https://blake.bcm.edu/emanwiki/ 2026-04-25T12:00:38+00:00 https://blake.bcm.edu/emanwiki/ https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2026-04-24T00:13:24+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:startup&rev=1776989604&do=diff Running EMEN2 at system boot For systems that will run EMEN2 continuously, I highly recommend creating a dedicated “emen2” account. This will run EMEN2 using regular user-level permissions instead of as root. Please see your operating system documentation for creating a new account. text/html 2026-04-24T00:12:41+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:emen2ctl&rev=1776989561&do=diff EMEN2 control script (emen2ctl) Similar to Apache's “apachectl” script, EMEN2 includes an “emen2ctl” script. This can be used to start and stop the server and perform some basic administration tasks. Running emen2ctl Note: Depending on how you installed EMEN2, emen2ctl may not be in your $PATH. On Linux, using the recommended installation, it will probably be $$HOME/test.db") or by setting the $ text/html 2026-04-24T00:11:12+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:install&rev=1776989472&do=diff Installing and configuring EMEN2 EMEN2 has a number of dependencies, which are described on the dependencies page. However, because EMEN2 is often used with EMAN2, we have packaged all of the EMEN2 dependencies along with binary builds of EMAN2, which greatly simplifies installation. See the $HOME/EMAN2, you would use $ text/html 2026-04-23T23:50:07+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:backups&rev=1776988207&do=diff EMEN2 Backups An EMEN2 environment contains a number of things: BerkeleyDB files: * _db.* (environment backing files) * data/ (databases) * journal/ (transaction journal) EMEN2-managed file attachments: * binary/ (file storage) * preview/ (thumbnails and other derived data) text/html 2026-04-23T23:40:01+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:public_data_server&rev=1776987601&do=diff EMEN2 (Electron Microscopy Electronic Notebook) EMEN2 Home Page EMEN2 is an object oriented database and electronic lab notebook. It is designed to store scientific data in a freeform way without limiting the ability to search/mine the results. Unlike a traditional database, where the contents of each record type (table) must be defined by a database administrator and strictly adhered to, each individual record in EMEN2 can have arbitrary additional parameters outside the record definition, a… text/html 2026-04-23T23:38:08+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:emdash:tutorial&rev=1776987488&do=diff EMDash EMDash is an EMEN2 client program for uploading images during a microscopy session. It includes tools for session management, commenting, viewing records, uploading, and watching data directories for new files. <<TableOfContents>> This is a screenshot of an active EMDash session. Each component in the interface will be described in the following sections. text/html 2026-04-23T23:37:23+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:emdash:install&rev=1776987443&do=diff EMDash Installation EMDash can be installed using “easy_install” or you may download the source and use “setup.py” Download EMDash sources Dependencies * PyQt4 * Python bindings for Nokia's Qt toolkit * You will want to install the Qt Library using Nokia's installer package. text/html 2026-04-23T23:36:20+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:extensions&rev=1776987380&do=diff # EMEN2 Extensions # Note: More to come... The EMEN2 web interface can be extended fairly easily. First, create a directory with the following structure: <ext>/ /%%__%%init%%__%%.py /views/ /views/%%__%%init%%__%%.py /views/example.py /templates/ /templates/example/ /templates/example/example.mako text/html 2026-04-23T23:31:38+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:rpc&rev=1776987098&do=diff Accessing the EMEN2 Public API using JSON-RPC and XML-RPC All public API methods are available via JSON-RPC, which is a language-neutral Remote Procedure Call protocol based on the JSON standard. We have published a simple JSON-RPC module for Python and JavaScript (described below) that can be used with EMEN2. In the future, we plan to provide similar access via a simpler REST text/html 2026-04-23T23:30:04+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:api&rev=1776987004&do=diff EMEN2 Public API Time * time.difference * time.now Utilities * version * ping Auth * auth.login * auth.logout * auth.check.context * auth.check.admin * auth.check.readadmin * auth.check.create Generic methods text/html 2026-04-23T23:25:19+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:dependencies&rev=1776986719&do=diff EMEN2 Dependencies To run the EMEN2 server, Berkeley DB, bsddb3, and dateutil are required for basic functionality. If you want to run the web server, you will also need Twisted, Markdown, Mako, and jsonrpc. Additional server features, such as thumbnails and image analysis, are provided by EMAN2 and ImageMagick. text/html 2026-04-08T16:08:02+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:install:condainstall&rev=1775664482&do=diff EMAN2 (Binary) Installation For up-to-date binary installations you must use the instructions on this page. The old binary installation images were retired in late 2023. They are still available for historical purposes, but are no longer updated. While the installation method on this page is fine, if you text/html 2026-04-08T16:05:02+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:install:sourceinstall&rev=1775664302&do=diff Standard instructions for installing EMAN2/3 on Linux, macOS and WSL2 (Windows) ---------- While the instructions look long, in reality it should only take 10-15 minutes to complete the entire process (with a decent network connection). * We use text/html 2026-04-07T19:12:48+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2gmm&rev=1775589168&do=diff THIS PAGE IS UNDER CONSTRUCTION * TODO - indicates incomplete tutorial sections * THE e2gmm program is under active development. STRONGLY encourage using an EMAN2 snapshot or source version dated 12/2022 or later. Even with a current version you may notice some small differences in the display, etc. text/html 2026-03-25T14:24:46+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programfiles&rev=1774448686&do=diff EMAN2 Output Files This page documents all of the various files produced by various tasks and workflows in EMAN2. While the format of the actual files will be one of the standard EMAN2 supported image formats in most cases, these pages will explain the contents of files with specific standard names. text/html 2026-03-20T17:45:20+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e3make3d_point&rev=1774028720&do=diff Preview of e3make3d_point for better 3-D reconstructions THE METHOD DESCRIBED ON THIS PAGE IS NOT YET PUBLISHED, IT IS PROVIDED TO GIVE PEOPLE THE OPPORTUNITY TO TRY IT OUT AS WE MAKE FINAL IMPROVEMENTS If you have any difficulties (or successes) with this method, please let us know, and feel free to ask questions (sludtke@bcm.edu).