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eman2:tutorials [2025/06/14 18:47] – steveludtkeeman2:tutorials [2025/06/24 01:20] (current) – [Archive of Workshop Material (Lectures, specific tutorials, etc.] steveludtke
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     * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Data Download]]     * [[http://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:tomoseg|Tomogram Annotation]]+    * [[EMAN2:Programs:e2tomoseg|Tomogram Annotation]]
   * More advanced topics for subtomogram averaging   * More advanced topics for subtomogram averaging
     * [[EMAN2:e2tomo_p22|Advanced SPT methods]] - Latest (2023) workflow for in situ SPT.     * [[EMAN2:e2tomo_p22|Advanced SPT methods]] - Latest (2023) workflow for in situ SPT.
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 ==== Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions) ==== ==== Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions) ====
-  * [[EMAN2:Programs/e2refinetorelion2d/e2refinetorelion2dtutorial|2D Class Averaging with Relion]] +  * [[EMAN2:Programs:e2refinetorelion2d:tutorial|2D Class Averaging with Relion]] 
-  * [[EMAN2:Programs/e2refinetorelion3d/e2refinetorelion3dtutorial|3D Refinement with Relion]] +  * [[EMAN2:Programs:e2refinetorelion3d:tutorial|3D Refinement with Relion]] 
-  * [[EMAN2:Programs/e2refinetofrealign/e2refinetofrealigntutorial|3D Refinement with FreAlign]]+  * [[EMAN2:Programs:e2refinetofrealign:tutorial|3D Refinement with FreAlign]]
  
 ===== Archive of Workshop Material (Lectures, specific tutorials, etc. ===== ===== Archive of Workshop Material (Lectures, specific tutorials, etc. =====
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     * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]     * [[http://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||&do=get]] (version 1)+    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-22Tutorial.pdf|PDF] (version 1)
       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]       * [[http://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||&do=get]] (version 1)+    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-21Tutorial.pdf|PDF]] (version 1)
       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]       * [[http://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||&do=get]]+    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-2Tutorial.pdf|PDF]]
       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]       * [[http://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||&do=get]]+    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-13_pre_Tutorial.pdf|PDF]]
       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
-    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-13_pre_Heterogeneity.pdf||&do=get]]+    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-13_pre_Heterogeneity.pdf|PDF]]
     * see also: http://www.sciencedirect.com/science/article/pii/S0076687916300362     * see also: http://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||&do=get]] +    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-12_Tutorial.pdf|PDF]] 
-    * Required data - [[http://blake.bcm.edu/dl/EMAN2/Bgal.zip||&do=get]] +    * Required data - [[http://blake.bcm.edu/dl/EMAN2/Bgal.zip]] 
-    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-12_Tutorial2_heterogeneity.pdf||&do=get]] +    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-12_Tutorial2_heterogeneity.pdf|PDF]] 
-    * Required data - [[http://blake.bcm.edu/dl/EMAN2/ribosome.zip||&do=get]]+    * Required data - [[http://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.
eman2/tutorials.1749926825.txt.gz · Last modified: by steveludtke