NYSBC - New York Structural Biology Center

Simons Electron Microscopy Center

The Simons Electron Microscopy Center provides expertise and resources for understanding both molecular and cellular structures. Molecular structure determination is enabled by high-end transmission electron microscopes (TEMs), direct detection cameras, and computational support for single particle analysis. Cellular structure determination is enabled by tomographic reconstructions using the TEMs and a focused ion beam (FIB) scanning electron microscope (SEM). SEMC is supported by dues from member institutions as well as the Simons Foundation.


SEMC Renovations Krios#2

Order in the control room has been restored.

Installing the Krios#2!

Members of the lab assist in positioning the base of the new Krios#2 in its case.

Installing the Krios#3!


The Krios#3 is currently in a testing stage.

Renovations to the SEMC suite are now complete. The Krios#1 is in normal operation and available, the Krios#2 is in open beta (see below), and the Krios#3 is being testing.

The BioTWIN screening microscope is now up and running. The addition of this instrument allows greater throughput for optimization of vitrified samples.

Click here to learn about scheduling microscope time.

Request For Applications (RFA) for Krios#2 Open Beta

INSTRUMENT: Krios#2 is a 300kV Titan Krios with: 1) Cs (image) corrector, 2) Phase Plates and 3) Gatan GIF Quantum Energy Filter.

WHO IS ELIGIBLE: Open beta is designed to streamline our workflows in preparation for normal operations. Mature projects will take higher priority, however all active users from our member institutions are encouraged to apply for EM time. The minimum requirement is for users to have screened similar cryo sample conditions (including preliminary data processing) for the grids that they will be loading into the instrument.

REQUIREMENTS: Interested users should submit a proposal. Users must have: 1) registered as a user, 2) registered their project and, 3) completed a SEMC New User Orientation session (offered once a month). To apply for this orientation email EMG@NYSBC.org.

SUPPORTED WORKFLOWS: Cryo-single particle and cryo-electron tomography workflows on the Gatan K2 Summit in counting mode will be supported.


BioTWIN The FEI T12 BioTWIN screening microscope is now open for general use. As established for the JEOL1230 screening microscope, member institution users may book time on the instrument within their institutional allocation. The addition of this instrument allows greater throughput for screening and optimization of too temperature and vitrified samples.

Until users are certified to be independent on this instrument they must email EMG@NYSBC.org to request staff assistance concurrent with their reservation.

Laboratory Supplies
All SEMC users must purchase their own consumable EM supplies. Grids, grid boxes, Krios cartridges and small personal tools must be purchased prior to your lab session. We encourage you to buy these directly from the vendors. There is new information on our "To Start" page regarding how to obtain the consumable laboratory supplies that users are required provide for their projects. To learn more about it, click here. If you choose to purchase items using the PayPal method explained in the link, you must bring proof of purchase with you to the lab in order to receive your supplies.

Upcoming/Ongoing Events

June 27th, 2017
SEMC Conference Room

This Appion Part 2 Workshop is a follow-on to the Part 1 workshop and will focus on 3D initial models and refinement. To register for this workshop, click here: https://www.surveymonkey.com/r/8R6N9RB. Attendance is limited to 10 participants.

May 30th, 2017
10am - 4pm
SEMC Conference Room

The Appion Part 1 Workshop provides hands-on training for the Appion single-particle data processing workflow. Appion is a "pipeline" for processing and analysis of EM images; it is integrated with Leginon data acquisition, but can also be used stand-alone after uploading images or particle stacks. Topics include analyzing the quality of your data collection, correcting the CTF, generating and cleaning up stacks, and generating 2D class averages. An Appion Part 2 Workshop will be offered in the future to provide training for making initial models and doing 3D reconstructions. To register for this workshop, click here: https://www.surveymonkey.com/r/8D2ZDW7. Attendance is limited to 10 participants.

May 25th, 2017
1pm - 3pm
SEMC Conference Room

This workshop will provide an overview of making holey gold films from holey carbon films supported on gold mesh. Holey gold films provide a stronger support film and reduce beam induced movement of the specimen. To register for this workshop, click here: https://www.surveymonkey.com/r/QBC5KXQ.

May 18th, 2017
Dragonfly, a Free but Valuable Platform for Image Visualization and Analysis
Mike Marsh, Object Research Systems

Dragonfly is a commercially supported image processing and visualization platform for 2D/3D/4D microscopy and other imaging data. To read the abstract, please click here.

Recent Events

SEMC Electron Microscopy Winter Course
The Winter Workshop has ended for 2017.

For more information about the course, please click here.

Please email EMG@NYSBC.org to inquire about registering for the next Winter Course.

May 9th, 2017
Appion Part 3 Workshop: Tomography
Leginon-Appion-Protomo: Semi-Automated Fiducial-less Tilt-Series Collection, Alignment, and Sub-Tomogram Processing

On May 9th, Alex Noble and Julia Brasch gave a workshop that is part of the Appion Workshop Series.

Tomography performed without fiducials has historically been an unreliable and innacurate task. At NYSBC we have developed a full workflow for fiducial-less tilt-series collection and alignment. This workshop teaches you how to perform tomography on all sample types, from single particle samples to FIB/SEM lamella for visualization in situ and for further processing with sub-tomogram alignment and averaging.

Users learn the basics of tilt-series collection in Leginon, tilt-series alignment with Appion-Protomo, and sub-tomogram processing with Dynamo. Appion-Protomo and Dynamo is partially hands-on.

No previous experience in tomography is required. Workshop attendees are encouraged to bring data in the form of tilt-series images, tomograms, or sub-tomograms for processing assistance.

Attendees should bring their own laptop in order to follow along during this hands-on workshop. Please email EMG@NYSBC.org to inquire about future workshop dates.

May 2, 2017
New User Training

New User Training is offered on the first Tuesday of every month. The morning session covers sample preparation (negative-staining and plunge freezing), and the afternoon session covers basic TEM use (loading samples and introduction to Leginon). Held this month on May 2nd, the training was attended by the people in the photo above. Please email EMG@NYSBC.org to inquire about future training session dates.

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