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| = EMAN2 TUTORIALS = | = EMAN2 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 .'' |
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| == Beginners (introductory tutorials) == | == Video tutorials and discussions == * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]] - These are a valuable supplement to the tutorials here, but are NOT a replacement |
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| ''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.'' |
== Standard Tutorials == === Tutorial Data Downloads === The actual tutorials are in the sections below, this section contains the various test data sets. |
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| 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: | |
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| Don't forget the [[EMAN2/VideoTutorials|Video Tutorials]]! | * http://blake.bcm.edu/dl/eman2_tutorials_all.zip |
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| ==== Single particle analysis (SPA) - 2D particles ==== | Alternatively, these individual data downloads cover the following standard workshop tutorial sequence: |
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| * [[EMAN2/Eman1Transition|EMAN1 to EMAN2 Transition Guide]] - Also with useful quickstart guides for users of other software * [[Ws2014|Tutorial from the 2014 Workshops in Shanghai, Brisbane and online]] - Based on EMAN2.1 beta4. 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+ |
* [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]] * [[http://blake.bcm.edu/dl/tutorial_tomo_small.zip|Small Tomography Tutorial (for low end machines/laptops)]] * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Tomography Tutorial (for standard workstations)]] * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Single Particle Tutorial Data]] * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]] |
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| ==== Single particle tomography (SPT) - 3D particles ==== | === Short tutorials and info sheets === * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022) * [[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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| BOTH the tutorial in .pdf format and the data needed for the tutorial in a .zip file are provided in the page linked below: | === 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_boxer_tutorial_2021_04.pdf|Particle picking tutorial (basic tutorial only)]] * [[EMAN2/Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance) * [[attachment:EMAN2_FlexibilityTutorial.pdf|2-D variability analysis tutorial]] * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]] * 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]] |
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| * [[SPT/Spt|Single particle tomography]] - Requires EMAN 2.05+ | === Tomography - tilt series through subtomogram averaging === * Complete workflow for tomography and subtomogram averaging (includes both small version (laptop ~12 Å) and large version (subnanometer on workstation)) * [[EMAN2/e2TomoSmall|Tomography and Subtomogram Averaging Tutorial]] * [[http://blake.bcm.edu/dl/tutorial_tomo_small.zip|Small Data Download]] * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Data Download]] * Automated Cellular Tomogram Annotation using Neural Networks * [[EMAN2/Programs/tomoseg|Tomogram Annotation]] * More advanced topics for subtomogram averaging * [[EMAN2/e2tomo_p22|Advanced SPT methods]] - Latest (2023) workflow for in situ SPT. * [[EMAN2/TomoSymmetry|Working with pseudosymmetric particles]] - Improving resolution and exploring variability in symmetric particles * [[EMAN2/e2tomo_more| Miscellaneous tools]] - Various SPT tools that may not be included in the main workflows. |
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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) |
=== Gaussian Mixture Model - for SPA and SPT data === * Heterogeneity analysis - Strongly suggest reading [[https://www.nature.com/articles/s41592-021-01220-5|the paper]] (PMC8363932). While there have been some very significant improvements, it lays a foundation. This project has also bifurcated, as explained in the first tutorial below. * [[EMAN2/e2gmm|GMM GUI Tutorial - supports both SPA and SPT projects]] - suggest starting here for most users * [[EMAN2/e2gmmOriginal|Original GMM tutorial accompanying the 2021 paper]] * Orientation refinement - Improve resolution for flexible structures. For detailed methods, see the [[https://www.nature.com/articles/s41592-023-02082-9| 2024 paper]]. * [[EMAN2/e2gmm_refine|GMM-based orientation refinement]] for SPA * [[EMAN2/e2tomo_p22#GMM-based_refinement|A brief tutorial]] on GMM based orientation refinement for SPT * [[EMAN2/e2gmm_model|Atomic model refinement]] - both single model and continuous movement. |
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| ==== Adding an e2program to the program manager workflow ==== * [[EMAN2PMWorkflow|Modifying the EMAN2 projectmanager workflow]] ==== Using the Built-In Modules from Other Software ==== |
=== Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions) === |
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| === Out of date tutorials (provided for data access, etc.) === | == 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 |
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| * [[Ws2011/Eman2|Tutorial from the 2011 EMAN2 workshop (Data on same page)]] - Based on EMAN2.01. 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 * [[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 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 - These are a valuable supplement to the tutorials here, but are NOT a replacement
Standard Tutorials
Tutorial Data Downloads
The actual tutorials are in the sections below, this section contains the various test data sets.
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:
Alternatively, these individual data downloads cover the following standard workshop tutorial sequence:
Short tutorials and info sheets
EMAN2/Jupyter - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022)
EMAN2/NegativeStain - special issues that impact processing negative stain single particle images
Single particle analysis (SPA) - 2D particles
Quick Introduction to the EMAN2 GUI (Start here if you have never used EMAN2!)
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
Tomography - tilt series through subtomogram averaging
- Complete workflow for tomography and subtomogram averaging (includes both small version (laptop ~12 Å) and large version (subnanometer on workstation))
- Automated Cellular Tomogram Annotation using Neural Networks
- More advanced topics for subtomogram averaging
Advanced SPT methods - Latest (2023) workflow for in situ SPT.
Working with pseudosymmetric particles - Improving resolution and exploring variability in symmetric particles
Miscellaneous tools - Various SPT tools that may not be included in the main workflows.
Gaussian Mixture Model - for SPA and SPT data
Heterogeneity analysis - Strongly suggest reading the paper (PMC8363932). While there have been some very significant improvements, it lays a foundation. This project has also bifurcated, as explained in the first tutorial below.
GMM GUI Tutorial - supports both SPA and SPT projects - suggest starting here for most users
Orientation refinement - Improve resolution for flexible structures. For detailed methods, see the 2024 paper.
GMM-based orientation refinement for SPA
A brief tutorial on GMM based orientation refinement for SPT
Atomic model refinement - both single model and continuous movement.
Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions)
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
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)