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start [2025/06/14 16:34] – created steveludtkestart [2025/08/07 12:17] (current) – steveludtke
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-====== EMAN2.99.47 ======+====== Ludtke Lab - Baylor College of Medicine ====== 
 +This is the main webserver for the Ludtke Lab. It documents several NIH supported projects, provides educational materials and has a range of historical resources, including some from the National Center for Macromolecular Imaging, a NIGMS P41 center which was at BCM for ~30 years.
  
-**//The EMAN2 wiki was undergoing a massive hacker attack, and we were forced to update to a newer Wiki system, we are still in the process of transitioning all of the pages, so past links may not work properly, and some current links may be broken while we update.//**+Note that the server was moved to a new system in July 2025, and some pages may not have migrated perfectly. If you find something you need is missing, please email sludtke_at_bcm.edu.
  
-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.+=== Projects === 
 +  * EMAN3 Documentation - coming soon 
 +  * [[eman2|EMAN2 Documentation]] 
 +  * [[eman1|EMAN1 Documentation/Downloads - Historical]] 
 +  * [[emen|EMEN Documentation]] 
  
-EMAN2 is a broadly based scientific image processing suite (largely greyscale) 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.+=== Historical Workshops === 
 +While software details may be dated, there is a lot of solid CryoEM theory information here  
 +  * [[ws2011|2011 NCMI Workshop]] 
 +  * [[ws2012|2012 NCMI Workshop]] 
 +  * [[ws2013|2013 NCMI Workshop]] 
 +  * [[ws2015|2015 NCMI Workshop]]
  
-Please also note that this is '''not''' the (related) [[EMEN2]] electronic notebook, but is EMAN2, a scientific image processing suite. +=== Introduction to Programming in Python === 
- +Historical course material for the course I've taught at BCM for the last 15+ years. After 2018 the material moved to BlackBoard which is internally available only. 
-===== Please Cite (and read) ===== +  * [[intro_programming:ip2011|2011]] 
-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: +  * [[intro_programming:ip2012|2012]] 
- +  * [[intro_programming:ip2013|2013]] 
-  * '''Primary EMAN2 paper:''' +  * [[intro_programming:ip2014|2014]] 
-    * 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 +  * [[intro_programming:ip2015|2015]] 
-  * '''Subnanometer resolution subtomogram averaging using PPPT methods:''' +  * [[intro_programming:ip2016|2016]] 
-    * 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 +  * [[intro_programming:ip2017|2017]] 
-  * '''Neural Network Based Tomogram Segmentation''' +  * [[intro_programming:ip2018|2018]]
-    * 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]] +
-  * [[EMAN2/Install/SourceInstall|Build from source (Linux/OSX/WSL2)]] (strongly suggested, may be easier than binary installs now) +
-  * Binary Installations (please use a Current Build) +
-     * [[EMAN2/Install/CondaInstall|Current Build]] {{https://anaconda.org/cryoem/eman-dev/badges/version.svg}} {{https://anaconda.org/cryoem/eman-dev/badges/latest_release_date.svg}}  +
-     * [[EMAN2/Install/BinaryInstallAnaconda/2.99|v2.99.47]] +
-     * [[EMAN2/Install/BinaryInstallAnaconda/2.91|v2.91]] +
-     * [[EMAN2/Install/BinaryInstallAnaconda|Older versions]] +
-  * [[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.+
  
 +=== Orphan Pages ===
 +[[Orphans]]
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