Differences between revisions 6 and 158 (spanning 152 versions)

EMAN2 TUTORIALS

Beginners (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

Written Tutorials

Tutorial Data

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
This covers the following standard workshop tutorial sequence:
- Quick Introduction to the EMAN2 GUI (30 min)
- 2-D variability analysis tutorial (30 min)
- Single particle analysis tutorial (1-4 hr plus some waiting)
- EMAN2 tomography workflow tutorial (small) (1-4 hr plus some waiting)

Short tutorials and info sheets

EMAN2/NegativeStain - special issues that impact processing negative stain single particle images
Information about images
Filtering and basic image processing
CTF Simulator

Single particle analysis (SPA) - 2D particles

Quick Introduction to the EMAN2 GUI (Start here if you have never used EMAN2!)
- eman2_samples.zip
Single particle analysis tutorial
- Tutorial Data Download
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. It will be fixed in the next release.
- Practice data for 2-D variability analysis
tutorial for the Neural network particle picker (requires CUDA for good performance)
These haven't been updated in a while, please ask if you have problems
- EMAN1 to EMAN2 Transition Guide - Also with useful quickstart guides for users of other software
- Tilt Validation tutorial
- Random Conical Tilt Tutorial

Tomography - tilt series through subtomogram averaging

Complete workflow for tomography and subtomogram averaging (subnanometer resolution, 2+ days, full workstation)
- 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 tomography workflow tutorial (small)
- Tomography Mini-tutorial Data Download
Automated Cellular Tomogram Annotation using Neural Networks
- Tomogram Annotation

Exchanging Data Between EMAN2 and Other Software

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

2019 May UTMB Workshop (full site with talks)
2019 January Tutorial for EMAN2.22
- EMAN2-22Tutorial.pdf (version 1)
  - Tutorial Data Download
2018 May Tutorial for EMAN2.21a
- EMAN2-21Tutorial.pdf (version 1)
  - Tutorial Data Download
2017 February Tutorial for EMAN2.2
- EMAN2-2Tutorial.pdf
  - Tutorial Data Download
2016 Summer Tutorial for EMAN2.12 June 2016 snapshots
2015 Fall Tutorial for EMAN2.12
- EMAN2-12_Tutorial.pdf
- Required data - Bgal.zip
- EMAN2-12_Tutorial2_heterogeneity.pdf
- Required data - ribosome.zip
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.
Single particle tomography - Tutorial for deprecated Single particle tomography (SPT) workflow.
Tutorial from the 2014 Workshops in Shanghai, Brisbane and online - Based on EMAN2.1 beta4. Full single particle reconstruction tutorial
Tutorial from the 2013 Workshop in Beijing (Data on same page) - Based on EMAN2.1alpha. Full single particle reconstruction tutorial
Tutorial from the 2012 Workshop in Singapore (Data on same page) - Based on EMAN2.06. Full single particle reconstruction tutorial
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 ( - Full tutorial on single particle reconstruction using the workflow (uses Workshop demo data DVD)

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+   ← Revision 158 as of 2020-01-31 16:20:32 → ⇥
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-== Using e2.py ==
* [:EMAN2/Tutorials/Display:Display a test image, and an ordinary image]
+= EMAN2 TUTORIALS =
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+Line 3:
-* [:EMAN2/Tutorials/RotateTranslate:Rotate and translate an image]
+== Beginners (introductory tutorials) ==
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+Line 5:
-* [:EMAN2/Tutorials/AddAndMultiply:Add images, and multiply by a constant]
+''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 8:
-* [:EMAN2/Galleries/Testimages:Generate a test image]
+=== Video tutorials and discussions ===
  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]

=== Written Tutorials ===

==== Tutorial Data ====
 * 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]]
 * This covers 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]] (1-4 hr plus some waiting)
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial (small)]] (1-4 hr plus some waiting)

==== Short tutorials and info sheets ====
 * [[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]]

==== 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_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. It will be fixed in the next release.
  * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
 * [[EMAN2/Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance)
 * 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 (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]]

==== 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]]

=== 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]])