Differences between revisions 90 and 138 (spanning 48 versions)

EMAN2 TUTORIALS

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 feel free to email sludtke@bcm.edu.

Video tutorials and discussions

EMAN2 Video Tutorials

Written Tutorials

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

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
tutorial for the Neural network particle picker (requires CUDA for good performance)
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 cellular tomography and subtomogram averaging
- EMAN2 tomography workflow tutorial
Automated Cellular Tomogram Annotation using Neural Networks
- Tomogram Annotation

Exchanging Data Between EMAN2 and Other Software

Advanced Users and Programmers

Change log level in EMAN2

Older tutorials (provided for data access, etc.)

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
Single particle reconstruction tutorial from 2008 Workshop ( - Full tutorial on single particle reconstruction using the workflow (uses Workshop demo data DVD)
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

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+=== Video tutorials and discussions ===
  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]

=== Written Tutorials ===

==== 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]]
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+ * 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]]
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+Line 32:
+ * [[EMAN2/Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance)
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- * [[Ws2012/Eman2|Tutorial from the 2012 Workshop in Singapore (Data on same page)]] - Based on EMAN2.06. Full single particle reconstruction tutorial
 * [[OxfordWs2012|Tilt Validation tutorial from the Oxford 2012 mini-workshop]] - Requires EMAN 2.05+
 * [[RctTutorial|Random Conical Tilt Tutorial]] - Requires EMAN 2.05+
+ * [[OxfordWs2012|Tilt Validation tutorial]]
 * [[RctTutorial|Random Conical Tilt Tutorial]]
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-==== Single particle tomography (SPT) - 3D particles ====
+==== Tomography - tilt series through subtomogram averaging ====
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-BOTH the tutorial in .pdf format and the data needed for the tutorial in a .zip file are provided in the page linked below:
+ * Complete workflow for cellular tomography and subtomogram averaging
  * [[e2tomo|EMAN2 tomography workflow tutorial]]
 * Automated Cellular Tomogram Annotation using Neural Networks
  * [[EMAN2/Programs/tomoseg|Tomogram Annotation]]
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+Line 44:
- * [[SPT/Spt|Single particle tomography]] - Requires EMAN 2.05+
+==== 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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-==== 2D assessment of heterogeneity ====
 * [[attachment:population_dynamics_2009_11.pdf|Full tutorial on 2-D analysis for assessment of structural heterogeneity and population dynamics]] (under construction)

==== Adding an e2program to the program manger workflow ====
 * [[EMAN2PMWorkflow|Modifying the EMAN2 projectmanager workflow]]

=== Out of date tutorials still provided for data access, etc. ===
 * 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]])
 * [[Ws2011/Eman2|Tutorial from the 2011 EMAN2 workshop (Data on same page)]] - Based on EMAN2.01. Full single particle reconstruction tutorial


== Advanced (EMAN2 through the ''e2.py'' Python prompt) ==
* [[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]]
+=== 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]]
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+Line 59:
-* [[EMAN2LogLevel|Change log level in EMAN2]]
+ * [[EMAN2LogLevel|Change log level in EMAN2]]

=== Older tutorials (provided for data access, etc.) ===
 * 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
 * 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]])
 * [[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