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 is rapidly being restored.

Installing the Krios#2!

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


Installation of the BioTWIN is proceeding ahead of schedule.

Renovations to the SEMC suite are nearly complete. The Krios#1 FEI Falcon II has been upgraded to the FEI Falcon III direct detector. NYSBC is the first site in the US that has had this upgrade completed. Over the next semester the Falcon III will undergo beta-testing and integration with our Leginon automated data acquisition software system. We have also installed a new Volta Phase Plate on the Krios#1, and this is currently undergoing testing and characterization.

The BioTWIN screening microscope has arrived, and installation is nearly complete. The addition of this instrument allows greater throughput for optimization of vitrified samples.

The Krios#2 has arrived and is in the process of being installed. Krios#2 will have a Cs corrector, a phase plate, and an energy filter. The instrument will be suitable for both single particle and electron tomography projects.

The Krios#3 room is ready, as we expect the instrument to arrive in early December.

Until the latest construction phase is fully completed, please continue to email EMG@NYSBC.org to schedule microscope use.

We look forward to the completion of this long but necessary renovation project, and look forward to seeing many of you back in our warm and friendly control room again soon.

Click here to view an updated renovation schedule.
Click here to learn about scheduling microscope time during the renovation period.

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.


SEMC Electron Microscopy Winter Course
SEMC will be offering a "reverse classroom" style EM course that will begin January 2017 and will run for 16 weeks, through May 2017. The course will be based on an online video class taught by Grant Jensen. Students will be expected to watch these lectures prior to a formal 90 minute class that will meet once per week for follow up materials and discussion.
If you wish to attend the course, please fill out an application form by December 31st, 2016. There will be a limit of 20 students and we may not be able to accept all applicants or any late comers.

For more information about the course, please click here.

To register for the course go to: https://www.surveymonkey.com/r/WinterCourse17.

December 8-9, 2016
Dynamo Workshop

This workshop will provide hands-on training in all practical aspects of sub-tomogram averaging using Dynamo. The new Dynamo catalogue system for organizing and centralizing tomograms will be featured along with new semi-automated picking procedures. All stages of the pipeline will be covered, including: tomogram visualization and archiving, particle picking, membrane picking, filament picking, averaging, refinement, and classification.

The workshop will begin on December 8 at noon with a SEMC@NYSBC Forum introducing Dynamo and continue all day December 9th.

No previous experience in sub-tomogram processing is required. Workshop attendees are encouraged to bring data, whether tomograms or sub-tomograms, for processing assistance at the end of the final day. Attendees should bring their own laptop in order to follow along during this hands-on workshop.

Register for the Dynamo Workshop here: https://www.surveymonkey.com/r/JHFDJ27.

December 7, 2016
Appion Part 3 Workshop

Tilt-series alignment is commonly performed by tracking fiducials in order to recover the three-dimensional structure and orientation of specimen in cryo-electron tomography, negative stain tomography, and tomography on plastic sections. However this approach is sometimes fraught with difficulty due to fiducial movement, fiducial aggregation, or the lack of fiducials in specimen such as FIB/SEM lamella.

In this workshop users will gain hand-on experience with a semi-automated implementation of Protomo into Appion. Protomo allows for fiducial-less alignment of tilt-series and refinement of specimen orientation on the grid through an iterative geometry refinement process. Appion-Protomo, which installs seamlessly with Appion, significantly reduces the effort and expertice required by the user to align fiducial-free tilt-series collected using any software package. All that is required is a stack of tilt images along with knowledge of their imaging conditions. Integrated within Appion-Protomo are pipelines for defocus estimation, CTF correction, and dose compensation, along with multiple reconstruction methods.

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

Attendees are encouraged to sign up for the Dynamo workshop on Dec 8 & 9 to learn how to extract and process subtomograms from their reconstructed tomograms.

Attendees should bring their own laptop in order to follow along during this hands-on workshop.

Register for the Appion Part 3 Workshop here: https://www.surveymonkey.com/r/SR2KWZT.

December 8, 2016
New User Training

Pictured here are the attendees of the December New User Training, offered 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). Please e-mail emg@nysbc.org to learn about future new user training sessions.

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