Policies

General Scheduling and Use Rules for all TEMs

Facility

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. The facility strives to provide service to our members, but has limited personnel and a major effort is made to provide training in the use of appropriate instruments to enable users to do their own microscopy.

All new users must register with the facility: http://semc.nysbc.org/new-users/to-start/ .

Please note SEMC is a BSL-1 facility.

Acknowledgement

Any use of the resources at SEMC requires acknowledgement of use of the resources in publications as follows:

Standard Acknowledgement:
“Some of this work was performed at the Simons Electron Microscopy Center and National Resource for Automated Molecular Microscopy located at the New York Structural Biology Center, supported by grants from the Simons Foundation (349247), NYSTAR, and the NIH National Institute of General Medical Sciences (GM103310) with additional support from [copy and paste depending on equipment]”

Krios1/K2: Agouron Institute [Grant Number: F00316] Krios1/Falcon : NIH S10 OD019994-01
Helios: NIH S10 RR029300-01

Training

SEMC offers several training outreach programs:

Project Discussion meetings [weekly]: Tuesday @ 3pm and Thursday @ 3pm
New user orientation [monthly]: Sample prep and TEM use
Appion workshop [quarterly]: Appion single particle data processing
EM course [yearly]: Theory of EM

All users of the center must be approved by their Institutional Representative prior to using any of the high-end instrumentation. This prior approval includes those who have been trained elsewhere in electron microscopy. The intent is not to limit access, but to ensure efficient usage of the EMs and protect the instruments from possible damage.

Scheduling Microscope Time

Once a user completes new user orientation they will be entered into the scheduling system. This is an online scheduler that enables users to schedule time on the screening EMs and sample preparation equipment without contacting Facility staff.

Time on the high-end EMs requires a project discussion meeting and preliminary cryo data. Users should notify their Institutional Representative and the SEMC staff to be placed on the queue. The intent of the following rules is to ensure access to the instruments for the largest number of users, not to limit access.

In general, users may sign up for up to 2 consecutive sessions (9am-1pm or 1pm-5pm on weekdays) or 1 day (9am-5pm on weekdays). Should a longer session be needed users should contact emg@nysbc.org and provide an explanation. Users may sign up for no more than 2 days in total.

Signing up less than 24 hours before a session begins will not count against your bookings allotment.

Last minute bookings:
Any session scheduled less than 24 hours in advance (or over a weekend or holiday) is considered a last minute booking. Last minute bookings will be approved during business hours and staff assistance cannot be guaranteed. We will do our best to accommodate all users, but if you require full staff assistance please book at least one week in advance.

Waitlist:
You may request to be put on the waitlist to access unused time or last minute cancellations for your institution’s time. However, you must have grids ready to go and be available to come to the center at a moment’s notice (less than 24 hours advanced notice).

Consecutive Sessions:
You may not request 3 consecutive sessions during weekday-daytime (9am-5pm) hours. It is OK and encouraged to do this with evening and weekend sessions or in combination with a daytime session (e.g. 9am to midnight on weekdays or 9am to 9am the following day on weekends) assuming you have All-Hours access.

Special Bookings:
Special case sign-up is available with the help of the SEMC Staff.

1) If you have a special need for more microscope time (e.g. you have to get a paper out quickly), please talk to the your Institutional Representative and email emg@nysbc.org to submit a request for extra time.

2) Should a multi-day session be needed users should contact the emg@nysbc.org and provide an explanation.

No Shows:
Failure to show up for sessions you booked in advance inconveniences everyone. If you find, for any reason, that you will not use a session you have booked – YOU MUST CANCEL 24 HOURS IN ADVANCE.

Lateness:
If you are more than 30 minutes late, you will forfeit your session, if others wish to use it. If you know you will be late in advance, please notify SEMC Staff.

Microscope down time/early termination of a session:
If there is an unexpected issue that leads to termination/cancellation of your session, though we will try to accommodate you, there should be no expectation of a makeup session.

An exception is if a pre-planned maintenance session must be rescheduled. We will work with you to reschedule your session for the next available time.

After-Hours Use of Instrumentation:

Users must be certified as independent on the instrumentation they are booking. Independence is defined as proper setup, usage and shutdown of the instrument without staff supervision. Users must also have a Certificate of Fitness for Non-Production Chemical Laboratories (C-14) issued by the NYC Fire Department.

Independence must be verified by two staff members on two separate occasions. Independence is awarded on a per-instrument basis. Staff has the right to revoke independence if additional training is required. Please email EMG in advance of your session in order to test for independence.

Users must request approval of after-hours use of instrumentation via email to EMG at emg@nysbc.org and session booking must be approved in PPMS.

Users will be issued an NYSBC Temporary Access Form for each session by an EMG staff member. You cannot stay past 5 pm without receiving this form.

Only NYSBC Temporary Access Form holders are allowed on-site outside of business hours. Each additional user must have their own NYSBC Temporary Access Form.

All liquid nitrogen dispensing must be completed by 5 pm. Please fill a couple LD4 dewars so that you have enough liquid nitrogen for your freezing session. If you cannot make it on-site before 5 pm, please email emg@nysbc.org and ask a staff member to fill LD4s for your session.

If you encounter any issues:

1. Notify EMG at emg@nysbc.org
2. Shutdown equipment (if possible)
3. Go home! If you cannot properly shutdown the instrumentation for any reason, please let us know and we will troubleshoot the next day.

In a case of an emergency please contact the laboratory safety officer. Emergency contact information can be found on signage in the dehumidified room and at both entrances to the lab.

Data policy

Please note that you are responsible for your data and samples. In general, direct detector data will be queued for deletion in a month. Leginon images from your session may be viewed at emgweb.nysbc.org. Your Leginon images are not backed up and may be converted to JPEG versions within 1 year. We will make our best efforts to preserve the functionality of the image viewer, but do not archive data.

Food and Drink

No food is allowed in the microscope rooms, drinks must not be left on the counter or microscope tables.

User Guest/Visitor Policy

Visitors must be announced at least 1 day in advance of their visit. Please email emg@nysbc.org with the following information: guest name, affiliation and position. See example below.
- Guest name: Bridget Carragher
- Affiliation: Simons Electron Microscopy Center
- Position: Principal Investigator
Visitors are only allowed to observe. They are not allowed to operate instrumentation or any other ancillary equipment.
Visitors are only allowed on-site from 9AM – 5PM.
Visitors must be at least 18 years of age.
Visitors are under the supervision and responsibility of the staff assignee for the duration of their session.
Visitors must check-in with their staff assignee to sign out a guest badge for the day.
Visitors must check-out with their staff assignee to return the guest badge at end of day.
Visitors must have their guest badge visible for the entirety of their visit.
If visitors will become regular users, they must attend New User Orientation and obtain an official ID at the NYSBC. Please email emg@nysbc.org to request access to the next New User Orientation.
EMG staff reserve the right to turn away visitors if any of the rules above are not followed.

Best practices at NYSBC Simons Electron Microscopy Center

Arrive on time for your session!
Try not to use microscope time for sample preparation. Whenever possible your grids should be ready to go at the start of your microscope session.
Sign up to use any microscope, sample preparation equipment, or computer workstations prior to your arrival.
Absolutely no food or drink in the lab.
Be courteous to other users: finish your session on time and clean up after yourself.
The dehumidified room often gets crowded; please leave any unnecessary belongings outside in the lab or in our lockers out in the hall.
Users who have not completed safety training and registered their C14s do not have 24 hour access and are only allowed to use the facility during business hours.
If you ever have any doubts on equipment use, please seek help from an EMG staff member.
Never use force on any equipment. If something is stuck leave it alone and call for help.
We would suggest that when possible you use the instruments as follows:
- JEOL1230: Negative stain screening
- FEI Tecnai F20: High-resolution cryoEM single particle (once sample conditions have been optimized) or advanced overnight RT data collection

Acknowledgement

Any use of the resources at SEMC requires acknowledgement of use of the resources in publications as follows:

Krios1/K2: Agouron Institute [Grant Number: F00316] Krios1/Falcon : NIH S10 OD019994-01
Helios: NIH S10 RR029300-01

Emergency contact numbers

Safety Officer:
Edward Eng
Normal Hours: x346

Second Contact:
Robert Gheorghita
Normal Hours: x309

Lab Heads:
Clint Potter
Normal Hours: x301

Bridget Carragher
Normal Hours: x302