Electron Microscopy Group

Leginon 3.6 release. Smart Leginon Autoscreen is the main new feature as described in https://doi.org/10.1101/2022.07.23.501225. EER format support is included, too.

More information regarding new user features in Leginon is here and same for Appion is here.

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 3.5 release.

If you download Leginon and/or Appion we strongly encourage you to register as a Leginon/Appion user at: https://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.

[1] http://leginon.org

[2] http://appion.org

Leginon [1] and Appion [2] V3.5 release. Updates include general speed up, microED, and support for TFS Falcon4 frame saving in MRC format. All features mentioned in http://dx.doi.org/10.1002/pro.3967 are included. Minor features affecting the user have also been added.

More information regarding new user features in Leginon is here and same for Appion is here.

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 3.4 release.

If you download Leginon and/or Appion we strongly encourage you to register as a Leginon/Appion user at: https://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.

[1] http://leginon.org

[2] http://appion.org

Leginon [1] and Appion [2] V3.4 release. Updates include support for TFS Falcon3 frame saving and handling and K3. The K2/K3 data collection and Appion frame transfer and frame alignment are now fully compatible with TIFF LZW compression. Evaluation of the improvement and calibration procedure for lens aberration correction of beam shift-image shift targeting are added. Minor features affecting the user have also been added.

More information regarding new user features in Leginon is here and same for Appion is here.

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 3.3 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.

[1] http://leginon.org

[2] http://appion.org

Leginon ¹ and Appion ² V3.3 release. Updates include support for Volta phase plate, Protomo, tilt data collection, ice thickness measuring, error notification. Current workflow routinely used at NRAMM and SEMC@NYSBC have been updated. Minor features affecting the user have also been added.

More information regarding new user features in Leginon is here and same for Appion is here.

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 3.3 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.

[1] http://leginon.org

[2] http://appion.org

Leginon¹ and Apppion² 3.2 is released mainly to mark the support for JEOL scopes, for data acquisition. Minor features affecting the user and installation experiences are also added.

More information regarding new features are available here and the general change log for Appion/Leginon 3.2

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 3.2 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.

[1] http://leginon.org

[2] http://appion.org

Hello,

We have decided to start a discussion forum related to instruments. We are not sure that this will be useful or effective but believe that it is worth a try. This is not meant to replace the 3DEM list but rather provide a place for highly technical discussions that may only be of interest to a subset of 3DEM subscribers.

The forum will be managed using redmine and can be found at:

http://emg.nysbc.org/projects/nramm-discussion-forum/boards

For now we envisage two major areas of interest: “Microscopes” and “Cameras”. We could obviously divide these areas into finer categories, and we may do that later if the forum gets too busy or crowded.

So, some suggestions for ground rules.

- The forum should be for questions and answers or discussions about technical matters. It is NOT meant to be a forum for rants and raves or even general grumblings and mutterings.

- We encourage participation from industry but do not encourage comparison of products or commercialism of any kind.

- The forum is available for anyone to read but if you want to contribute you will need to register. This is just for basic protection against spam.

Please feel free to make other suggestions.

Please pass this along to anyone you think may be interested in participating.

Regards,

The NRAMM Team

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