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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. 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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==== 2D single particle analysis (SPA) ====
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 * The old SPR tutorial - [[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]])
 * [[Ws2011/Eman2|The NEW tutorial from the 2011 EMAN2 workshop, compatible with EMAN 2.01 (Data on same page)]]
 * [[attachment:rct_tutorial.pdf|Tutorial on using EMAN2 for Random Conical Tilt reconstructions]]		 == Video tutorials and discussions ==
  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]
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==== 3D single particle tomography (SPT) ====
 * NEW single particle tomography USERS' GUIDE. [Partially used for the SPT tutorial at the 2011 EMAN2 workshop].
 [[attachment:e2spt_users_guide.pdf| e2spt_users_guide.pdf|&do=get]]
 * UPDATED on April 18, 2011. '''It SHOULD be a valid PDF'''. If not, please report it, and try to open in with OpenOffice or Word. 		== Written Tutorials ==
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=== Tutorial Data Downloads ===
The actual tutorials are in the sections below, this section contains the various test data sets.
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==== 2D assessment of heterogeneity ====
 * [[attachment:population_dynamics_2009_11.pdf|Full tutorial on 2-D analysis for assessment of structural heterogeneity and population dynamics]]		 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]]
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== Advanced (EMAN2 through the ''e2.py'' Python prompt) ==
* [[EMAN2/Galleries/Testimages|Generate and display an EMAN2 test image]]		 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)
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* [[EMAN2/Tutorials/RotateTranslate|Rotate, translate, scale or mirror an image]] === Short tutorials and info sheets ===
 * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW)
 * [[EMAN2/NegativeStain]] - special issues that impact processing negative stain single particle images
 * [[attachment:image_info.pdf|Information about images]]
 * [[attachment:image_proc.pdf|Filtering and basic image processing]]
 * [[attachment:ctf_sim.pdf|CTF Simulator]]
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* [[EMAN2/Tutorials/AddAndMultiply|Add and multiply images, add and multiply by constants]] === 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]]
  * 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
  * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
 * [[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]]
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* [[EMAN2/Tutorials/ri2ap|Convert a real/imaginary image into an amplitude/phase image and vice versa]] === Tomography - tilt series through subtomogram averaging ===
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* [[EMAN2/Tutorials/iter_pixels|Iterate through the pixels of an image]]  * Complete workflow for tomography and subtomogram averaging (subnanometer resolution, 2+ days, full workstation)
  * [[EMAN2/e2tomo|EMAN2 tomography workflow tutorial (large)]]
  * Data link is in the tutorial text
 * 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 tutorial (small)]]
  * [[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]]
 * 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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* [[EMAN2/Tutorials/make_a_projection|Make a projection of a 3D model, project through the asymmetric unit]] === 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]]
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{{attachment:2d_image_3dplot_2.png}}

* [[EMAN2LogLevel|Change log level in EMAN2]]		 == 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]]
 * 2019 January Tutorial for EMAN2.22
  * [[attachment:EMAN2-22Tutorial.pdf||&do=get]] (version 1)
   * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * 2018 May Tutorial for EMAN2.21a
  * [[attachment:EMAN2-21Tutorial.pdf||&do=get]] (version 1)
   * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * 2017 February Tutorial for EMAN2.2
  * [[attachment:EMAN2-2Tutorial.pdf||&do=get]]
   * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * 2016 Summer Tutorial for EMAN2.12 June 2016 snapshots
  * [[attachment:EMAN2-13_pre_Tutorial.pdf||&do=get]]
   * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
  * [[attachment:EMAN2-13_pre_Heterogeneity.pdf||&do=get]]
  * see also: http://www.sciencedirect.com/science/article/pii/S0076687916300362
 * 2015 Fall Tutorial for EMAN2.12
  * [[attachment:EMAN2-12_Tutorial.pdf||&do=get]]
  * Required data - [[attachment:Bgal.zip||&do=get]]
  * [[attachment:EMAN2-12_Tutorial2_heterogeneity.pdf||&do=get]]
  * Required data - [[attachment:ribosome.zip||&do=get]]
 * [[Ws2015|2015 Workshop Tutorials and Demo data]] - This includes updated tutorials on both high resolution single particle analysis and 2D/3D heterogeneity analysis along with sample data, freshly updated for the EMAN2.12 release. The workshop also included a number of other related topics also available on that page.
 * [[SPT/Spt|Single particle tomography]] - Tutorial for deprecated Single particle tomography (SPT) workflow.
 * [[Ws2014|Tutorial from the 2014 Workshops in Shanghai, Brisbane and online]] - Based on EMAN2.1 beta4. Full single particle reconstruction tutorial
 * [[Ws2013/EMAN2|Tutorial from the 2013 Workshop in Beijing (Data on same page)]] - Based on EMAN2.1alpha. Full single particle reconstruction tutorial
 * [[Ws2012/EMAN2|Tutorial from the 2012 Workshop in Singapore (Data on same page)]] - Based on EMAN2.06. Full single particle reconstruction tutorial
 * [[Ws2011/Eman2|Tutorial from the 2011 EMAN2 workshop (Data on same page)]] - Based on EMAN2.01. Full single particle reconstruction tutorial
 * 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 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)