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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]] |
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| ''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.'' |
== Written 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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| === Video tutorials and discussions === * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]] |
* http://blake.bcm.edu/dl/eman2_tutorials_all.zip |
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| === Written Tutorials === | Alternatively, these individual data downloads cover the following standard workshop tutorial sequence: |
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| ==== Tutorial Data ==== * 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: * [[http://blake.bcm.edu/dl/eman2_tutorials_all.zip]] * This covers the following standard workshop tutorial sequence: * [[attachment:EMAN2_GUITutorial.pdf|Quick Introduction to the EMAN2 GUI]] (30 min) * [[attachment:EMAN2_FlexibilityTutorial.pdf|2-D variability analysis tutorial]] (30 min) * [[attachment:EMAN2_SingleParticleTutorial.pdf|Single particle analysis tutorial]] (3-4 hr plus some waiting) * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial (small)]] (3-4 hr plus some waiting) |
* [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]] * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]] * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] * [[http://blake.bcm.edu/dl/tutorial_tomo_mini.zip|Tomography Mini-tutorial Data Download]] |
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| ==== Short tutorials and info sheets ==== | === Short tutorials and info sheets === * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW) |
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| ==== Single particle analysis (SPA) - 2D particles ==== | === Single particle analysis (SPA) - 2D particles === |
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| * [[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) |
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| * WARNING - there seems to be a bug in EMAN2.31 so the realign and rerefine buttons do not work properly. Skip that step in the tutorial. It will be fixed in the next release. | * WARNING - there seems to be a bug in EMAN2.31 so the realign and rerefine buttons do not work properly. Skip that step in the tutorial |
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| * [[EMAN2/Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance) | * [[EMAN2/e2gmm|3-D variability analysis using GMM (Gaussian Mixture Model) and deep learning]] (requires CUDA, still under active development) |
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| ==== 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 (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. |
=== 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)) |
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| * [[http://blake.bcm.edu/dl/tutorial_tomo_mini.zip|Tomography Mini-tutorial Data Download]] | * [[http://blake.bcm.edu/dl/tutorial_tomo_small.zip|Small Data Download]] * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Data Download]] |
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| * More advanced topics for subtomogram averaging * [[EMAN2/e2tomo_more|Advanced Subtomo]] * Preview tutorial for the new version of integrated subtomogram averaging (under development) * [[EMAN2/e2tomo_new|New Subtomogram Averaging]] |
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| ==== Exchanging Data Between EMAN2 and Other Software ==== | === Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions) === |
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| === Archive of Workshop Material (Lectures, specific tutorials, etc. === | == Archive of Workshop Material (Lectures, specific tutorials, etc. == |
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
Written 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)
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)
2-D variability analysis tutorial
- WARNING - there seems to be a bug in EMAN2.31 so the realign and rerefine buttons do not work properly. Skip that step in the tutorial
3-D variability analysis using GMM (Gaussian Mixture Model) and deep learning (requires CUDA, still under active development)
- 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
- Preview tutorial for the new version of integrated subtomogram averaging (under development)
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)