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| == EMAN2 == EMAN2 is now stable enough to be a complete replacement for EMAN1 for most tasks. It is capable of single particle reconstructions at near-atomic resolution, and can process very large data sets (>100,000 particles). |
= EMAN2.2 = 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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| '''''Please read this [[EMAN2/DatabaseWarning|Important Warning]]''''' | 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. |
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| * [[EMAN2/Install|Installation Instructions and Tips]] | Please also note that this is '''not''' the (related) [[EMEN2]] electronic notebook, but is EMAN2, a scientific image processing suite. === Please Cite === 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 * '''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 * '''Methods for subtomogram averaging:''' * J.G. Galaz-Montoya, C.W. Hecksel, P.R. Baldwin, E. Wang, S.C. Weaver, M.F. Schmid, S.J. Ludtke & W. Chiu. (2016) Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography. J Struct Biol. 194, 383-394. PMC4846534 == Download EMAN2 == * [[EMAN2/Eman22Release|EMAN2.2 Release Notes]] * [[http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222|Download EMAN2]] (binaries) * [[https://github.com/cryoem/eman2|Download EMAN2]] (source code) == Install EMAN2 == * [[EMAN2/Install|Installation Guides]] (binary and source) * [[EMAN2/Remote|EMAN2 Remote GUI use (for clusters and remote workstations)]] == Documentation == * Tutorials * [[https://www.youtube.com/c/SteveLudtke|YouTube Tutorials]] (Archived video tutorials and mini-tutorials) * [[EMAN2/Tutorials|Tutorials]] (Full PDF tutorials with data covering many different tasks) |
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| * [[EMAN2/Tutorials|EMAN2 Tutorials (START HERE!)]] * [[EMAN2/Programs|Individual Programs]] * [[EMAN2/Concepts|Concepts and Conventions in EMAN2]] * [[EMAN2/Parallel|Parallel Computing (multiple cores, linux clusters, sets of 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/Parallel|Clusters]] (Running EMAN2 on clusters and multi-core workstations) * [[EMAN2/Gpu|GPGPU Computing]] (use the graphics processor for image processing) |
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| * [[EMAN2/Eman1Transition|EMAN1 -> EMAN2 Transition Guide]] * [[EMAN2/Obsolete|Old Docs]] (Out of date documentation) * Mailing list for EMAN2 discussions: * 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 |
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| * [[EMAN2/GitTutorials|GitHub (Transitioning from CVS to Git)]] | |
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| * [[EMAN2/FAQ|FAQ - Ask your questions here]] | * [[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 the successor to [[EMAN1|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. |
== 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. |
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| EMAN2 is now a fully usable reconstruction package, including initial parallelism support. However, it was designed so both EMAN1 and EMAN2 can be installed in the same user account with no conflicts, in case you need some EMAN1 functionality. 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. | 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. |
EMAN2.2
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 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.
Please also note that this is not the (related) EMEN2 electronic notebook, but is EMAN2, a scientific image processing suite.
Please Cite
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
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
Methods for subtomogram averaging:
J.G. Galaz-Montoya, C.W. Hecksel, P.R. Baldwin, E. Wang, S.C. Weaver, M.F. Schmid, S.J. Ludtke & W. Chiu. (2016) Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography. J Struct Biol. 194, 383-394. PMC4846534
Download EMAN2
Download EMAN2 (binaries)
Download EMAN2 (source code)
Install EMAN2
Installation Guides (binary and source)
Documentation
- Tutorials
YouTube Tutorials (Archived video tutorials and mini-tutorials)
Tutorials (Full PDF tutorials with data covering many different tasks)
- User Documentation
File Descriptions (Folders and files in an EMAN2 Project)
Standards (File Formats, Symmetry, Box Size, etc.)
Programs (Individual Program Documentation)
Clusters (Running EMAN2 on clusters and multi-core workstations)
GPGPU Computing (use the graphics processor for image processing)
Old Docs (Out of date documentation)
- Mailing list for EMAN2 discussions:
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
Advanced Users & Programmers
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.
