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---- /!\ '''Edit conflict - other version:''' ---- ---- /!\ '''Edit conflict - other version:''' ---- * [[attachment:image_info.pdf|Information about images]] * [[image_proc.pdf|Filtering and basic image processing]] * [[ctf_sim.pdf|CTF Simulator]] ---- /!\ '''Edit conflict - your version:''' ---- |
* [[EMAN2/NegativeStain]] - special issues that impact processing negative stain single particle images |
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| ---- /!\ '''End of edit conflict''' ---- | ==== Single particle analysis (SPA) - 2D particles ==== * [[attachment:EMAN2-31Tutorial.pdf|Latest EMAN2.31 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]] * [[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]] |
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| ==== Tomography - tilt series through subtomogram averaging ==== | |
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| ---- /!\ '''Edit conflict - other version:''' ---- ---- /!\ '''Edit conflict - your version:''' ---- * [[attachment:image_info.pdf|Information about images]] * [[attachment:image_proc.pdf|Filtering and basic image processing]] * [[attachment:ctf_sim.pdf|CTF Simulator]] |
* 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 tutoria (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]] |
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| ---- /!\ '''End of edit conflict''' ---- | ==== 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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| == 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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| ---- /!\ '''Edit conflict - your version:''' ---- | {{attachment:2d_image_3dplot_2.png}} |
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| ---- /!\ '''End of edit conflict''' ---- ==== Single particle analysis (SPA) - 2D particles ==== |
* [[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]] |
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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
EMAN2/NegativeStain - special issues that impact processing negative stain single particle images
Single particle analysis (SPA) - 2D particles
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
Tomography - tilt series through subtomogram averaging
- Complete workflow for tomography and subtomogram averaging (subnanometer resolution, 2+ days, full workstation)
- 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.
- Automated Cellular Tomogram Annotation using Neural Networks
Exchanging Data Between EMAN2 and Other Software
Advanced Users and Programmers
Convert a real/imaginary image into an amplitude/phase image and vice versa
Make a projection of a 3D model, project through the asymmetric unit
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)
- 2018 May Tutorial for EMAN2.21a
EMAN2-21Tutorial.pdf (version 1)
- 2017 February Tutorial for EMAN2.2
- 2016 Summer Tutorial for EMAN2.12 June 2016 snapshots
- 2015 Fall Tutorial for EMAN2.12
Required data - Bgal.zip
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