Differences between revisions 142 and 180 (spanning 38 versions)
⇤ ← Revision 142 as of 2019-02-19 20:29:20 →
Size: 5417
Editor: SteveLudtke
Comment:
← Revision 180 as of 2024-04-05 01:50:10 → ⇥
Size: 8234
Editor: MuyuanChen
Comment: re-organize gmm part
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]] - These are a valuable supplement to the tutorials here, but are NOT a replacement
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.''		 == Standard 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/tutorial_tomo_small.zip|Small Tomography Tutorial (for low end machines/laptops)]]
 * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Tomography Tutorial (for standard workstations)]]
 * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Single Particle Tutorial Data]]
 * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]

=== Short tutorials and info sheets ===
 * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022)
Line 21: Line 30:
==== Single particle analysis (SPA) - 2D particles ==== === 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]]
  * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * [[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]]
  * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
 * 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]]

=== Tomography - tilt series through subtomogram averaging ===
 * Complete workflow for tomography and subtomogram averaging (includes both small version (laptop ~12 Å) and large version (subnanometer on workstation))
  * [[EMAN2/e2TomoSmall|Tomography and Subtomogram Averaging Tutorial]]
  * [[http://blake.bcm.edu/dl/tutorial_tomo_small.zip|Small Data Download]]
  * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Data Download]]
 * Automated Cellular Tomogram Annotation using Neural Networks
  * [[EMAN2/Programs/tomoseg|Tomogram Annotation]]
 * More advanced topics for 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 - for SPA and SPT data ===
 * Heterogeneity analysis - 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/e2gmmOriginal|Original GMM tutorial accompanying the 2021 paper]]
 * Orientation refinement - Improve resolution for flexible structures. For detailed methods, see the [[https://www.nature.com/articles/s41592-023-02082-9| 2024 paper]].
  * [[EMAN2/e2gmm_refine|GMM-based orientation refinement]] for SPA
  * [[A brief EMAN2/e2tomo_p22#GMM-based_refinement| tutorial]] on GMM based orientation refinement for SPT
 * [[EMAN2/e2gmm_model|Atomic model refinement]] - both single model and continuous movement.

=== Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions) ===
 * [[EMAN2/Programs/e2refinetorelion2d/e2refinetorelion2dtutorial|2D Class Averaging with Relion]]
 * [[EMAN2/Programs/e2refinetorelion3d/e2refinetorelion3dtutorial|3D Refinement with Relion]]
 * [[EMAN2/Programs/e2refinetofrealign/e2refinetofrealigntutorial|3D Refinement with FreAlign]]

== Archive of Workshop Material (Lectures, specific tutorials, etc. ==
 * [[UTMBWorkshop2019|2019 May UTMB Workshop]] (full site with talks)
  * [[https://blake.bcm.edu/emanwiki/UTMBWorkshop2019?action=AttachFile&do=get&target=EMAN2-3Tutorial.pdf|Latest EMAN2.3 single particle tutorial PDF]]
  * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
  * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
Line 31: Line 84:

 * [[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]]

==== Tomography - tilt series through subtomogram averaging ====

 * Complete workflow for tomography and subtomogram averaging (subnanometer resolution, 2+ days, full workstation)
  * [[EMAN2/e2tomo|EMAN2 tomography workflow tutorial]]
  * Data link is in the tutorial text
 * Small version of workflow for tomography and subtomogram averaging (~15 A, 1 day, possible on a laptop)
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial]]
  * [[http://blake.bcm.edu/dl/tutorial_tomo_mini.zip|Tomography Mini-tutorial Data Download]]
 * Automated Cellular Tomogram Annotation using Neural Networks
  * [[EMAN2/Programs/tomoseg|Tomogram Annotation]]

==== Exchanging Data Between EMAN2 and Other Software ====
 * [[EMAN2/Programs/e2refinetorelion2d/e2refinetorelion2dtutorial|2D Class Averaging with Relion]]
 * [[EMAN2/Programs/e2refinetorelion3d/e2refinetorelion3dtutorial|3D Refinement with Relion]]
 * [[EMAN2/Programs/e2refinetofrealign/e2refinetofrealigntutorial|3D Refinement with FreAlign]]

== 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]]

=== Older tutorials (provided for data access, etc.) ===
Line 79: Line 97:
 * 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 83: Line 100:
 * 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

  • 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 - for SPA and SPT data

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)