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= EMAN2.1 =
EMAN2 is the successor to [[EMAN1]]. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing very large data sets (>100,000 particle) very efficiently (up to 20x faster than EMAN1).
= EMAN2.9 =
Most of the pages are editable by any user that has registered an account on the server. To prevent spam, you need to email sludtke@bcm.edu to get an account on the system if you wish to contribute changes. If you just wish to browse, you don't need an account.
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EMAN2.1 has now been officially released!
 * Much easier to use, but flexibility still available
 * True "gold standard" refinements with automatic filtration
 * BDB is gone!
EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing large data sets (>100,000 particle) very efficiently.
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'''''UNDER (RE)CONSTRUCTION''''' - Note that the current website contains a bit of a mix of 2.0X and 2.1 information. We are gradually updating things to 2.1 as time goes on. If you find something confusing or self-contradictory, please let us know or ask about it. === Please Cite (and read) ===
EMAN is free software, supported by NIH Grants. It is critical that you cite EMAN2 when you use it in a publication in any significant way, to help us document usage when trying to renew our funding. Feel free to cite any of these:
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== Download EMAN2 ==
 * [[EMAN2/Eman21Release|IMPORTANT notice about EMAN2.1]]
 * [[http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222|Main EMAN2 Download Page]]
 * Please note that nightly snapshots have been temporarily disabled for the last two weeks of December 2015, as part of the GitHub conversion.
 * '''Primary EMAN2 paper:'''
  * G. Tang, L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees & S.J. Ludtke. (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol. 157, 38-46. PMID: 16859925
 * '''Subnanometer resolution subtomogram averaging using PPPT methods:'''
  * Chen M, Bell JM, Shi X, Sun SY, Wang Z, Ludtke SJ. Nat Methods. (2019) A complete data processing workflow for cryo-ET and subtomogram averaging, Nat. Methods, 16(11):1161-1168, PMC31611690
 * '''Neural Network Based Tomogram Segmentation'''
  * Chen M, Dai W, Sun SY, Jonasch D, He CY, Schmid MF, et al. (2017). Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Nat. Methods, 14(10), 983–5. PMCID: PMC5623144
 * '''Neural Network Particle Picker'''
  * Bell JM, Chen M, Durmaz T, Fluty AC, Ludtke SJ. (2018). New software tools in EMAN2 inspired by EMDatabank map challenge. J. Struct. Biol. Elsevier;, 204(2), 283–90.
 * '''EMAN2 high resolution refinement methods:'''
  * J.M. Bell, M. Chen, P.R. Baldwin & S.J. Ludtke. (2016) High Resolution Single Particle Refinement in EMAN2.1. Methods. 100, 25-34. PMC4848122
 * '''Methods for analysis of conformational and compositional variability:'''
  * Ludtke, S. J. "Single-Particle Refinement and Variability Analysis in EMAN2.1." in Methods Enzymol 579159-189 (Elsevier, United States, 2016). PMC5101015
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 * [[EMAN2/Install|Installation Instructions and Tips]]
 * Please check this [[EMAN2/ChangeLog|CHANGELOG]] after upgrading to a new version
 * Download (PLEASE READ INSTRUCTIONS):
  * [[http://cryoem.bcm.edu/cryoem/downloads/view_eman2_versions|EMAN2 binaries]]
  * [[http://github.com/cryoem/eman2|EMAN2 source code]]
 * [[EMAN2/Eman22Release|EMAN2 Release Notes]]
 * [[EMAN2/Install/BinaryInstallAnaconda/2.91|Binary Installation 2.91]]
 * [[EMAN2/COMPILE_EMAN2_ANACONDA|Source Installation (Linux and OSX)]]
 * [[EMAN2/Install|Installation Details and Guides, including earlier versions]]
 * [[EMAN2/Remote|EMAN2 Remote GUI setup/use (for clusters and remote workstations)]]
 * [[EMAN2/FAQ/Computer|What sort of computer should I buy?]]

== Tutorials ==
 * [[EMAN2/Tutorials|Tutorials]] (Full PDF tutorials with data covering many different tasks)
 * [[https://www.youtube.com/c/SteveLudtke|YouTube Tutorials]] (Archived video tutorials and mini-tutorials)
 * [[EMAN2/AdvancedTutorials|Advanced Tutorials]] (A few simple Python-level tutorials for programmers and Power Users)
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 * Upcoming Live Tutorials
  * None currently scheduled
  * See the archived tutorials: [[https://www.youtube.com/c/SteveLudtke]]
 * User Documentation
  * [[EMAN2/Eman1Transition|EMAN1 -> EMAN2 Transition Guide]]
  * [[EMAN2/Tutorials|EMAN2 Tutorials (START HERE!)]]
  * [[EMAN2/DirectoryStructure|Standard Folders in an EMAN2 Project]]
  * [[EMAN2/Concepts|File Formats, Image Processing Functions, Mathematical Conventions]]
  * [[EMAN2/Programs|Individual Program Documentation]]
  * [[EMAN2/ProgramFiles|Output file descriptions and details]]
  * [[EMAN2/Parallel|Parallel Computing (multiple cores, linux clusters, sets of workstations)]]
  * [[EMAN2/Gpu|GPGPU Computing (use the graphics processor for image processing)]]
  * [[EMAN2/Galleries|Galleries]]
  * [[EMAN2/Obsolete|Obsolete Pages]]
 * Advanced Users & Programmers
  * [[EMAN2/Library|Python/C++ Programmers Documentation]]
  * [[http://blake.grid.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|Direct link to docs for EMData (image) class]]
  * [[http://blake.grid.bcm.edu/eman2/doxygen_html/classEMAN_1_1Transform.html|Direct link to docs for Transform (orientation/Euler angle) class]]
  * [[EMAN2/GitTutorials|Transitioning from CVS to Git (under construction)]]
 * [[EMAN2/FAQ|FAQ]] - Please ask your questions in the Google Group, answers to common questions will be posted here as well as in the Group
 * Mailing list for EMAN2 discussions:
  * http://groups.google.com/group/eman2
  * eman2@googlegroups.com (must join the group before you can post)
  * http://groups.google.com/group/eman2-developers (This is the group for discussions among developers, likely less interesting for users)
 * [[EMAN2/Important|Things You Need to Know / FAQ]]
 * [[EMAN2/Remote|EMAN2 Remote GUI setup/use (for clusters and remote workstations)]]
 * [[EMAN2/Parallel|Clusters]] (Running EMAN2 on clusters and multi-core workstations)
 * [[EMAN2/DirectoryStructure|File Descriptions]] (Folders and files in an EMAN2 Project)
 * [[EMAN2/Concepts|Standards]] (File Formats, Symmetry, Box Size, etc.)
 * [[EMAN2/Programs|Programs]] (Individual Program Documentation)
 * [[EMAN2/Gpu|GPGPU Computing]] (use the graphics processor for image processing)
 * [[EMAN2/Galleries|Galleries]]
 * [[EMAN2/Eman1Transition|EMAN1 -> EMAN2 Transition Guide]]
 * [[EMAN2/Obsolete|Old Docs]] (Out of date documentation)

== Ask For Help ==
We prefer to provide assistance via the Google group below, since this archives all discussions and makes them searchable. You must join the group to post, but can browse/search old content anonymously.
 * http://groups.google.com/group/eman2 (Main discussion list for EMAN2)
 * http://groups.google.com/group/eman2-developers (Discussions among developers, likely less interesting for users)
 * [[EMAN2/FAQ|FAQ]] - Please ask your questions in the Google Group which has a searchable archive. This page is somewhat out of date
 * NOTE - If you are located in a country that blocks Google (China) or prefer not to post publicly, please feel free to email sludtke@bcm.edu directly. The Google Group is used because it creates a persistent searchable archive of past questions, but direct emails are completely acceptable.

== Advanced Users & Programmers (Python) ==
 * [[EMAN2/Library|Python/C++ Programmers Documentation]]
 * [[http://blake.grid.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|Direct link to docs for EMData (image) class]]
 * [[http://blake.grid.bcm.edu/eman2/doxygen_html/classEMAN_1_1Transform.html|Direct link to docs for Transform (orientation/Euler angle) class]]
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EMAN2 is now a fully usable reconstruction package, including parallelism support. However, in case you aren't ready to abandon EMAN1 yet, EMAN1 and EMAN2 can be installed in the same user account with no conflicts. All EMAN2 programs, including GUI programs, are written in the easy-to-learn Python scripting language. This permits knowledgeable end-users to customize any of the code with unprecedented ease. If you aren't an advanced user, you can still make use of the integrated GUI and all of EMAN2's command-line programs. Any programs in EMAN2 with an EMAN1 equivalent are likely substantially improved over their EMAN1 equivalents. For example e2pdb2mrc.py is ~10x faster than the EMAN1 pdb2mrc. 3-D refinements are typically 5-25x faster than in EMAN1 (with the correct options). All EMAN2 programs, including GUI programs, are written in the easy-to-learn Python scripting language. This permits knowledgeable end-users to customize any of the code with unprecedented ease. If you aren't an advanced user, you can still make use of the integrated GUI and all of EMAN2's command-line programs.

EMAN2.9

Most of the pages are editable by any user that has registered an account on the server. To prevent spam, you need to email sludtke@bcm.edu to get an account on the system if you wish to contribute changes. If you just wish to browse, you don't need an account.

EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing large data sets (>100,000 particle) very efficiently.

Please also note that this is not the (related) EMEN2 electronic notebook, but is EMAN2, a scientific image processing suite.

Please Cite (and read)

EMAN is free software, supported by NIH Grants. It is critical that you cite EMAN2 when you use it in a publication in any significant way, to help us document usage when trying to renew our funding. Feel free to cite any of these:

  • Primary EMAN2 paper:

    • G. Tang, L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees & S.J. Ludtke. (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol. 157, 38-46. PMID: 16859925

  • Subnanometer resolution subtomogram averaging using PPPT methods:

    • Chen M, Bell JM, Shi X, Sun SY, Wang Z, Ludtke SJ. Nat Methods. (2019) A complete data processing workflow for cryo-ET and subtomogram averaging, Nat. Methods, 16(11):1161-1168, PMC31611690
  • Neural Network Based Tomogram Segmentation

    • Chen M, Dai W, Sun SY, Jonasch D, He CY, Schmid MF, et al. (2017). Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Nat. Methods, 14(10), 983–5. PMCID: PMC5623144
  • Neural Network Particle Picker

    • Bell JM, Chen M, Durmaz T, Fluty AC, Ludtke SJ. (2018). New software tools in EMAN2 inspired by EMDatabank map challenge. J. Struct. Biol. Elsevier;, 204(2), 283–90.
  • EMAN2 high resolution refinement methods:

    • J.M. Bell, M. Chen, P.R. Baldwin & S.J. Ludtke. (2016) High Resolution Single Particle Refinement in EMAN2.1. Methods. 100, 25-34. PMC4848122

  • Methods for analysis of conformational and compositional variability:

    • Ludtke, S. J. "Single-Particle Refinement and Variability Analysis in EMAN2.1." in Methods Enzymol 579159-189 (Elsevier, United States, 2016). PMC5101015

Install EMAN2

Tutorials

  • Tutorials (Full PDF tutorials with data covering many different tasks)

  • YouTube Tutorials (Archived video tutorials and mini-tutorials)

  • Advanced Tutorials (A few simple Python-level tutorials for programmers and Power Users)

Documentation

Ask For Help

We prefer to provide assistance via the Google group below, since this archives all discussions and makes them searchable. You must join the group to post, but can browse/search old content anonymously.

  • http://groups.google.com/group/eman2 (Main discussion list for EMAN2)

  • http://groups.google.com/group/eman2-developers (Discussions among developers, likely less interesting for users)

  • FAQ - Please ask your questions in the Google Group which has a searchable archive. This page is somewhat out of date

  • NOTE - If you are located in a country that blocks Google (China) or prefer not to post publicly, please feel free to email sludtke@bcm.edu directly. The Google Group is used because it creates a persistent searchable archive of past questions, but direct emails are completely acceptable.

Advanced Users & Programmers (Python)

About EMAN2

EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. Image processing in a suite like EMAN differs from consumer image processing packages like Photoshop in that pixels in images are represented as floating-point numbers rather than small (8-16 bit) integers. In addition, image compression is avoided entirely, and there is a focus on quantitative analysis rather than qualitative image display.

All EMAN2 programs, including GUI programs, are written in the easy-to-learn Python scripting language. This permits knowledgeable end-users to customize any of the code with unprecedented ease. If you aren't an advanced user, you can still make use of the integrated GUI and all of EMAN2's command-line programs.

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EMAN2 (last edited 2021-04-21 18:14:49 by SteveLudtke)