[3dem] Using SerialEM and Leginon on same scope

[Matthias Wolf]

I may have created the impression of preferably endorsing EPU and SerialEM. I did not intend to suggest this.
The former is just often preferred by users and facility managers due its simplicity. The latter offers most functionality for tomography acquisition.

For a larger center with more than one or two scopes, leginon wins hands down - this is because of its integrated database, which facilitates the tracking of projects, scope parameters, gain references, storage locations, logical separation of non-affiliated groups by access permissions, etc. Leginon has also had on-the-fly features for the last 10 years such as background data transfer from the acquisition file server, automated CTF and particle selection all the way to 2D and 3D processing with Appion.

While SerialEM is great, it does not offer any project management features. The Jensen lab has long been using the leginon/Appion pipeline for batch tomography and everyone knows that they have great results.

Only recently, with the advent of dedicated on-the-fly software like Scipion, TranSphire, Focus and Warp, standalone-packages like EPU, UCSFImage, Gatan's Latitude and SerialEM have become more integrated into the general workflow, which allows for additional flexibility in creating custom processing pipelines.

   Matthias
________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Rice, William <William.Rice at nyulangone.org>
Sent: Saturday, August 31, 2019 2:32 AM
To: Grassucci, Robert <rg2502 at cumc.columbia.edu>; 3DEM List (3dem at ncmir.ucsd.edu) <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] Using SerialEM and Leginon on same scope


Hi Bob,


I can also say that they coexist well at NYU, where we have a Krios and an Arctica. As Matthias said, I don't run them at the same time. We also have EPU on the Krios but it is very seldomly used (only for the Falcon 3 -- no advanced scripting installed yet)


Bill


William J. Rice, PhD

Director, Cryo-Electron Microscopy Laboratory

NYU Langone Health

Smilow, SR C-10

522 First Ave., New York, NY 10016

________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Grassucci, Robert <rg2502 at cumc.columbia.edu>
Sent: Friday, August 30, 2019 9:44:59 AM
To: 3DEM List (3dem at ncmir.ucsd.edu)
Subject: [3dem] Using SerialEM and Leginon on same scope


Hi All,

With the commissioning of our 4 new scopes we are debating if we should put SerialEM and Leginon on the same microscopes.  I have heard from some people that there may be some problems that arise during the transition.  We have mostly been using Leginon so have a great deal of experience with it and use SerialEM for our limited tomography users.  I cannot see any reason they should conflict but want to ask the 3DEM community if they have any specific experience where this has been a problem.  Thank you and I look forward to your advice.

Regards,

Bob





Robert Grassucci

Co Director CryoEM Core Facility

Columbia University Medical Center

Biochemistry and Molecular Biophysics Dept.

Black Building 2-221

650 W 168 Street

New York, NY 10032

Phone: 212-305-9520


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