Policies & Rules

Independent User

An independent user is one who can work independently, meaning the user is certified to (also) work during weekends, holidays and overnight without the supervision of staff. To be independent, individual users must demonstrate proficiency in performing all required steps and tasks independently, including but not limited to: 1) handling holders, 2) microscope alignments, 3) low dose imaging and data collection, 4) ending of session, and 5) basic troubleshooting (and being able to assess what does/does not constitute “basic troubleshooting” vs problems that require immediate notification of the staff). Users should be able to perform all necessary steps mostly without having to refer to their notes, and while operating all instrument components safely.

Work Area

Users must clean up their work areas, return all used items to their proper storage location and leave all rooms, microscopes and accessory instruments in a condition such that they are ready for the next user.

For negative staining, fresh stocks of 2% UA solutions, blotting paper, tweezers, gloves are available.

Users can store your grids in the desiccator cabinet provided in the EMRL lab.


  • For T12 microscope, the first user for the day can start using the microscope 30 min in advance and cool the ACD, ramp up HT and filament.
  • Equipment signup is allowed for up to 14 days in advance. Cancellation of your session is allowed up to 1 hr in advance of your session.
  • The minimum reservation time on TF20 is 4 hours. The slots are split into 9 AM-1 PM and 1 PM-5 PM, 5 PM-9 PM
  • The minimum reservation time on T12 is 2 hours.
  • Reservation time on Cryo Plungers is 1 hour
  • The use of the microscope and contributions of the staff must be acknowledged in the “Materials and Methods” and “Acknowledgment “sections respectively.
  • The Cryo-EM Screening Facility does not provide cryo-EM data processing and reconstruction services.
  • Never insert a USB device of your own into any of the computers in the facility. 
  • Never step on any cables or wander behind the microscope.
  • Only trained users will be allowed to operate the microscope independently.
  • Do not forget to fill in the logbook after your session.
  • The beam settings in the low dose setup should not be changed in Search or Focus mode. You are allowed to change the magnification only in the Exposure mode.
  • VERY IMPORTANT: If users experience any problems while operating the instruments (hardware issues or software/computer errors), the user should not attempt to resolve the problem. On the microscopes: stop operations, close the column valves and contact core director immediately (24-hour contact is posted). Attempting to correct a malfunction and inadvertently damaging the microscopes can void our service agreement with FEI. If an error causes termination of the session the user will not be billed for the remainder of the booked time.

Protein Sample Quality Check

The quality of the protein is often the bottleneck in a successful cryoEM session. We highly recommend using light scattering such as DLS to estimate the quality of the protein before performing the Cryo-EM experiment.

Please contact Dr. Kushol Gupta (kgupta@pennmedicine.upenn.edu) for accessing his core facility and DLS instrument and usage.

All users (Internal and External) will have a folder on the shared network drive called “T12_D3” that is connected to the cloud Box. Internal users can access Penn+Box to download data. All external users will be given a downloadable link from Box server. The images collected on T12 or Tf20 will automatically sync to your account and stored on your Box account. Please be sure to download the images monthly on your personal computer and backup your data.

The disks on the T12 and Tf20 data computers will be periodically cleaned and facility will not backup any data.

If you would like to use Falcon III camera in counting mode then bring an external hard drive with you and copy them onto the external drive.

The Falcon III camera is highly sensitive to electrons and so the user has to be in nanoprobe mode while operating Falcon III camera.

If your project requires the active participation of EMRL staff in preparing grids or optimizing the conditions for imaging, then the work done at EMRL is considered as collaborative work. All collaborative projects that result in publication should list the staff member as a co-author. Any additional help required for the successful submission of the manuscript will also be provided by the staff.

Publications that result from using the EMRL Instrumentation should acknowledge the facility and the personnel assisted in data collection.

All the Cryo-EM Maps that are deposited to EMData Bank should be reported to EMRL. 

EMRL will store cryo-grids for 2 years and will be automatically disposed of after that.

Supplies such as buttons for grid storage, falcon tubes, string, a label for storing cryo grids are provided by EMRL.

For negative stain grids, fresh stocks of stain solutions, grids for negative stain, blotting paper, tweezers, gloves are available.

Please label appropriately and store all your negative stain grids in the desiccator cabinet provided in the EMRL lab.

All users must sign-up for instruments on the iLab website. You can reserve up to 14 days in advance. You can modify or cancel your reservation up to 24 hrs prior to your reserved time slot. During this 24 hrs, you could still cancel the reservation, but you will be charged if the canceled slot is not booked by anyone.

A User will be charged for the entire reserved slot, even if the user finishes early (so plan accordingly).

If an error causes termination of the session, the user will not be billed for the remainder of the booked time. However, it's absolutely your responsibility to follow up with staff to make sure that the session has been canceled and not billed for the unused instrument time.