Using the Facility

Intro to Flow Cytometry

The Introduction to Flow Cytometry Class is a series of three 90-minute lectures offered monthly.  The class is led by UWCCC Flow Lab Certified Cytometrists and is designed for newcomers and old pros alike.

This class is the required first step of our training program. All investigators that use or plan to use Flow & Image Cytometry and/or Cell Sorting in their research are required to attend this lecture series.

All lectures will be held from 9-10:30am on a Monday, Wednesday, and Friday, unless otherwise noted.

Registration closes the Friday prior to the start of class at 4:30pm.

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Class schedule & location

Hybrid: In-person at WIMR, with option to join via Teams.

Email confirmation will be sent to registrants the week prior to class.


  • January 22, 24, 26
  • February 19, 21, 23
  • March 18, 20, 22
  • April 15, 17, 19
  • May 13, 15, 17
  • June 17, 19, 21
  • July 15, 17, 19
  • August 12, 14, 16
  • September 16, 18, 20
  • October 14, 16, 18
  • November 11, 13, 15
  • December 16, 18, 20

Topics Covered

  1. How a flow cytometer works
  2. The importance of controls
  3. Fluorescence and choosing fluorochromes
  4. What compensation is all about
  5. Sample preparation
  6. Experimental Design, Optimization, and Standardization
  7. Image Cytometry
  8. Cell Sorting
  9. Data analysis
  10. Common Flow and Image Cytometry applications
  11. Flow Lab policies and procedures
  12. Other topics of your choice, questions encouraged


Cancer Center Members: $78.03
Non-Cancer Center Members: $111.48
Wm S Middleton VA: $123.74
External Academic: $176.81
Industry: $266.30

Prices effective January 1, 2024


To register for a Flow Lab Lecture Series, please fill in the information requested below and press submit.


Instrument Training

Hands-On Training is required of all new users after completion of the Introduction to Flow Cytometry class and and is instrument specific.  Training covers instrument operation, data collection, biosafety, troubleshooting, and general maintenance. Within iLab, reserve duration of time listed below on the instrument of choice for Hands-On Training on the Flow Cytometers. Initial training often uses fluorescent beads, some instrumentation training requires cells as noted below.

For training on the ImageStream, please reserve 2.5 to 3 hours.  Training works best on this instrument with actual samples, so please bring experimental samples for your first training on the ImageStream.  This will provide an opportunity to assess sample prep, suggest steps for optimizing your assay going forward, and a data set to use for learning the IDEAS image cytometry data analysis software.

Please feel free to contact the Flow Lab Staff with any questions regarding training, choosing the right instrument for your experiments, and preparing cells for trainings requiring cells:

Training appointments are available at the following times:

  • ThermoFisher Attune (Thunder & Lightning):
    • Lightning: Mondays, 11am-12:45pm, or 1pm-2:45pm
    • Thunder: Thursdays, 11am-12:45pm, or 1pm-2:45pm
  • BD LSR Fortessa:
    • Wednesdays, 11am-12:45pm, or 1pm-2:45pm
  • Aurora Spectral Cytometer:  Tuesdays, 11am-3pm.
  • ImageStream:  Wednesdays, 12-3pm.
    • Cells required for training, please bring prepared experimental samples.
    • Email to schedule experimental consult prior to training
  • Sony MA900 Cell Sorter
    • Tuesdays, Wednesdays, Thursdays
      • Startup & QC Training: 9:30 – 11:30am
      • Sorting & Shutdown Training: 1:30 – 3:30pm
        • Cells required. Please bring prepared experimental samples.

After completion of Hands-On Training, users will schedule Assisted appointment(s) with actual experimental samples.  These Assisted appointments will focus on optimizing instrument settings for their specific experiments. Training will be complete when both the user and Flow Lab staff feel the user is competent to operate the instrument(s) independently.  Users will be checked off as trained in iLab for individual instrument(s) allowing user access to reserve instrument(s) outside of the reserved training times.

Additional Training

As part of our Educational Outreach Program, the UWCCC Flow Lab will come to your lab meeting, department meeting, journal club, class, or other group meeting to discuss topics of interest.  To schedule a seminar contact the Flow Lab. Our current list of common topics related to cytometry are listed below.  If you are interesting in something not listed please contact the Flow Lab at and suggest a topic.

  • Best Practices in Cytometry
  • Rigor and Reproducibility in Cytometry
  • Panel Design and Optimization
  • Overview of Computational Data Analysis Methods in Flow Cytometry
  • Compensation with Confidence
  • Data Analysis Basics
  • Getting Started with FlowJo
  • Getting Started with FCS Express

Biosafety Level

The Flow Cytometry Laboratory (Flow Lab) is approved by the Institutional Biosafety Committee to handle samples of biosafety level 2 (BSL2) and below. Cytometers create aerosols. All users must provide the Flow Lab with a Biosafety Protocol number that indicates that all materials brought to the Flow Lab are below BSL-3 and approved for use on a sorter or benchtop cytometer. Please feel free to contact the UW Office of Biological Safety with specific biological safety questions.

Transportation of Samples

All samples transported to the Flow Lab must be transported in compliance with Biological Materials Transport on UW Campus Guidance.

This requires 3 levels of containment and applies to transportation within a building, as well as between buildings:

  1. Primary Specimen container with secure closure
  2. Secondary Specimen container with secure closure (containing primary container(s))
  3. Outer container with secure closure, made of rigid material and labeled with appropriate contact information (name, phone, lab name, lab location), and appropriate specimen description such as “Biological Research Samples”, “Research Samples, Non-Infectious”, “Animal Specimens for Research”.  Other suggestions available in the Biological Materials Transport on UW Campus Guidance document available here:

Transportation of biological specimens in private vehicles is not allowed and may violate federal regulations.

Biological Safety Protocol Information for Researchers using the Flow Lab

The Office of Biological Safety and the Institutional Biosafety Committee are in the process of transitioning paper Biosafety Protocols into Bio-ARROW, the online Biosafety Protocol Form.

Samples exceeding BSL-2 cannot be analyzed or sorted in the Flow Lab unless the biohazards are inactivated through fixation. Please review our Flow Cytometry Standard Operating Procedures (pdf). All samples for sorting must be listed on your lab’s biological safety protocol and approved by the Office of Biological Safety.

Flow Lab Hood Certification Dates

  • Baker BioProtect Aria “Jill” Cell Sorter (7018B WIMR), SN 120708, Cert. Date: 11/28/24
  • Baker BioProtect Aria “Jack” Cell Sorter (7018B WIMR), SN 108121, Cert. Date: 11/28/24
  • Baker BCC300AMS Sony MA900 Cell Sorter (7018C WIMR), SN 138210, Cert. Date: 11/28/24
  • BioBubble Aria “Jayne” Cell Sorter (2360 Biotech), SN PU2525-0159, Cert. Date: 03/11/24
  • 4′ Baker SteriGuardIII Advance (7018E WIMR), SN 93707, Cert. Date: 11/27/24
  • 6′ Baler SteroGuardIII Advance (7018E WIMR), SN 95206, Cert. Date: 11/27/24
  • 4′ Baker SteriGuardIII Advance (2360 Biotech), SN 90115, Cert. Date: 03/11/24

If you have not used the Flow Lab before, see our FAQs about getting started, below.

  1. To use the Flow Cytometry equipment, you must make an appointment using iLab with your own account.  We do not allow users to make appointments for other users.  Abuse of this policy may result in removal of access to the Flow Lab instrumentation.
  2. Make note of the cancellation, no show and login password policies noted in the online scheduler. Remember that you may need a lead time of at least 96 hours for benchtop analysis and as much as two weeks for sorting. Plan ahead.
  3. We encourage all users to learn to run the benchtop cytometers themselves. Attendance at the monthly lecture series is required for all benchtop training sessions. Once you have the attended the lecture series, make an appointment for training.
  4. If you have not been trained to run the cytometers, or if you need assay-specific instruction, make an Assisted Benchtop appointment. Email us about experimental design, fluorochrome selection, and appropriate instrumentation.
  5. Access to self-appointments is restricted until you have completed training and are able to operate the instrument(s) independently.
  6. Rescheduling & Cancellation.  Any self-use reservation may be cancelled by the user up to 15 minutes before the start of the reservation at no charge.  Staff-assisted reservations, Training, Assisted, and Cell Sorting can be cancelled by the user up to 24 hours before the start of the reservation.  If cancellation is necessary within that 24 hour window, please call the Flow Lab at 263-0313 (WIMR) or 265-5547 (Biotech). No Call/No Show reservations are charged in full for time reserved.
  7. If you encounter scheduling difficulties or problems finding appropriate times for your experiments, always contact Flow Lab staff. We can help.
  1. The Flow Lab is staffed from 9am-5pm Monday through Friday. Requests for staff-assisted reservations for after-hours will be evaluated on a case-by-case bases and should be made well in advance.
  2. The Flow Lab is available at all times to trained users.
  3. Benchtop analyzers are user-operated. We strongly encourage all users to learn to operate these cytometers. Attendance at the introductory lecture series is required before instruction will be provided.
  4. All users are expected to learn basic data analysis.
  5. The BD FACS Aria sorting cytometers are staff-operated only.
  6. The Flow Lab is closed on: Martin Luther King Day, Memorial Day, Fourth of July, Labor Day, Veteran’s Day, Thanksgiving Day, Christmas Eve through New Year’s Day and the Friday of our annual regional meeting of the Great Lakes International Imaging and Flow Cytometry Association (GLIIFCA).

Appointments can be cancelled online or by calling the office (263-0313) without penalty according to the following schedule:

Benchtop Analysis Cytometers

Users are able to create, edit, and cancel appointments right up to the start time of the reservation. No Call/No Show appointments will be charged for the full reserved time.  Users are charged from their reserved start time until the end of the reservation or until they have logged off the instrument, which ever is longer.  Reserved time is unavailable to other users and will be charged to the reservation owner, regardless of log out times.  Please edit your reservations if you feel you will require less time than originally booked.


Online cancellation up to 24 hours prior to the appointment. Cancellations cannot be made online less than 24 hours before the appointment. Please call the Flow Lab to cancel if less than 24 hours before a sort to avoid charges. The facility maintains a wait list for these cancellations. Sorting appointments cancelled with less than 24 hours notice will be billed for a minimum of one hour of sorting time.

Failure to keep an appointment will result in a charge for the amount of time scheduled.


  1. You must provide all the supplies necessary to analyze or sort your samples. These include: sample tubes, dilution buffers, propidium iodide or other vital dye, collection tubes, and serum for cell collection after sorting.
  2. Check your samples. If there are visible particulates, the samples must be filtered before being placed on the cytometers. All samples to be placed on the sorters must be filtered just prior to the sort. The Flow Lab will provide these filters.


  1. You are responsible for keeping users of the Flow Lab safe. You are required to inform us via the online appointment form if your samples contain a biohazard.
  2. You must use disposable gloves when operating the cytometer.
  3. You are responsible for cleaning the area around the cytometer after its use. Dispose of sample tubes in the appropriate containers and wipe up any spills.
  4. You are also responsible for the care of the instrument when you complete your analysis. The staff will instruct you on proper instrument care at the end of your run.
  5. Our biosafety cabinet is available for general use, unless posted. No yeast or bacteria allowed in the BSC, centrifuges, or incubators.


  1. You are the primary caretaker of your data. Data is acquired on a cytometer and immediately transferred to our data server. You may download the data to your own computer by accessing the server from your own computer. Instructions for connecting to the Flow Lab data server.
  2. The server is for current raw data only. You are responsible for coming to the Flow Lab and collecting older data. You may not place analyzed data, power point presentations or old data on the server.  In compliance with HIPPA regulations, no PHI is allowed to be stored on the Flow Lab data server.


  1. Offline computers are available for analysis. You may schedule a computer or may use them on a first come/first served basis.
  2. There is no charge for the use of these computers for analyzing data generated in the UWCCC Flow Lab.
  3. We are available to teach data analysis, but please check with us to schedule a time.  The Flow Lab offers walk-in Data Analysis Office Hours at CSC K4/532 every Wednesday morning from 10:00am to noon.

Contact us to discuss experimental design, protocol development, data analysis, or one-on-one data analysis at a computer station with one of the flow cytometry lab staff.

Phone: 608-263-0313