflow_tutorial_2010_08_25.pdf|Full tutorial on single particle reconstruction using the workflow]] (uses [[http://blake.grid.bcm.edu/dl/data/workshop5.iso|Workshop demo data DVD]])

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 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

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)