[3dem] NRAMM Appion 2.1

[Bridget Carragher]

The National Resource for Automated Molecular Microscopy,
Sponsored by the National Center for Research Resources,

Announces the Release of Appion 2.1

Appion[1] is a "pipeline" for processing and analysis of EM images.   
Appion is integrated with Leginon[2] 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: EMAN[3],  
Spider[4], Frealign[5], Imagic[6], XMIPP[7], IMOD[8], ProTomo[9],  
ACE[10], CTFFind and CTFTilt[11], findEM[12], DogPicker[13],  
TiltPicker[14], RMeasure5, EM-BFACTOR[15], and Chimera[16].  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://ami.scripps.edu/redmine/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://ami.scripps.edu/redmine/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 at 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://ami.scripps.edu/redmine/projects/ami/wiki/FindEM

[13] http://ami.scripps.edu/redmine/projects/ami/wiki/DoGpicker

[14] http://ami.scripps.edu/redmine/projects/ami/wiki/TiltPicker

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

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

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Bridget Carragher, Associate Professor
Automated Molecular Imaging Group, Department of Cell Biology
The Scripps Research Institute, MC CB129,10550 North Torrey Pines  
Road, La Jolla, CA 92037
tel: (858) 784-9070; fax: (858) 784-9090; bcarr at scripps.edu; http://ami.scripps.edu
National Resource for Automated Molecular Microscopy: http://nramm.scripps.edu
Office Location: Room 117,  Carr-B Building,  3215 Merryfield Row, San  
Diego, CA 92121.
Map and Directions: http://cimbio.scripps.edu/misc/building/
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