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| eman2:tutorials [2025/06/24 01:20] – [Archive of Workshop Material (Lectures, specific tutorials, etc.] steveludtke | eman2:tutorials [2025/08/04 16:52] (current) – steveludtke |
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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: | 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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| * http://blake.bcm.edu/dl/eman2_tutorials_all.zip | * https://blake.bcm.edu/dl/eman2_tutorials_all.zip |
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| Alternatively, these individual data downloads cover the following standard workshop tutorial sequence: | Alternatively, these individual data downloads cover the following standard workshop tutorial sequence: |
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| * [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]] | * [[https://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)]] | * [[https://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)]] | * [[https://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]] | * [[https://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]] | * [[https://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]] |
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| ==== Short tutorials and info sheets ==== | ==== Short tutorials and info sheets ==== |
| * [[EMAN2:Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022) | * [[EMAN2:Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022) |
| * [[EMAN2:NegativeStain]] - special issues that impact processing negative stain single particle images | * [[EMAN2:NegativeStain]] - special issues that impact processing negative stain single particle images |
| * [[http://blake.bcm.edu/dl/EMAN2/image_info.pdf|Information about images]] | * [[https://blake.bcm.edu/dl/EMAN2/image_info.pdf|Information about images]] |
| * [[http://blake.bcm.edu/dl/EMAN2/image_proc.pdf|Filtering and basic image processing]] | * [[https://blake.bcm.edu/dl/EMAN2/image_proc.pdf|Filtering and basic image processing]] |
| * [[http://blake.bcm.edu/dl/EMAN2/ctf_sim.pdf|CTF Simulator]] | * [[https://blake.bcm.edu/dl/EMAN2/ctf_sim.pdf|CTF Simulator]] |
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| ==== Single particle analysis (SPA) - 2D particles ==== | ==== Single particle analysis (SPA) - 2D particles ==== |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2_GUITutorial.pdf|Quick Introduction to the EMAN2 GUI]] (Start here if you have never used EMAN2!) | * [[https://blake.bcm.edu/dl/EMAN2/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]] | * [[https://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]] |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2_SingleParticleTutorial.pdf|Single particle analysis tutorial]] | * [[https://blake.bcm.edu/dl/EMAN2/EMAN2_SingleParticleTutorial.pdf|Single particle analysis tutorial]] |
| * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] | * [[https://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2_boxer_tutorial_2021_04.pdf|Particle picking tutorial (basic tutorial only)]] | * [[https://blake.bcm.edu/dl/EMAN2/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) | * [[EMAN2:Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance) |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2_FlexibilityTutorial.pdf|2-D variability analysis tutorial]] | * [[https://blake.bcm.edu/dl/EMAN2/EMAN2_FlexibilityTutorial.pdf|2-D variability analysis tutorial]] |
| * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]] | * [[https://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 | * 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 | * [[EMAN2:Eman1Transition|EMAN1 to EMAN2 Transition Guide]] - Also with useful quickstart guides for users of other software |
| * Complete workflow for tomography and subtomogram averaging (includes both small version (laptop ~12 Å) and large version (subnanometer on workstation)) | * 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]] | * [[EMAN2:e2TomoSmall|Tomography and Subtomogram Averaging Tutorial]] |
| * [[http://blake.bcm.edu/dl/tutorial_tomo_small.zip|Small Data Download]] | * [[https://blake.bcm.edu/dl/tutorial_tomo_small.zip|Small Data Download]] |
| * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Data Download]] | * [[https://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Data Download]] |
| * Automated Cellular Tomogram Annotation using Neural Networks | * Automated Cellular Tomogram Annotation using Neural Networks |
| * [[EMAN2:Programs:e2tomoseg|Tomogram Annotation]] | * [[EMAN2:Programs:e2tomoseg|Tomogram Annotation]] |
| * [[UTMBWorkshop2019|2019 May UTMB Workshop]] (full site with talks) | * [[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]] | * [[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]] | * [[https://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]] | * [[https://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]] |
| * 2019 January Tutorial for EMAN2.22 | * 2019 January Tutorial for EMAN2.22 |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-22Tutorial.pdf|PDF] (version 1) | * [[https://blake.bcm.edu/dl/EMAN2/EMAN2-22Tutorial.pdf|PDF] (version 1) |
| * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] | * [[https://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] |
| * 2018 May Tutorial for EMAN2.21a | * 2018 May Tutorial for EMAN2.21a |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-21Tutorial.pdf|PDF]] (version 1) | * [[https://blake.bcm.edu/dl/EMAN2/EMAN2-21Tutorial.pdf|PDF]] (version 1) |
| * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] | * [[https://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] |
| * 2017 February Tutorial for EMAN2.2 | * 2017 February Tutorial for EMAN2.2 |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-2Tutorial.pdf|PDF]] | * [[https://blake.bcm.edu/dl/EMAN2/EMAN2-2Tutorial.pdf|PDF]] |
| * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] | * [[https://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] |
| * 2016 Summer Tutorial for EMAN2.12 June 2016 snapshots | * 2016 Summer Tutorial for EMAN2.12 June 2016 snapshots |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-13_pre_Tutorial.pdf|PDF]] | * [[https://blake.bcm.edu/dl/EMAN2/EMAN2-13_pre_Tutorial.pdf|PDF]] |
| * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] | * [[https://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]] |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-13_pre_Heterogeneity.pdf|PDF]] | * [[https://blake.bcm.edu/dl/EMAN2/EMAN2-13_pre_Heterogeneity.pdf|PDF]] |
| * see also: http://www.sciencedirect.com/science/article/pii/S0076687916300362 | * see also: https://www.sciencedirect.com/science/article/pii/S0076687916300362 |
| * 2015 Fall Tutorial for EMAN2.12 | * 2015 Fall Tutorial for EMAN2.12 |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-12_Tutorial.pdf|PDF]] | * [[https://blake.bcm.edu/dl/EMAN2/EMAN2-12_Tutorial.pdf|PDF]] |
| * Required data - [[http://blake.bcm.edu/dl/EMAN2/Bgal.zip]] | * Required data - [[https://blake.bcm.edu/dl/EMAN2/Bgal.zip]] |
| * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-12_Tutorial2_heterogeneity.pdf|PDF]] | * [[https://blake.bcm.edu/dl/EMAN2/EMAN2-12_Tutorial2_heterogeneity.pdf|PDF]] |
| * Required data - [[http://blake.bcm.edu/dl/EMAN2/ribosome.zip]] | * Required data - [[https://blake.bcm.edu/dl/EMAN2/ribosome.zip]] |
| * [[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. | * [[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. | * [[SPT/Spt|Single particle tomography]] - Tutorial for deprecated Single particle tomography (SPT) workflow. |
| * [[Ws2012/EMAN2|Tutorial from the 2012 Workshop in Singapore (Data on same page)]] - Based on EMAN2.06. 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 | * [[Ws2011/Eman2|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 ( - [[http://blake.bcm.edu/dl/EMAN2/workflow_tutorial_2010_08_25.pdf|Full tutorial on single particle reconstruction using the workflow]] (uses [[http://blake.grid.bcm.edu/dl/data/workshop5.iso|Workshop demo data DVD]]) | * Single particle reconstruction tutorial from 2008 Workshop ( - [[https://blake.bcm.edu/dl/EMAN2/workflow_tutorial_2010_08_25.pdf|Full tutorial on single particle reconstruction using the workflow]] (uses [[https://blake.grid.bcm.edu/dl/data/workshop5.iso|Workshop demo data DVD]]) |
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