= EMAN2.99.47 = 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 == * [[EMAN2/Eman22Release|EMAN2 Release Notes]] * Binary Installations * [[EMAN2/Install/BinaryInstallAnaconda/2.99|v2.99.47 (latest)]] * [[EMAN2/Install/BinaryInstallAnaconda/2.91|v2.91]] * [[EMAN2/Install/BinaryInstallAnaconda/ContinuousBuild|Continuous Build]] * [[EMAN2/Install/BinaryInstallAnaconda|Older versions]] * [[EMAN2/Install/SourceInstall|Build from source (Linux/OSX/WSL2)]] * [[EMAN2/Install|Legacy instructions for older EMAN2 releases]] * [[EMAN2/Parallel|Parallel computing in EMAN2]] (threads and MPI) * [[EMAN2/Remote|EMAN2 Remote GUI setup/use (for clusters and remote workstations)]] * [[EMAN2/FAQ/Computer|What sort of computer should I buy?]] * Direct Download (PLEASE READ INSTRUCTIONS): * [[http://cryoem.bcm.edu/cryoem/downloads/view_eman2_versions|EMAN2 binaries]] * [[http://github.com/cryoem/eman2|EMAN2 source code]] == Tutorials == * [[EMAN2/Tutorials|Standard Tutorials]] Detailed tutorials on specific tasks, like single particle reconstruction or subtomogram averaging. Start here! * [[EMAN2/VideoTutorials|Tutorial Videos]] It is impossible to provide complete details in a video format, but these are excellent supplements to the standard tutorials above. * [[EMAN2/AdvancedTutorials|Advanced Tutorials]] A mix of tutorials and discussions on more advanced topics, like specialized projects and using EMAN2 from Python * [[EMAN2/OtherTutorials|Related Topics]] Tutorials on related topics, such as FFTs, etc. == 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.) * [[https://blake.bcm.edu/doxygen/programs_help_html/|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.bcm.edu/doxygen/classEMAN_1_1EMData.html|Direct link to docs for EMData (image) class]] * [[http://blake.bcm.edu/doxygen/classEMAN_1_1Transform.html|Direct link to docs for Transform (orientation/Euler angle) class]] == 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}}