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Revision 117 as of 2016-01-28 22:55:59
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== EMAN2 alpha == = 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).
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Note that EMAN2 is still in alpha-testing. It can do some useful things, but is not completely stable yet. EMAN2.1 has now been officially released!
 * Much easier to use, but flexibility still available
 * True "gold standard" refinements with automatic filtration
 * BDB is gone!
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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.
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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.
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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.
== 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]]

== Install EMAN2 ==
 * [[EMAN2/Install|Installation Instructions and Tips]]
 * Please check this [[EMAN2/ChangeLog|CHANGELOG]] after upgrading to a new version

== Documentation ==
 * 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)

== 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.

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).

{{attachment:idea_5_c.png}}

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).

EMAN2.1 has now been officially released!

  • Much easier to use, but flexibility still available
  • True "gold standard" refinements with automatic filtration
  • BDB is gone!

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

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.

Download EMAN2

Install EMAN2

Documentation

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.

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).

idea_5_c.png

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