Policies

Data storage

Because an enormous amount of data (in terabytes) is collected during data acquisition and quality monitoring via cryoSPARC Live, the facility offers only temporary data storage for a maximum period of one week. It is critical to keep the microscope storage free to avoid instrument downtime caused by full drives. Collected data must be transferred to user-designated storage for further processing. The facility does not offer IT support or computational tools to process data. No raw data will be permanently stored at the facility; it is the user's responsibility to maintain raw data in their own storage systems once collected and transferred.

No external hard drives or flash storage devices are permitted to connect to the microscope PC or support PC. All data must be transferred using the local network or through a Globus account.

New labs navigating cryo-EM research are encouraged to explore data storage and processing options by contacting the Center for Research Computing (CRC) at Notre Dame or commercial High-Performance Computing (HPC) providers such as Amazon Web Services (AWS), Microsoft Azure, or Google Cloud Platform (GCP).

Instrument use

To avoid instrument downtime and maintain equipment in optimal operating condition, all Cryo-TEM Core Facility users must adhere to the following rules and guidelines at all times:

· Only core facility personnel are authorized to provide instrument training through established training packages based on user experience levels. Trained users are not permitted to train others.

· Unassisted use is strictly restricted to regular office hours (Monday–Friday, 8:00 AM–5:00 PM). No unassisted bookings outside of office hours are allowed for sample preparation or sample screening.

· Facility managers reserve the right to deny any booking or instrument use until the user successfully completes all required training sessions.

· Users must reserve instruments in the iLab calendar prior to use. Failure to do so will result in restricted access.

· Users must log in using the Kiosk interface during instrument use to track active time. Billing is primarily based on logged instrument usage rather than reserved time.

· Instrument bookings must be canceled at least 24 hours in advance for the Vitrobot and 48 hours in advance for the Glacios 2. This minimizes instrument downtime and allows other users to utilize the equipment.

· Core facility personnel reserve the right to cancel any booking with email notification if an instrument requires maintenance or troubleshooting.

· Users must not attempt to fix or troubleshoot instruments. Regardless of the issue's size, bring it to a facility manager's attention immediately.

· Principal Investigators (PIs) are financially responsible for equipment damage resulting from mishandling or negligence by group members.

· To maximize instrument utilization, extended experiments (such as long-term data acquisition) should be scheduled overnight or during weekends.

· Once grids are plunge-frozen using the Vitrobot, clip and store them in dedicated, properly labeled grid storage boxes for facility managers to load for screening.

· Users are responsible for purchasing all consumables required for Cryo-TEM grid preparation, including grids (Quantifoil, Lacey, C-Flat, etc.), O-rings, C-clips, and grid storage boxes. If the facility provides any consumables, users must log the items and quantities for billing.

· Whenever storing clipped grids in the 35L dewar, verify that sufficient liquid nitrogen remains to preserve sample quality. If the liquid level is low ( 2/3 full), refill the dewar.

· Do not pour liquid nitrogen containing moisture into the 35L dewar, as this causes ice crystal formation and degrades stored grid quality. Ensure the lid is replaced immediately after use to minimize evaporation and crystalline ice buildup.

· Always close all three ethane gas valves after use and bleed off any excess gas remaining in the line.

· After completing plunge-freezing on the Vitrobot: remove water from the humidity chamber, remove blotting paper, place the O-ring in the designated box next to the instrument, and leave the chamber door open. The ethane container and Styrofoam block must be placed inside the fume hood.

· Following grid clipping, place all tweezers, insertion tools, grid container tools, and autogrid tweezers on the aluminum tray to dry. Do not turn on heating elements, as high temperatures can damage heat-sensitive tools.

· Instruments and lab areas must be vacated promptly at the conclusion of scheduled sessions and left clean and in good working order.

· Access to the Cryo-TEM Core Facility will be revoked for failure to comply with facility policies.

Laboratory Policy and Agreement Contract

Users must sign the Laboratory Policy and Agreement Contract prior to using the facility or its equipment. Physical copies are available at the Cryo-TEM Core Facility in B002 McCourtney Hall-East, or digital copies can be downloaded from the lab website for printing.