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URMC / Research / Flow Cytometry / Policies/Procedures


The following guidelines apply to all URMC Flow Cytometry Core Instruments. If you have questions about these guidelines, please contact Matt Cochran.


  • In the event the instrument you are booked on is down, the core personnel will notify you as soon as possible, and will make every effort to reschedule your experiment as close to your initial time as possible. This may require the use of a different instrument. If you are uncomfortable running this instrument, the core will assist you and waive the operator assist fee.

  • If your run is taking longer than expected and will run into another users time, they have the right to bump you at the time their run is to start.
  • After hours, the instrument should always be turned off after use to prevent issues with it being left on.  If another user is on the calendar they can re-start as needed.
  • Do not give after hours access to the facility or instruments to someone who
    doesn't have access. If a person's ID doesn't allow them access to the
    facility after hours, there is a reason for that.
  • The cancellation policy is as follows:
    • For sorting during normal hours (ending at 5pm)- Users must cancel their time 48 hours in advance of their scheduled appointment to avoid being charged for the time. If it is outside the 48 hour lock this can be done by going to PPMS and cancelling your reservation. If it is inside the 48 hour lock you can cancel through PPMS but may incur charges.
    • For the CyTOF- Reservations must be cancelled 48 hours in advance of the scheduled appointment to avoid being charged for the time.  Cancellations must be made via email.
    • For "Evening Hours Sorting"- Users must cancel their time 7 days in advance of their scheduled appointment to avoid being charged for the time. If it is outside the calendar lock this can be done by going to PPMS and cancelling your reservation. If it is inside the lock you can cancel through PPMS but may incur charges.
    • For analysis - Users must cancel their time no less than 24 hours in advance of their scheduled appointment to avoid being charged. If it is outside the 24 hour lock this can be done by going to PPMS and cancelling your reservation. If your reservation is locked, you can cancel through PPMS but may incur charges.
    • For analysis instruments- reservations from 6pm to 8am may be cancelled any time before the start of your run at no charge by cancelling through PPMS.
    • For "Evening Sort Hours"- reservations from 5pm to 9pm may be cancelled through PPMS any time before the start of the run with a charge of $43/hr.
    • No charges will be applied for cancelled time, regardless of when it was cancelled if another user schedules that time.
  • Failure to adhere to these policies will result in additional charges to your account as well as loss of access to the facility. Access will be restored after meeting with Matt or Tim. Persistent offenders (more than three violations in a calendar year) will be required to undergo training and additional requirements as determined by the Flow Core staff.

Access and Training

  • Each investigator must be registered with the FCR prior to being trained on the instruments or getting access to the cell sorters and CyTOF.
  • Before getting access to any core instrument, you will need to be trained in the proper use of the equipment. If you have not been trained, please visit the training page of the website to understand the training process.
  • For any training to be done, please fill out a training request for the specific type.
  • If you anticipate needing to use the machine after hours, you must undergo after hours training to be sure you understand fully how to change the fluidics and shut down the instrument.
  • It is against core policy to make reservations for anyone other than yourself.
  • If you access the instruments in non-standard business hours (M-F after 5pm or weekends), you are responsible for checking the calendar (refresh the calendar) and shutting down the instrument if you are the last user for the day. Failure to shut down the instrument will result in the following penalties:
    • Immediate loss of access to the flow core until you have met with Matt and Tim.
    • Your account being charged for the time the instrument was left on.

After-Hours Access

The Flow Core is open during normal business hours (8am to 5pm) from Monday through Friday, though specific instrument times may vary slightly.

After hours access is a privilege granted to experienced investigators that have completed the after hours training. In order to be eligible for after hours training and access a user must have a minimum of 20hrs of usage on the requested instrument within the previous 4 months. If the 20hr limit is reached in less than 4 months after hours training can be requested, however all requests from individuals that have not reached 20 hrs will be denied until the limit is reached. To receive after-hours access, the investigator must fill out the afterhours access form. A separate training session (free, approximately ½ hour) will be scheduled to review the specifics of after-hours access and instrument troubleshooting. After this session, the investigator must pass a written afterhours access exam and practical demonstration. If they fail, they must wait two weeks to reschedule the test. An investigator can schedule this test any time after they have normal access to the instrument.

Instrumentation Usage

  • Do not change the filter configuration without first discussing changes with the Flow Core staff. Inappropriate filter configuration can lead to erroneous data. If the filters are changed for a particular experiment, they should be returned to the default configuration when you are finished.
  • Follow all posted cleaning guidelines. Guidelines are posted on or near each instrument.
  • For the FACSDiva instruments:
    • There are lines on the waste tank to determine when it should be emptied. If the waste is at or above that line, it must be emptied and bleach put in the bottom.
    • Additionally, if you empty the waste, the sheath must be filled. The fill line for the sheath tank is marked by the weld line on the inside of the tank
  • If the instrument maintenance policies are not followed, there will be a $43 fee charged. Policies include but are not limited to cleaning protocols, not shutting down the instrument if you are the last investigator for the day, changing the data export pathways, etc.

Data Handling

  • FACSDiva data export pathways:

    • Experiment files: D:\BD export\experiment\"current year"\"current month"
    • FCS files: D:\BD export\FCS (File format must remain FCS 3.0)
  • The data export pathways should never be changed. If the pathways are changed that investigator will be responsible for a maintenance fee, as above.

  • Experiments should be deleted from the acquisition software immediately after they are exported. If they are not deleted at the completion of the run they can/will be deleted by the next user to keep the database clean.

  • Experiment files that have been exported to the proper location will be archived automatically on a daily basis. The experiment files will be deleted off the local computer at the end of the month.
  • Exported FCS files will be deleted off the computer once a week during long cleans. The Core will not back up this data. If you are missing FCS files, they can be recovered from archived experiments.
  • Data exported to any location other than the above pathways will be deleted immediately.

Billing Practices

  • Time for instruments will be billed based on the time reserved and/or time used, whichever is longer.
  • Instrumentation rates are found on the Billing and Fees page.
  • If you change labs or accounts, please fill out the change of information form immediately so that your account can be updated correctly.

Tips and Tricks

  • When designing poly-chromatic experiments, it is strongly encouraged to make an appointment with a member of the Flow Core staff to review the experimental design to make sure that it can be run on one of our instruments
  • Bring the proper controls!
  • Check the website for frequent updates and information.