Appion

Leginon¹ is a system designed for automated collection of images from a transmission electron microscope. Appion² is integrated with Leginon as a "pipeline" for processing and analysis of EM images. The 3.0 release of these packages includes major changes in two areas. First, many aspects of the software have been updated to run on newer operating systems. The officaial target operating system is now CentOS 6. Second, Leginon and Appion have expanded support for the newest generation of cameras. In addition to the previously supported Direct Electron DE12, Leginon now supports data acquisition using the Gatan K2 Summit and FEI Falcon direct detectors. Movies acquired by the K2 or DE direct electron detectors are passed to Appion, which handles frame alignments; the user can select which frames are used in the rest of the Appion pipeline.

More information regarding new features are available at the Leginon Change Log and the Appion Change Log.

Leginon and Appion are open source software packages released under the Apache License, Version 2.0, and are available for download at: http://leginon.org and http://appion.org. Instructions are also available for upgrading existing installations of Leginon and Appion to the current 3.0 release.

If you download Leginon and/or Appion we strongly encourage you to register as a Leginon/Appion user at: http://emg.nysbc.org/account/register. This will allow us to keep you informed of new releases, bug fixes, and other useful information, and also allow us to keep track of the user base which is important to ensure future support of the software.

Questions or comments? Contact us at amisoftware@scripps.edu.

[1] http://leginon.org

[2] http://appion.org

Appion¹ is a "pipeline" for processing and analysis of EM images. Appion is integrated with Leginon² data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs), or particle stacks, using tools provided as part of the package. Appion consists of a web based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output and communication between packages is managed using tightly integrated SQL databases. The goal is to have all control of the processing pipeline managed from a web based user interface and all output from the processing presented using web based viewing tools.

Appion provides wrappers for a variety of software including: EMAN³, Spider⁴, Frealign⁵, Imagic⁶, XMIPP⁷, IMOD⁸, ProTomo⁹, ACE¹⁰, CTFFind and CTFTilt¹¹, findEM¹², DogPicker¹³, TiltPicker¹⁴, RMeasure5, EM-BFACTOR¹⁵, and Chimera¹⁶. These packages are not part of the distribution and must be downloaded separately under their own license agreements. These packages must also be acknowledged by appropriate citations when used within Appion. Appropriate citations are provided on the individual pages in Appion as well as at: http://emg.nysbc.org/projects/appion/wiki/Appion_citations

Appion is open source software released under the Apache License, Version 2.0, and is available for download at: http://appion.org.

If you download Appion we strongly encourage you to register as an Appion user at: http://emg.nysbc.org/account/register. This will allow us to keep you informed of new releases, bug fixes, and other useful information, and also allow us to keep track of the user base which is important to ensure future support of the software.

Please contact us at appion@scripps.edu to report any errors or omissions.

[1] http://appion.org

[2] http://leginon.org

[3] http://blake.bcm.edu/eman

[4] http://www.wadsworth.org/spider_doc/spider/docs/spider.html

[5] http://emlab.rose2.brandeis.edu/

[6] http://imagescience.de/imagic/

[7] http://xmipp.cnb.csic.es/

[8] http://bio3d.colorado.edu/imod/

[9] http://www.electrontomography.org/

[10] http://nramm.scripps.edu/software/ace/

[11] http://emlab.rose2.brandeis.edu/

[12] http://emg.nysbc.org/projects/ami/wiki/FindEM

[13] http://emg.nysbc.org/projects/ami/wiki/DoGpicker

[14] http://emg.nysbc.org/projects/ami/wiki/TiltPicker

[15] http://www.ual.es/~jjfdez/SW/embfactor.html

[16] http://www.cgl.ucsf.edu/chimera