Differences between revisions 106 and 141 (spanning 35 versions)
Revision 106 as of 2016-06-15 14:49:09
Size: 3867
Editor: SteveLudtke
Comment:
Revision 141 as of 2019-02-19 18:39:55
Size: 5419
Editor: SteveLudtke
Comment:
Deletions are marked like this. Additions are marked like this.
Line 15: Line 15:
==== 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]]
Line 16: Line 22:
 * 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]]

 * [[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/tomoworkflow_2019_02.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 18: Line 68:
  * use Required data from 2015 tutorial    * [[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
Line 25: Line 77:
 * [[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]]
 * [[EMAN2/Programs/convnet_pickparticle|An experimental new particle picker]] (requires installation of additional libraries)

==== Single particle tomography (SPT) - 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]]

==== 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.
Line 43: Line 80:
 * [[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
Line 44: Line 83:
 * [[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)