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| == EMAN2 alpha == Note that EMAN2 is still in alpha-testing. It can do some useful things, but is not completely stable yet. |
= EMAN2 = |
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| Also note that this Wiki has just (1/2007) been started, and doesn't contain much yet. | 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. EMAN2 is capable of processing very large data sets (>100,000 particle) very efficiently (up to 20x faster than EMAN1). |
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| * [:EMAN2/Install:Installation Instructions and Tips] * [:EMAN2/Programs:Individual Program Documentation] * [:EMAN2/Library:Python/C++ Programmers Documentation] * [:EMAN2/Bugs:Report a Bug] |
Please also note that this is NOT the (related) [[EMEN2]] electronic notebook, but is EMAN2, a scientific image processing suite. |
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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. |
'''Note for EMAN1 users - ''' If you are still using EMAN1 due to some missing functionality in EMAN2, please email sludtke@bcm.edu or post a message on the Google group telling what you are still doing in EMAN1. We will either explain how to do it in EMAN2, or add it to the list of projects. Please also note that there is an EMAN1->EMAN2 transition guide available below. Thanks ! = Download EMAN2 = * [[http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222|Main EMAN2 Download Page]] * [[http://ncmi.bcm.edu/ncmi/software/counter_222/software_86|Nightly builds - direct link]] (<-- We normally suggest using this version, which is updated every night) * [[http://ncmi.bcm.edu/ncmi/software/counter_222/software_120|Last stable version - direct link]] = Install EMAN2 = * [[EMAN2/Install|Installation Instructions and Tips]] * Please check this [[EMAN2/ChangeLog|CHANGELOG]] after upgrading to a new version * '''''Please read this [[EMAN2/DatabaseWarning|Important Warning]]''''' = Documentation = * User Documentation * [[EMAN2/Eman1Transition|EMAN1 -> EMAN2 Transition Guide]] * [[EMAN2/Tutorials|EMAN2 Tutorials (START HERE!)]] * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]] * [[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]] * Advanced Users & Programmers * [[EMAN2/Library|Python/C++ Programmers Documentation]] * [[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|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
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).
Please also note that this is NOT the (related) EMEN2 electronic notebook, but is EMAN2, a scientific image processing suite.
Note for EMAN1 users - If you are still using EMAN1 due to some missing functionality in EMAN2, please email sludtke@bcm.edu or post a message on the Google group telling what you are still doing in EMAN1. We will either explain how to do it in EMAN2, or add it to the list of projects. Please also note that there is an EMAN1->EMAN2 transition guide available below. Thanks !
Download EMAN2
Nightly builds - direct link (<-- We normally suggest using this version, which is updated every night)
Install EMAN2
Please check this CHANGELOG after upgrading to a new version
Please read this Important Warning
Documentation
- User Documentation
Advanced Users & Programmers
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:
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).
