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== EMAN2 alpha == = EMAN2.91 =
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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Note that EMAN2 is still in alpha-testing. It can do some useful things, but is not completely stable yet. 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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 * [wiki:/Install Installation Instructions and Tips]
 * [wiki:/Programs Individual Program Documentation]
 * [wiki:/Library Python/C++ Library Documentation]
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 ==
 * 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)

== Documentation ==
 * [[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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==== About EMAN2 ====
EMAN2 is not (yet) a replacement for EMAN1, but can enhance EMAN1's capabilities.
It was designed so both 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 knowledgable
end-users to customize any of the code with unprecendented ease. If you aren't an advanced
user, you can still make use of all of EMAN2's command-line programs, all of which start
with 'e2'. 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.
== 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.

{{attachment:idea_5_c.png}}

EMAN2.91

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.

idea_5_c.png

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