Differences between revisions 123 and 144 (spanning 21 versions)
Revision 123 as of 2017-09-06 07:13:02
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Revision 144 as of 2019-02-20 02:18:36
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 * [[EMAN2/NegativeStain]] - special issues that impact processing negative stain single particle images
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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]]
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 * [[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 ====

 * Small version of workflow for tomography and subtomogram averaging (~15 A, 1 day, possible on a laptop)
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutoria (small)l]]
  * [[http://blake.bcm.edu/dl/tutorial_tomo_mini.zip|Tomography Mini-tutorial Data Download]]
 * 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
 * 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.) ===
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 * [[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]]

==== Single particle tomography (SPT) - subtomogram averaging - 3D Particles ====
BOTH the tutorial in .pdf format and the data needed for the tutorial in a .zip file are provided in the page linked below:

 * [[SPT/Spt|Single particle tomography]]

==== Automated Cellular Tomogram Annotation using Neural Networks ====
 * [[EMAN2/Programs/tomoseg|Tomogram Annotation]]

==== Using the Built-In Modules from 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]]

=== Out of date tutorials (provided for data access, etc.) ===
 * [[SPT/Spt|Single particle tomography]] - Tutorial for deprecated Single particle tomography (SPT) workflow.
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 * [[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
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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
 * [[Ws2013/EMAN2|Tutorial from the 2013 Workshop in Beijing (Data on same page)]] - Based on EMAN2.1alpha. 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]]

{{attachment:2d_image_3dplot_2.png}}

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

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

Written Tutorials

Short tutorials and info sheets

Single particle analysis (SPA) - 2D particles

Tomography - tilt series through subtomogram averaging

Exchanging Data Between EMAN2 and Other Software

Advanced Users and Programmers

2d_image_3dplot_2.png

Older tutorials (provided for data access, etc.)

EMAN2/Tutorials (last edited 2024-04-05 01:51:27 by MuyuanChen)